{"id":16,"date":"2024-02-09T11:01:11","date_gmt":"2024-02-09T02:01:11","guid":{"rendered":"https:\/\/www.bioreg.kyushu-u.ac.jp\/ext\/epicode\/wp\/?page_id=16"},"modified":"2024-05-09T12:53:20","modified_gmt":"2024-05-09T03:53:20","slug":"publications","status":"publish","type":"page","link":"https:\/\/www.bioreg.kyushu-u.ac.jp\/ext\/epicode\/publications","title":{"rendered":"\u7814\u7a76\u5b9f\u7e3e"},"content":{"rendered":"\n<h2 class=\"wp-block-heading\">\u7814\u7a76\u5b9f\u7e3e<\/h2>\n\n\n<div class=\"teachpress_pub_list\"><form name=\"tppublistform\" method=\"get\"><a name=\"tppubs\" id=\"tppubs\"><\/a><div class=\"teachpress_filter\"><select class=\"default\" name=\"yr\" id=\"yr\" tabindex=\"2\" onchange=\"teachpress_jumpMenu('parent',this, 'https:\/\/www.bioreg.kyushu-u.ac.jp\/ext\/epicode\/publications?')\">\r\n                   <option value=\"tgid=&amp;type=&amp;auth=&amp;usr=&amp;yr=#tppubs\">All years<\/option>\r\n                   <option value = \"tgid=&amp;type=&amp;auth=&amp;usr=&amp;yr=2026#tppubs\" >2026<\/option><option value = \"tgid=&amp;type=&amp;auth=&amp;usr=&amp;yr=2025#tppubs\" >2025<\/option><option value = \"tgid=&amp;type=&amp;auth=&amp;usr=&amp;yr=2024#tppubs\" >2024<\/option>\r\n                <\/select><select class=\"default\" name=\"type\" id=\"type\" tabindex=\"3\" onchange=\"teachpress_jumpMenu('parent',this, 'https:\/\/www.bioreg.kyushu-u.ac.jp\/ext\/epicode\/publications?')\">\r\n                   <option value=\"tgid=&amp;yr=&amp;auth=&amp;usr=&amp;type=#tppubs\">All types<\/option>\r\n                   <option value = \"tgid=&amp;yr=&amp;auth=&amp;usr=&amp;type=article#tppubs\" >Journal Articles<\/option><option value = \"tgid=&amp;yr=&amp;auth=&amp;usr=&amp;type=inbook#tppubs\" >Book Chapters<\/option><option value = \"tgid=&amp;yr=&amp;auth=&amp;usr=&amp;type=unpublished#tppubs\" >Unpublished<\/option>\r\n                <\/select><select class=\"default\" name=\"tgid\" id=\"tgid\" tabindex=\"4\" onchange=\"teachpress_jumpMenu('parent',this, 'https:\/\/www.bioreg.kyushu-u.ac.jp\/ext\/epicode\/publications?')\">\r\n                   <option value=\"yr=&amp;type=&amp;auth=&amp;usr=&amp;tgid=#tppubs\">All tags<\/option>\r\n                   <option value = \"yr=&amp;type=&amp;auth=&amp;usr=&amp;tgid=15#tppubs\" >Chromatin<\/option><option value = \"yr=&amp;type=&amp;auth=&amp;usr=&amp;tgid=22#tppubs\" >Chromatin remodeler<\/option><option value = \"yr=&amp;type=&amp;auth=&amp;usr=&amp;tgid=24#tppubs\" >Cryo-electron microscopy<\/option><option value = \"yr=&amp;type=&amp;auth=&amp;usr=&amp;tgid=6#tppubs\" >Fukaya G<\/option><option value = \"yr=&amp;type=&amp;auth=&amp;usr=&amp;tgid=11#tppubs\" >Gotoh G<\/option><option value = \"yr=&amp;type=&amp;auth=&amp;usr=&amp;tgid=18#tppubs\" >H2A.B<\/option><option value = \"yr=&amp;type=&amp;auth=&amp;usr=&amp;tgid=9#tppubs\" >Hattori G<\/option><option value = \"yr=&amp;type=&amp;auth=&amp;usr=&amp;tgid=17#tppubs\" >Histone Variant<\/option><option value = \"yr=&amp;type=&amp;auth=&amp;usr=&amp;tgid=21#tppubs\" >Homologous recombination<\/option><option value = \"yr=&amp;type=&amp;auth=&amp;usr=&amp;tgid=8#tppubs\" >Horikoshi G<\/option><option value = \"yr=&amp;type=&amp;auth=&amp;usr=&amp;tgid=13#tppubs\" >Kawashima G<\/option><option value = \"yr=&amp;type=&amp;auth=&amp;usr=&amp;tgid=2#tppubs\" >Kimura G<\/option><option value = \"yr=&amp;type=&amp;auth=&amp;usr=&amp;tgid=4#tppubs\" >Kurumizaka G<\/option><option value = \"yr=&amp;type=&amp;auth=&amp;usr=&amp;tgid=20#tppubs\" >Miyamoto G<\/option><option value = \"yr=&amp;type=&amp;auth=&amp;usr=&amp;tgid=27#tppubs\" >Nakajima G<\/option><option value = \"yr=&amp;type=&amp;auth=&amp;usr=&amp;tgid=7#tppubs\" >Nakayama G<\/option><option value = \"yr=&amp;type=&amp;auth=&amp;usr=&amp;tgid=14#tppubs\" >Nucleosome<\/option><option value = \"yr=&amp;type=&amp;auth=&amp;usr=&amp;tgid=3#tppubs\" >Ochiai G<\/option><option value = \"yr=&amp;type=&amp;auth=&amp;usr=&amp;tgid=1#tppubs\" >Ohkawa G<\/option><option value = \"yr=&amp;type=&amp;auth=&amp;usr=&amp;tgid=26#tppubs\" >Osakabe G<\/option><option value = \"yr=&amp;type=&amp;auth=&amp;usr=&amp;tgid=23#tppubs\" >RAD51<\/option><option value = \"yr=&amp;type=&amp;auth=&amp;usr=&amp;tgid=19#tppubs\" >Tachibana G<\/option><option value = \"yr=&amp;type=&amp;auth=&amp;usr=&amp;tgid=10#tppubs\" >Takahashi G<\/option><option value = \"yr=&amp;type=&amp;auth=&amp;usr=&amp;tgid=12#tppubs\" >Takemoto G<\/option><option value = \"yr=&amp;type=&amp;auth=&amp;usr=&amp;tgid=16#tppubs\" >Transcription<\/option><option value = \"yr=&amp;type=&amp;auth=&amp;usr=&amp;tgid=5#tppubs\" >Yamagata G<\/option><option value = \"yr=&amp;type=&amp;auth=&amp;usr=&amp;tgid=25#tppubs\" >Yamaguchi G<\/option>\r\n                <\/select><select class=\"default\" name=\"auth\" id=\"auth\" tabindex=\"5\" onchange=\"teachpress_jumpMenu('parent',this, 'https:\/\/www.bioreg.kyushu-u.ac.jp\/ext\/epicode\/publications?')\">\r\n                   <option value=\"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=#tppubs\">All authors<\/option>\r\n                   <option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=133#tppubs\" >Naruhiko Adachi<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=207#tppubs\" >Munetaka Akatsu<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=8#tppubs\" >Kanta Ando<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=126#tppubs\" >Mari Aoki<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=93#tppubs\" >Kyohei Arita<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=171#tppubs\" >Yoshimasa Asada<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=161#tppubs\" >Yuta Asayama<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=145#tppubs\" >Yuto Azumaya<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=35#tppubs\" >Akemi Baba<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=39#tppubs\" >Yoshihiro Baba<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=3#tppubs\" >Ryoma Bise<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=104#tppubs\" >Scott R. Burlingham<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=316#tppubs\" >Yi-Chen Chen<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=197#tppubs\" >Ting Cheng<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=184#tppubs\" >Konrad Chudzik<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=194#tppubs\" >Radostin Danev<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=103#tppubs\" >Jacob DeRoo<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=200#tppubs\" >Jinghan Diao<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=67#tppubs\" >Da\u2010Qiao Ding<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=303#tppubs\" >Yuanchao Dong<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=115#tppubs\" >Kenta Echigoya<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=46#tppubs\" >Haruhiko Ehara<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=82#tppubs\" >Masaki Endo<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=311#tppubs\" >Yoko Endo-Takahashi<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=107#tppubs\" >Hallie P. Febvre<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=105#tppubs\" >Gretchen Fixen<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=189#tppubs\" >Geoffrey Fudenberg<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=2#tppubs\" >Takeru Fujii<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=44#tppubs\" >Risa Fujita<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=274#tppubs\" >Yohsuke T. Fukai<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=41#tppubs\" >Takashi Fukaya<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=181#tppubs\" >Yoshiyuki Fukuda<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=170#tppubs\" >Noritaka Fukunaga<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=169#tppubs\" >Akira Funahashi<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=130#tppubs\" >Ayako Furukawa<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=236#tppubs\" >Kanji Furuya<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=101#tppubs\" >Gabriel Galindo<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=204#tppubs\" >Shan Gao<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=301#tppubs\" >Xiaohui Gao<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=113#tppubs\" >Brian J. Geiss<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=110#tppubs\" >Soham Ghosh<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=125#tppubs\" >Mie Goto<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=20#tppubs\" >Naoki Goto<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=121#tppubs\" >Yukiko Gotoh<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=175#tppubs\" >Misuzu Habazaki<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=305#tppubs\" >Nobuhito Hamano<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=178#tppubs\" >Kayo Hanada<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=24#tppubs\" >Tetsuya Handa<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=13#tppubs\" >Akihito Harada<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=52#tppubs\" >Tokuko Haraguchi<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=108#tppubs\" >Ryan Hasbrook<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=268#tppubs\" >Kana Hashimoto<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=54#tppubs\" >Michihiro Hashimoto<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=163#tppubs\" >Yu Hatano<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=180#tppubs\" >Suguru Hatazawa<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=95#tppubs\" >Yukako Hattori<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=91#tppubs\" >Aki Hayashi<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=152#tppubs\" >Shinichi Hayashi<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=127#tppubs\" >Masami Henmi<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=34#tppubs\" >Ryota Higuchi<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=217#tppubs\" >Toshiaki Hino<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=43#tppubs\" >Seiya Hirai<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=158#tppubs\" >Tatsuki Hirai<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=81#tppubs\" >Hisato Hirano<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=208#tppubs\" >Rina Hirano<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=51#tppubs\" >Yasushi Hiraoka<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=192#tppubs\" >Cheng-Han Ho<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=86#tppubs\" >Naoki Horikoshi<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=4#tppubs\" >Kazufumi Hosoda<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=168#tppubs\" >Yoshihiko Hosoi<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=317#tppubs\" >Shuo-Wen Hsu<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=250#tppubs\" >Akane Ichiki<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=223#tppubs\" >Chisato Ida<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=57#tppubs\" >Masahito Ikawa<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=164#tppubs\" >Hiroki Ikeda<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=226#tppubs\" >Haruka Ikegami<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=65#tppubs\" >Rintaro Inoue<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=177#tppubs\" >Hisashi Ishida<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=285#tppubs\" >Miho Ito<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=118#tppubs\" >Tomoko Ito<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=299#tppubs\" >Yuzuru Itoh<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=272#tppubs\" >Shigenori Iwai<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=148#tppubs\" >Atsushi Iwama<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=281#tppubs\" >Mitsutaka Kadota<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=144#tppubs\" >Satoshi Kaito<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=300#tppubs\" >Tetsuji Kakutani<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=146#tppubs\" >Yugo R. Kamimura<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=151#tppubs\" >Motomu Kanai<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=276#tppubs\" >Setsuko Kanamura<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=98#tppubs\" >Eiichiro Kanatsu<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=149#tppubs\" >Atsushi Kaneda<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=203#tppubs\" >Kensuke Kataoka<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=78#tppubs\" >Junko Kato<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=284#tppubs\" >Michiko Kato<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=283#tppubs\" >Kyogo Kawaguchi<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=53#tppubs\" >Takayuki Kawaguchi<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=139#tppubs\" >Osamu Kawasaki<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=150#tppubs\" >Shigehiro A. Kawashima<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=99#tppubs\" >Yoshitaka Kawasoe<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=256#tppubs\" >Kazuhiko Kawata<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=183#tppubs\" >Masahide Kikkawa<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=312#tppubs\" >Yamato Kikkawa<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=17#tppubs\" >Hiroshi Kimura<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=42#tppubs\" >Tomoaki Kimura<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=116#tppubs\" >Yusuke Kishi<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=231#tppubs\" >Tomoya S Kitajima<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=140#tppubs\" >Iori Kiyokawa<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=302#tppubs\" >Chaebeen Ko<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=157#tppubs\" >Hisato Kobayashi<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=295#tppubs\" >Takehiko Kobayashi<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=304#tppubs\" >Yoshiaki Kobayashi<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=182#tppubs\" >Yuki Kobayashi<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=179#tppubs\" >Hidetoshi Kono<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=214#tppubs\" >Peter Koopman<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=251#tppubs\" >Yukino Kudo<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=26#tppubs\" >Tomoya Kujirai<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=172#tppubs\" >Kazuki Kurimoto<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=211#tppubs\" >Shunsuke Kuroki<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=27#tppubs\" >Hitoshi Kurumizaka<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=80#tppubs\" >Tsukasa Kusakizako<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=254#tppubs\" >Khoa Minh Le<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=225#tppubs\" >Yuna Lee<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=199#tppubs\" >Haicheng Li<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=220#tppubs\" >Zhihua Liang<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=288#tppubs\" >Zezhen Lu<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=210#tppubs\" >Ryo Maeda<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=14#tppubs\" >Kazumitsu Maehara<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=102#tppubs\" >Daiki Maejima<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=40#tppubs\" >Shiho Makino<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=120#tppubs\" >Hiroshi Masumoto<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=228#tppubs\" >Shogo Matoba<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=70#tppubs\" >Atsushi Matsuda<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=249#tppubs\" >Chihiro Matsuda<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=230#tppubs\" >Kazuya Matsumoto<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=267#tppubs\" >Syota Matsumoto<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=224#tppubs\" >Yuki Matsuo<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=111#tppubs\" >E. Handly Mayton<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=222#tppubs\" >Tomoya Mimura<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=9#tppubs\" >Ryoma Minami<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=56#tppubs\" >Ryunosuke Minami<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=219#tppubs\" >Yasuki Miyagawa<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=87#tppubs\" >Ryosuke Miyake<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=232#tppubs\" >Kei Miyamoto<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=128#tppubs\" >Sayako Miyamoto-Kohno<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=290#tppubs\" >Ken-Ich Mizutani<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=235#tppubs\" >Shoko Mizutani<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=239#tppubs\" >Akihiro Mori<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=12#tppubs\" >Seiichi Mori<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=106#tppubs\" >Tatsuya Morisaki<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=64#tppubs\" >Ken Morishima<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=279#tppubs\" >Satoshi Morita<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=36#tppubs\" >Daisuke Murakami<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=94#tppubs\" >Yota Murakami<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=237#tppubs\" >Ayumi Mure<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=314#tppubs\" >Hiroki Nagai<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=77#tppubs\" >Reina Nagamura<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=123#tppubs\" >Masahiro Naganuma<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=242#tppubs\" >Kohjiro Nagao<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=15#tppubs\" >Masao Nagasaki<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=55#tppubs\" >Reiko Nakagawa<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=38#tppubs\" >Takashi Nakagawa<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=315#tppubs\" >Yu-ichiro Nakajima<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=92#tppubs\" >Rinko Nakamura<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=291#tppubs\" >Toru Nakano<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=58#tppubs\" >Jun-ichi Nakayama<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=72#tppubs\" >Jun\u2010ichi Nakayama<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=18#tppubs\" >Masashi Narita<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=132#tppubs\" >Tatsuki Negami<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=119#tppubs\" >Lumi Negishi<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=313#tppubs\" >Yoichi Negishi<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=264#tppubs\" >Gohei Nishibuchi<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=246#tppubs\" >Daichi Nishiguchi<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=23#tppubs\" >Hidenori Nishihara<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=61#tppubs\" >Masahiro Nishimura<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=138#tppubs\" >Yoshifumi Nishimura<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=202#tppubs\" >Junhua Niu<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=173#tppubs\" >Tamiko Nozaki<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=63#tppubs\" >Kayo Nozawa<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=85#tppubs\" >Osamu Nureki<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=37#tppubs\" >Stephen L Nutt<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=310#tppubs\" >Mizuki Obara<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=122#tppubs\" >Chikashi Obuse<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=6#tppubs\" >Hiroshi Ochiai<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=50#tppubs\" >Haruka Oda<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=45#tppubs\" >Mitsuo Ogasawara<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=229#tppubs\" >Atsuo Ogura<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=7#tppubs\" >Hiroaki Ohishi<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=19#tppubs\" >Yasuyuki Ohkawa<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=227#tppubs\" >Miho Ohsugi<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=143#tppubs\" >Atsushi Okabe<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=68#tppubs\" >Kasumi Okamasa<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=209#tppubs\" >Naoki Okashita<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=266#tppubs\" >Masaya Oki<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=75#tppubs\" >Shuichi Onami<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=174#tppubs\" >Mayu Onoda<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=297#tppubs\" >Akihisa Osakabe<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=74#tppubs\" >Hitoshi Owada<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=294#tppubs\" >Eriko Oya<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=89#tppubs\" >Tomoyuki Oya<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=257#tppubs\" >Manabu Ozawa<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=190#tppubs\" >Michael I. Robson<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=117#tppubs\" >Mai Saeki<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=84#tppubs\" >Hiroaki Saika<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=233#tppubs\" >Raku Saito<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=32#tppubs\" >Yuichi Saito<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=97#tppubs\" >Reihi Sakamoto<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=240#tppubs\" >Nozomu Sakurai<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=252#tppubs\" >Mika Saotome<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=212#tppubs\" >Kyona Sasaki<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=62#tppubs\" >Nobuhiro Sato<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=193#tppubs\" >Shoko Sato<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=25#tppubs\" >Yuko Sato<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=188#tppubs\" >Lothar Schermelleh<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=47#tppubs\" >Shun-Ichi Sekine<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=134#tppubs\" >Toshiya Senda<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=292#tppubs\" >Li Shen<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=96#tppubs\" >Karin Shigenobu-Ueno<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=298#tppubs\" >Wataru Shihoya<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=135#tppubs\" >Kentaro Shimizu<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=59#tppubs\" >Masahiro Shimizu<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=137#tppubs\" >Nobutaka Shimizu<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=318#tppubs\" >Eisuke Shimokita<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=49#tppubs\" >Tomoko Shindo<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=73#tppubs\" >Soya Shinkai<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=258#tppubs\" >Takuro Shioi<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=129#tppubs\" >Mikako Shirouzu<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=79#tppubs\" >Yutaro Shuto<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=112#tppubs\" >Christopher D. Snow<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=88#tppubs\" >Chizuru Sogawa-Fujiwara<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=191#tppubs\" >Irina Solovei<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=114#tppubs\" >Timothy J. Stasevich<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=273#tppubs\" >Kaoru Sugasawa<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=165#tppubs\" >Satoshi Sugimura<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=66#tppubs\" >Masaaki Sugiyama<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=262#tppubs\" >Suguru Hatazawa, Yoshimasa Takizawa, Hitoshi Kurumizaka<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=241#tppubs\" >Takuto Suito<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=21#tppubs\" >Kazuma Suke<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=153#tppubs\" >Hitomi Suzuki<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=162#tppubs\" >Yuka Suzuki<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=263#tppubs\" >Mieko Suzuki\u2010Matsubara<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=270#tppubs\" >Haruna Tachibana<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=215#tppubs\" >Makoto Tachibana<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=11#tppubs\" >Taro Tachibana<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=265#tppubs\" >Hideaki Tagami<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=154#tppubs\" >Shinji Takada<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=100#tppubs\" >Tatsuro S Takahashi<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=248#tppubs\" >Tatsuro S. Takahashi<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=238#tppubs\" >Yuuki Takahashi<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=142#tppubs\" >Shinpei Takamaru<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=216#tppubs\" >Atsushi Takasu<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=253#tppubs\" >Chihiro Takayama<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=286#tppubs\" >Marina Takechi<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=155#tppubs\" >Tatsuya Takemoto<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=29#tppubs\" >Maoko Takenoshita<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=218#tppubs\" >Osamu Takenouchi<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=176#tppubs\" >Yuma Takeuchi<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=48#tppubs\" >Yoshimasa Takizawa<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=60#tppubs\" >Hiroki Tanaka<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=10#tppubs\" >Kaori Tanaka<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=90#tppubs\" >Mayo Tanaka<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=221#tppubs\" >Shota Tanaka<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=296#tppubs\" >Yusaku Tanaka<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=280#tppubs\" >Chiharu Tanegashima<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=5#tppubs\" >Yosuke Taniguchi<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=247#tppubs\" >Kensuke Tatsukawa<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=136#tppubs\" >Tohru Terada<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=83#tppubs\" >Seiichi Toki<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=160#tppubs\" >Mikiko Tokoro<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=159#tppubs\" >Yuta Tokuoka<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=1#tppubs\" >Kosuke Tomimatsu<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=187#tppubs\" >Watanya Trakarnphornsombat<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=309#tppubs\" >Naoko Tsubaki<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=16#tppubs\" >Seiichi Uchida<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=255#tppubs\" >Satoshi Uchino<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=31#tppubs\" >Jun Ueda<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=124#tppubs\" >Tamami Uejima<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=245#tppubs\" >Tadashi Uemura<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=30#tppubs\" >Miku Ueoka<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=186#tppubs\" >Simon Ullrich<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=243#tppubs\" >Masato Umeda<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=282#tppubs\" >Takashi Umehara<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=234#tppubs\" >Yusuke Umemura<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=213#tppubs\" >Yoko Uno<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=33#tppubs\" >Miho Ushijima<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=275#tppubs\" >Masatoshi Wakamori<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=244#tppubs\" >Kaori Watanabe<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=269#tppubs\" >Wenjie Xu<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=167#tppubs\" >Takahiro G Yamada<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=28#tppubs\" >Kazuo Yamagata<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=293#tppubs\" >Shinpei Yamaguchi<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=307#tppubs\" >Taiki Yamaguchi<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=206#tppubs\" >Yuki Yamaguchi<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=271#tppubs\" >Junpei Yamamoto<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=205#tppubs\" >Kyoka Yamamoto<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=71#tppubs\" >Takaharu G. Yamamoto<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=76#tppubs\" >Takashi Yamamoto<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=166#tppubs\" >Takuya Yamamoto<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=141#tppubs\" >Yuki Yamanashi<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=147#tppubs\" >Kenzo Yamatsugu<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=277#tppubs\" >Lisa Yamauchi<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=185#tppubs\" >Xingchi Yan<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=306#tppubs\" >Yusuke Yano<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=156#tppubs\" >Tatsuma Yao<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=308#tppubs\" >Karin Yokota<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=131#tppubs\" >Kento Yonezawa<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=22#tppubs\" >Nao Yonezawa<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=69#tppubs\" >Yuriko Yoshimura<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=289#tppubs\" >Ying Zeng<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=278#tppubs\" >Somayeh Zeraati<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=198#tppubs\" >Jiachen Zhang<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=201#tppubs\" >Wenxin Zhang<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=109#tppubs\" >Ning Zhao<\/option><option value = \"tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=287#tppubs\" >Yezhang Zhu<\/option>\r\n                <\/select><\/div><\/form><div class=\"tablenav\"><div class=\"tablenav-pages\"><span class=\"displaying-num\">61 entries<\/span> <a class=\"page-numbers button disabled\">&laquo;<\/a> <a class=\"page-numbers button disabled\">&lsaquo;<\/a> 1 of 2 <a href=\"https:\/\/www.bioreg.kyushu-u.ac.jp\/ext\/epicode\/publications?limit=2&amp;tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=&amp;tsr=#tppubs\" title=\"next page\" class=\"page-numbers button\">&rsaquo;<\/a> <a href=\"https:\/\/www.bioreg.kyushu-u.ac.jp\/ext\/epicode\/publications?limit=2&amp;tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=&amp;tsr=#tppubs\" title=\"last page\" class=\"page-numbers button\">&raquo;<\/a> <\/div><\/div><div class=\"teachpress_publication_list\"><h3 class=\"tp_h3\" id=\"tp_h3_2026\">2026<\/h3><div class=\"tp_publication tp_publication_article\"><div class=\"tp_pub_number\">61.<\/div><div class=\"tp_pub_info\"><p class=\"tp_pub_author\">Yi-Chen Chen,  Shuo-Wen Hsu,  Eisuke Shimokita,  Tatsuya Takemoto<\/p><p class=\"tp_pub_title\"><a class=\"tp_title_link\" href=\"https:\/\/dx.doi.org\/10.3389\/fbioe.2026.1785893\" title=\"Eye pigmentation\u2013based in-ovo chicken sexing via precision breeding\" target=\"blank\">Eye pigmentation\u2013based in-ovo chicken sexing via precision breeding<\/a> <span class=\"tp_pub_type article\">Journal Article<\/span> <\/p><p class=\"tp_pub_additional\"><span class=\"tp_pub_additional_in\">In: <\/span><span class=\"tp_pub_additional_journal\">Front. Bioeng. Biotechnol., <\/span><span class=\"tp_pub_additional_volume\">vol. 14, <\/span><span class=\"tp_pub_additional_year\">2026<\/span>, <span class=\"tp_pub_additional_issn\">ISSN: 2296-4185<\/span>.<\/p><p class=\"tp_pub_menu\"><span class=\"tp_abstract_link\"><a id=\"tp_abstract_sh_61\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('61','tp_abstract')\" title=\"Show abstract\" style=\"cursor:pointer;\">Abstract<\/a><\/span> | <span class=\"tp_resource_link\"><a id=\"tp_links_sh_61\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('61','tp_links')\" title=\"Show links and resources\" style=\"cursor:pointer;\">Links<\/a><\/span> | <span class=\"tp_pub_tags_label\">\u30bf\u30b0: <\/span><a rel=\"nofollow\" href=\"https:\/\/www.bioreg.kyushu-u.ac.jp\/ext\/epicode\/publications?tgid=12#tppubs\" title=\"Show all publications which have a relationship to this tag\">Takemoto G<\/a><\/p><div class=\"tp_bibtex\" id=\"tp_bibtex_61\" style=\"display:none;\"><div class=\"tp_bibtex_entry\"><pre>@article{Chen2026,<br \/>\r\ntitle = {Eye pigmentation\u2013based in-ovo chicken sexing via precision breeding},<br \/>\r\nauthor = {Yi-Chen Chen and Shuo-Wen Hsu and Eisuke Shimokita and Tatsuya Takemoto},<br \/>\r\ndoi = {10.3389\/fbioe.2026.1785893},<br \/>\r\nissn = {2296-4185},<br \/>\r\nyear  = {2026},<br \/>\r\ndate = {2026-04-01},<br \/>\r\nurldate = {2026-04-01},<br \/>\r\njournal = {Front. Bioeng. Biotechnol.},<br \/>\r\nvolume = {14},<br \/>\r\npublisher = {Frontiers Media SA},<br \/>\r\nabstract = {The systematic culling of male layer chicks raises ethical concerns, leading to bans in Germany and other European countries and spurring the search for reliable in-ovo sexing methods. Most existing strategies rely on integration of exogenous DNA or are limited to specific chicken strains, and none meet commercial requirements. Here, we present a broadly applicable in-ovo sexing method that avoids exogenous DNA integration. We developed precision-bred chickens with targeted disruption of the Z-linked SLC45A2 gene, which encodes a transporter essential for pigmentation. Hemizygous knockout females (ZW; SLC45A2KO\/W) exhibited eye depigmentation at embryonic day 7 (E7), whereas heterozygous knockout males (ZZ; SLC45A2KO\/+) retained normal pigmentation. This clear visual dimorphism enables accurate sexing by routine egg candling. Fertility and reproductive performance of knockouts were comparable to wild-type chickens, and genotyping confirmed 100% prediction accuracy. Unlike many current technologies, our approach requires no complex instrumentation and allows early detection during incubation. This work provides a practical and ethical solution to chick sexing, with significant advantages for commercial hatcheries. More broadly, this study illustrates the potential of precision breeding to address pressing animal welfare concerns in the modern poultry industry.},<br \/>\r\nkeywords = {Takemoto G},<br \/>\r\npubstate = {published},<br \/>\r\ntppubtype = {article}<br \/>\r\n}<br \/>\r\n<\/pre><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('61','tp_bibtex')\">Close<\/a><\/p><\/div><div class=\"tp_abstract\" id=\"tp_abstract_61\" style=\"display:none;\"><div class=\"tp_abstract_entry\">The systematic culling of male layer chicks raises ethical concerns, leading to bans in Germany and other European countries and spurring the search for reliable in-ovo sexing methods. Most existing strategies rely on integration of exogenous DNA or are limited to specific chicken strains, and none meet commercial requirements. Here, we present a broadly applicable in-ovo sexing method that avoids exogenous DNA integration. We developed precision-bred chickens with targeted disruption of the Z-linked SLC45A2 gene, which encodes a transporter essential for pigmentation. Hemizygous knockout females (ZW; SLC45A2KO\/W) exhibited eye depigmentation at embryonic day 7 (E7), whereas heterozygous knockout males (ZZ; SLC45A2KO\/+) retained normal pigmentation. This clear visual dimorphism enables accurate sexing by routine egg candling. Fertility and reproductive performance of knockouts were comparable to wild-type chickens, and genotyping confirmed 100% prediction accuracy. Unlike many current technologies, our approach requires no complex instrumentation and allows early detection during incubation. This work provides a practical and ethical solution to chick sexing, with significant advantages for commercial hatcheries. More broadly, this study illustrates the potential of precision breeding to address pressing animal welfare concerns in the modern poultry industry.<\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('61','tp_abstract')\">Close<\/a><\/p><\/div><div class=\"tp_links\" id=\"tp_links_61\" style=\"display:none;\"><div class=\"tp_links_entry\"><ul class=\"tp_pub_list\"><li><i class=\"ai ai-doi\"><\/i><a class=\"tp_pub_list\" href=\"https:\/\/dx.doi.org\/10.3389\/fbioe.2026.1785893\" title=\"Follow DOI:10.3389\/fbioe.2026.1785893\" target=\"_blank\">doi:10.3389\/fbioe.2026.1785893<\/a><\/li><\/ul><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('61','tp_links')\">Close<\/a><\/p><\/div><\/div><\/div><div class=\"tp_publication tp_publication_article\"><div class=\"tp_pub_number\">60.<\/div><div class=\"tp_pub_info\"><p class=\"tp_pub_author\">Hiroki Nagai,  Yu-ichiro Nakajima<\/p><p class=\"tp_pub_title\"><a class=\"tp_title_link\" href=\"https:\/\/dx.doi.org\/10.1016\/j.semcdb.2026.103670\" title=\"Epithelial cell plasticity in metazoans: Evolutionary insights into roles and mechanisms\" target=\"blank\">Epithelial cell plasticity in metazoans: Evolutionary insights into roles and mechanisms<\/a> <span class=\"tp_pub_type article\">Journal Article<\/span> <\/p><p class=\"tp_pub_additional\"><span class=\"tp_pub_additional_in\">In: <\/span><span class=\"tp_pub_additional_journal\">Seminars in Cell &amp; Developmental Biology, <\/span><span class=\"tp_pub_additional_volume\">vol. 179-180, <\/span><span class=\"tp_pub_additional_year\">2026<\/span>, <span class=\"tp_pub_additional_issn\">ISSN: 1084-9521<\/span>.<\/p><p class=\"tp_pub_menu\"><span class=\"tp_abstract_link\"><a id=\"tp_abstract_sh_60\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('60','tp_abstract')\" title=\"Show abstract\" style=\"cursor:pointer;\">Abstract<\/a><\/span> | <span class=\"tp_resource_link\"><a id=\"tp_links_sh_60\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('60','tp_links')\" title=\"Show links and resources\" style=\"cursor:pointer;\">Links<\/a><\/span> | <span class=\"tp_pub_tags_label\">\u30bf\u30b0: <\/span><a rel=\"nofollow\" href=\"https:\/\/www.bioreg.kyushu-u.ac.jp\/ext\/epicode\/publications?tgid=27#tppubs\" title=\"Show all publications which have a relationship to this tag\">Nakajima G<\/a><\/p><div class=\"tp_bibtex\" id=\"tp_bibtex_60\" style=\"display:none;\"><div class=\"tp_bibtex_entry\"><pre>@article{Nagai2026,<br \/>\r\ntitle = {Epithelial cell plasticity in metazoans: Evolutionary insights into roles and mechanisms},<br \/>\r\nauthor = {Hiroki Nagai and Yu-ichiro Nakajima},<br \/>\r\ndoi = {10.1016\/j.semcdb.2026.103670},<br \/>\r\nissn = {1084-9521},<br \/>\r\nyear  = {2026},<br \/>\r\ndate = {2026-03-03},<br \/>\r\njournal = {Seminars in Cell & Developmental Biology},<br \/>\r\nvolume = {179-180},<br \/>\r\npublisher = {Elsevier BV},<br \/>\r\nabstract = {Epithelial tissues function as multicellular communities that preserve tissue integrity while adapting to diverse environmental stresses by altering cell behaviors. A striking manifestation of such adaptability is cell plasticity, the ability of differentiated cells to revert to stem-like states or adopt alternative fates. Once considered rare and confined to highly regenerative species, cell plasticity is now recognized across the metazoan tree. In early-branching animals such as sponges and cnidarians, transdifferentiation and dedifferentiation are integral to life-cycle transitions and regeneration, whereas in more complex organisms, these processes typically emerge under stress, including stem cell loss or environmental perturbations. Here, we examine epithelial cell plasticity through evolutionary, cellular, and molecular perspectives. Focusing on the intestinal epithelium, we explore findings from mammalian and Drosophila models showing that progenitors and even terminally differentiated cells can dedifferentiate in response to external stimuli that disrupt homeostasis, such as pathogen infection and nutrient fluctuations. We further discuss conserved mechanisms involving intercellular signaling (e.g., Notch, EGFR, and JAK-STAT) and chromatin states primed for reprogramming, modulated by metabolic cues. Together, these insights position cell plasticity as an ancient environmental adaptation strategy, shaped by conserved molecular toolkits and refined by species- and cell lineage-specific innovations.},<br \/>\r\nkeywords = {Nakajima G},<br \/>\r\npubstate = {published},<br \/>\r\ntppubtype = {article}<br \/>\r\n}<br \/>\r\n<\/pre><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('60','tp_bibtex')\">Close<\/a><\/p><\/div><div class=\"tp_abstract\" id=\"tp_abstract_60\" style=\"display:none;\"><div class=\"tp_abstract_entry\">Epithelial tissues function as multicellular communities that preserve tissue integrity while adapting to diverse environmental stresses by altering cell behaviors. A striking manifestation of such adaptability is cell plasticity, the ability of differentiated cells to revert to stem-like states or adopt alternative fates. Once considered rare and confined to highly regenerative species, cell plasticity is now recognized across the metazoan tree. In early-branching animals such as sponges and cnidarians, transdifferentiation and dedifferentiation are integral to life-cycle transitions and regeneration, whereas in more complex organisms, these processes typically emerge under stress, including stem cell loss or environmental perturbations. Here, we examine epithelial cell plasticity through evolutionary, cellular, and molecular perspectives. Focusing on the intestinal epithelium, we explore findings from mammalian and Drosophila models showing that progenitors and even terminally differentiated cells can dedifferentiate in response to external stimuli that disrupt homeostasis, such as pathogen infection and nutrient fluctuations. We further discuss conserved mechanisms involving intercellular signaling (e.g., Notch, EGFR, and JAK-STAT) and chromatin states primed for reprogramming, modulated by metabolic cues. Together, these insights position cell plasticity as an ancient environmental adaptation strategy, shaped by conserved molecular toolkits and refined by species- and cell lineage-specific innovations.<\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('60','tp_abstract')\">Close<\/a><\/p><\/div><div class=\"tp_links\" id=\"tp_links_60\" style=\"display:none;\"><div class=\"tp_links_entry\"><ul class=\"tp_pub_list\"><li><i class=\"ai ai-doi\"><\/i><a class=\"tp_pub_list\" href=\"https:\/\/dx.doi.org\/10.1016\/j.semcdb.2026.103670\" title=\"Follow DOI:10.1016\/j.semcdb.2026.103670\" target=\"_blank\">doi:10.1016\/j.semcdb.2026.103670<\/a><\/li><\/ul><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('60','tp_links')\">Close<\/a><\/p><\/div><\/div><\/div><div class=\"tp_publication tp_publication_article\"><div class=\"tp_pub_number\">59.<\/div><div class=\"tp_pub_info\"><p class=\"tp_pub_author\">Raku Saito,  Yusuke Umemura,  Shiho Makino,  Takashi Fukaya<\/p><p class=\"tp_pub_title\"><a class=\"tp_title_link\" href=\"https:\/\/dx.doi.org\/10.1126\/sciadv.ady7568\" title=\"Decoding the molecular logic of rapidly evolving ZAD zinc finger proteins in                    <i>Drosophila<\/i>\" target=\"blank\">Decoding the molecular logic of rapidly evolving ZAD zinc finger proteins in                    <i>Drosophila<\/i><\/a> <span class=\"tp_pub_type article\">Journal Article<\/span> <\/p><p class=\"tp_pub_additional\"><span class=\"tp_pub_additional_in\">In: <\/span><span class=\"tp_pub_additional_journal\">Sci. Adv., <\/span><span class=\"tp_pub_additional_volume\">vol. 12, <\/span><span class=\"tp_pub_additional_number\">no. 9, <\/span><span class=\"tp_pub_additional_year\">2026<\/span>, <span class=\"tp_pub_additional_issn\">ISSN: 2375-2548<\/span>.<\/p><p class=\"tp_pub_menu\"><span class=\"tp_abstract_link\"><a id=\"tp_abstract_sh_59\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('59','tp_abstract')\" title=\"Show abstract\" style=\"cursor:pointer;\">Abstract<\/a><\/span> | <span class=\"tp_resource_link\"><a id=\"tp_links_sh_59\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('59','tp_links')\" title=\"Show links and resources\" style=\"cursor:pointer;\">Links<\/a><\/span> | <span class=\"tp_pub_tags_label\">\u30bf\u30b0: <\/span><a rel=\"nofollow\" href=\"https:\/\/www.bioreg.kyushu-u.ac.jp\/ext\/epicode\/publications?tgid=6#tppubs\" title=\"Show all publications which have a relationship to this tag\">Fukaya G<\/a><\/p><div class=\"tp_bibtex\" id=\"tp_bibtex_59\" style=\"display:none;\"><div class=\"tp_bibtex_entry\"><pre>@article{Saito2026,<br \/>\r\ntitle = {Decoding the molecular logic of rapidly evolving ZAD zinc finger proteins in                    \\textit{Drosophila}},<br \/>\r\nauthor = {Raku Saito and Yusuke Umemura and Shiho Makino and Takashi Fukaya},<br \/>\r\ndoi = {10.1126\/sciadv.ady7568},<br \/>\r\nissn = {2375-2548},<br \/>\r\nyear  = {2026},<br \/>\r\ndate = {2026-02-27},<br \/>\r\nurldate = {2026-02-27},<br \/>\r\njournal = {Sci. Adv.},<br \/>\r\nvolume = {12},<br \/>\r\nnumber = {9},<br \/>\r\npublisher = {American Association for the Advancement of Science (AAAS)},<br \/>\r\nabstract = {The zinc finger\u2013associated domain (ZAD)\u2013containing C2H2 zinc finger proteins (ZAD-ZnFs) represent the most abundant class of transcription factors that emerged during insect evolution, yet their molecular diversity and biological functions remain largely unclear. Here, we established a systematic CRISPR-based protein-tagging approach that enables direct, unambiguous comparison of nuclear localization and genome-wide binding profiles of endogenous ZAD-ZnFs in developing Drosophila embryos. Evidence is provided that a subset of ZAD-ZnFs forms nuclear condensates through the stacking of the N-terminal ZAD dimerization surface. Disruption of condensation activity leads to misregulation of genome-wide binding profiles and lethality, underscoring its functional and physiological significance in development. Integrative chromatin immunoprecipitation sequencing and Micro-C analyses reveal that many ZAD-ZnFs colocalize with core insulator proteins such as CCCTC-binding factor and Centrosomal protein 190 kD to control the formation of topological boundaries. We suggest that the diverse molecular functions of ZAD-ZnFs have evolutionarily arisen from their ancestral role as insulator-binding proteins.},<br \/>\r\nkeywords = {Fukaya G},<br \/>\r\npubstate = {published},<br \/>\r\ntppubtype = {article}<br \/>\r\n}<br \/>\r\n<\/pre><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('59','tp_bibtex')\">Close<\/a><\/p><\/div><div class=\"tp_abstract\" id=\"tp_abstract_59\" style=\"display:none;\"><div class=\"tp_abstract_entry\">The zinc finger\u2013associated domain (ZAD)\u2013containing C2H2 zinc finger proteins (ZAD-ZnFs) represent the most abundant class of transcription factors that emerged during insect evolution, yet their molecular diversity and biological functions remain largely unclear. Here, we established a systematic CRISPR-based protein-tagging approach that enables direct, unambiguous comparison of nuclear localization and genome-wide binding profiles of endogenous ZAD-ZnFs in developing Drosophila embryos. Evidence is provided that a subset of ZAD-ZnFs forms nuclear condensates through the stacking of the N-terminal ZAD dimerization surface. Disruption of condensation activity leads to misregulation of genome-wide binding profiles and lethality, underscoring its functional and physiological significance in development. Integrative chromatin immunoprecipitation sequencing and Micro-C analyses reveal that many ZAD-ZnFs colocalize with core insulator proteins such as CCCTC-binding factor and Centrosomal protein 190 kD to control the formation of topological boundaries. We suggest that the diverse molecular functions of ZAD-ZnFs have evolutionarily arisen from their ancestral role as insulator-binding proteins.<\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('59','tp_abstract')\">Close<\/a><\/p><\/div><div class=\"tp_links\" id=\"tp_links_59\" style=\"display:none;\"><div class=\"tp_links_entry\"><ul class=\"tp_pub_list\"><li><i class=\"ai ai-doi\"><\/i><a class=\"tp_pub_list\" href=\"https:\/\/dx.doi.org\/10.1126\/sciadv.ady7568\" title=\"Follow DOI:10.1126\/sciadv.ady7568\" target=\"_blank\">doi:10.1126\/sciadv.ady7568<\/a><\/li><\/ul><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('59','tp_links')\">Close<\/a><\/p><\/div><\/div><\/div><div class=\"tp_publication tp_publication_article\"><div class=\"tp_pub_number\">58.<\/div><div class=\"tp_pub_info\"><p class=\"tp_pub_author\">Nobuhito Hamano,  Yusuke Yano,  Taiki Yamaguchi,  Karin Yokota,  Naoko Tsubaki,  Mizuki Obara,  Yoko Endo-Takahashi,  Mitsuo Ogasawara,  Yoshimasa Takizawa,  Hitoshi Kurumizaka,  Yamato Kikkawa,  Yoichi Negishi<\/p><p class=\"tp_pub_title\"><a class=\"tp_title_link\" href=\"https:\/\/dx.doi.org\/10.1021\/acsanm.5c05403\" title=\"ImmuBubbles: Antibody-Shelled Gas-Core Nanobubbles as Ultrasound Contrast Agents\" target=\"blank\">ImmuBubbles: Antibody-Shelled Gas-Core Nanobubbles as Ultrasound Contrast Agents<\/a> <span class=\"tp_pub_type article\">Journal Article<\/span> <\/p><p class=\"tp_pub_additional\"><span class=\"tp_pub_additional_in\">In: <\/span><span class=\"tp_pub_additional_journal\">ACS Appl. Nano Mater., <\/span><span class=\"tp_pub_additional_year\">2026<\/span>, <span class=\"tp_pub_additional_issn\">ISSN: 2574-0970<\/span>.<\/p><p class=\"tp_pub_menu\"><span class=\"tp_abstract_link\"><a id=\"tp_abstract_sh_58\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('58','tp_abstract')\" title=\"Show abstract\" style=\"cursor:pointer;\">Abstract<\/a><\/span> | <span class=\"tp_resource_link\"><a id=\"tp_links_sh_58\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('58','tp_links')\" title=\"Show links and resources\" style=\"cursor:pointer;\">Links<\/a><\/span> | <span class=\"tp_pub_tags_label\">\u30bf\u30b0: <\/span><a rel=\"nofollow\" href=\"https:\/\/www.bioreg.kyushu-u.ac.jp\/ext\/epicode\/publications?tgid=4#tppubs\" title=\"Show all publications which have a relationship to this tag\">Kurumizaka G<\/a><\/p><div class=\"tp_bibtex\" id=\"tp_bibtex_58\" style=\"display:none;\"><div class=\"tp_bibtex_entry\"><pre>@article{Hamano2026,<br \/>\r\ntitle = {ImmuBubbles: Antibody-Shelled Gas-Core Nanobubbles as Ultrasound Contrast Agents},<br \/>\r\nauthor = {Nobuhito Hamano and Yusuke Yano and Taiki Yamaguchi and Karin Yokota and Naoko Tsubaki and Mizuki Obara and Yoko Endo-Takahashi and Mitsuo Ogasawara and Yoshimasa Takizawa and Hitoshi Kurumizaka and Yamato Kikkawa and Yoichi Negishi},<br \/>\r\ndoi = {10.1021\/acsanm.5c05403},<br \/>\r\nissn = {2574-0970},<br \/>\r\nyear  = {2026},<br \/>\r\ndate = {2026-02-11},<br \/>\r\nurldate = {2026-02-11},<br \/>\r\njournal = {ACS Appl. Nano Mater.},<br \/>\r\npublisher = {American Chemical Society (ACS)},<br \/>\r\nabstract = {Ultrasound (US)-responsive nanobubbles (NBs) enable image-guided, localized delivery of biologics; however, the surface area of conventional antibody-loaded NBs limits their loading capacity. Although antibodies such as trastuzumab (Herceptin) offer high target specificity and prolonged half-lives, their penetration into solid tumors is impeded by abnormal vasculature and a dense extracellular matrix. To address these challenges, we developed ImmuBubbles (IBs), self-assembled antibody-shelled gas-core NBs produced by high-speed agitation of trastuzumab solutions in perfluoropropane. Hydrophobic residues within the IgG Fc region promoted self-assembly at the gas\u2013liquid interface, forming shells without lipid incorporation. Herceptin-shelled IBs (Her-IBs) were uniform (\u223c95 nm) and positively charged (\u03b6 \u2248 + 10 mV) and generated US contrast both in vitro and in vivo. Moreover, cryo-transmission electron microscopy revealed spherical shells enclosing electron-lucent cores, consistent with a gas-filled morphology. To improve in vivo persistence, Pluronic L61 (L61) was coincorporated, yielding L61-Her-IBs with increased particle yield and enhanced echogenicity in cardiac imaging, with detectable contrast in tumor imaging. Antibody-dependent cellular cytotoxicity activity was preserved for L61-Her-IBs after high-speed mixing and therapeutic US (TUS; 1 MHz) exposure, consistent with maintained bioactivity. In SKOV3 xenografts, systemic L61-Her-IBs + TUS showed a trend toward tumor growth suppression compared with Herceptin monotherapy, without evident systemic toxicity. Collectively, these findings demonstrate that antibody-shelled NBs can function as US-responsive contrast agents while retaining antibody-mediated biological activity. To the best of our knowledge, this is the first report of self-assembled antibody-shelled NBs as ultrasound contrast agents that retain antibody function. With additional shell stabilization, such as covalent cross-linking using antibody-drug conjugate-style linkers, IBs may provide a platform for improving the precision of therapeutic ultrasound\u2013guided interventions in solid tumors and tissues protected by restrictive biological barriers, including the central nervous system.},<br \/>\r\nkeywords = {Kurumizaka G},<br \/>\r\npubstate = {published},<br \/>\r\ntppubtype = {article}<br \/>\r\n}<br \/>\r\n<\/pre><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('58','tp_bibtex')\">Close<\/a><\/p><\/div><div class=\"tp_abstract\" id=\"tp_abstract_58\" style=\"display:none;\"><div class=\"tp_abstract_entry\">Ultrasound (US)-responsive nanobubbles (NBs) enable image-guided, localized delivery of biologics; however, the surface area of conventional antibody-loaded NBs limits their loading capacity. Although antibodies such as trastuzumab (Herceptin) offer high target specificity and prolonged half-lives, their penetration into solid tumors is impeded by abnormal vasculature and a dense extracellular matrix. To address these challenges, we developed ImmuBubbles (IBs), self-assembled antibody-shelled gas-core NBs produced by high-speed agitation of trastuzumab solutions in perfluoropropane. Hydrophobic residues within the IgG Fc region promoted self-assembly at the gas\u2013liquid interface, forming shells without lipid incorporation. Herceptin-shelled IBs (Her-IBs) were uniform (\u223c95 nm) and positively charged (\u03b6 \u2248 + 10 mV) and generated US contrast both in vitro and in vivo. Moreover, cryo-transmission electron microscopy revealed spherical shells enclosing electron-lucent cores, consistent with a gas-filled morphology. To improve in vivo persistence, Pluronic L61 (L61) was coincorporated, yielding L61-Her-IBs with increased particle yield and enhanced echogenicity in cardiac imaging, with detectable contrast in tumor imaging. Antibody-dependent cellular cytotoxicity activity was preserved for L61-Her-IBs after high-speed mixing and therapeutic US (TUS; 1 MHz) exposure, consistent with maintained bioactivity. In SKOV3 xenografts, systemic L61-Her-IBs + TUS showed a trend toward tumor growth suppression compared with Herceptin monotherapy, without evident systemic toxicity. Collectively, these findings demonstrate that antibody-shelled NBs can function as US-responsive contrast agents while retaining antibody-mediated biological activity. To the best of our knowledge, this is the first report of self-assembled antibody-shelled NBs as ultrasound contrast agents that retain antibody function. With additional shell stabilization, such as covalent cross-linking using antibody-drug conjugate-style linkers, IBs may provide a platform for improving the precision of therapeutic ultrasound\u2013guided interventions in solid tumors and tissues protected by restrictive biological barriers, including the central nervous system.<\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('58','tp_abstract')\">Close<\/a><\/p><\/div><div class=\"tp_links\" id=\"tp_links_58\" style=\"display:none;\"><div class=\"tp_links_entry\"><ul class=\"tp_pub_list\"><li><i class=\"ai ai-doi\"><\/i><a class=\"tp_pub_list\" href=\"https:\/\/dx.doi.org\/10.1021\/acsanm.5c05403\" title=\"Follow DOI:10.1021\/acsanm.5c05403\" target=\"_blank\">doi:10.1021\/acsanm.5c05403<\/a><\/li><\/ul><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('58','tp_links')\">Close<\/a><\/p><\/div><\/div><\/div><div class=\"tp_publication tp_publication_article\"><div class=\"tp_pub_number\">57.<\/div><div class=\"tp_pub_info\"><p class=\"tp_pub_author\">Xiaohui Gao,  Chaebeen Ko,  Yuanchao Dong,  Takeru Fujii,  Satoshi Uchino,  Yoshiaki Kobayashi,  Akihito Harada,  Hiroaki Ohishi,  Yasuyuki Ohkawa,  Hiroshi Kimura,  Hiroshi Ochiai<\/p><p class=\"tp_pub_title\"><a class=\"tp_title_link\" href=\"https:\/\/dx.doi.org\/10.64898\/2026.02.08.704500\" title=\"Minute-scale coupling of chromatin marks and transcriptional bursts\" target=\"blank\">Minute-scale coupling of chromatin marks and transcriptional bursts<\/a> <span class=\"tp_pub_type article\">Journal Article<\/span> <\/p><p class=\"tp_pub_additional\"><span class=\"tp_pub_additional_in\">In: <\/span><span class=\"tp_pub_additional_journal\">bioRxiv, <\/span><span class=\"tp_pub_additional_year\">2026<\/span>.<\/p><p class=\"tp_pub_menu\"><span class=\"tp_abstract_link\"><a id=\"tp_abstract_sh_57\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('57','tp_abstract')\" title=\"Show abstract\" style=\"cursor:pointer;\">Abstract<\/a><\/span> | <span class=\"tp_resource_link\"><a id=\"tp_links_sh_57\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('57','tp_links')\" title=\"Show links and resources\" style=\"cursor:pointer;\">Links<\/a><\/span> | <span class=\"tp_pub_tags_label\">\u30bf\u30b0: <\/span><a rel=\"nofollow\" href=\"https:\/\/www.bioreg.kyushu-u.ac.jp\/ext\/epicode\/publications?tgid=2#tppubs\" title=\"Show all publications which have a relationship to this tag\">Kimura G<\/a>, <a rel=\"nofollow\" href=\"https:\/\/www.bioreg.kyushu-u.ac.jp\/ext\/epicode\/publications?tgid=3#tppubs\" title=\"Show all publications which have a relationship to this tag\">Ochiai G<\/a>, <a rel=\"nofollow\" href=\"https:\/\/www.bioreg.kyushu-u.ac.jp\/ext\/epicode\/publications?tgid=1#tppubs\" title=\"Show all publications which have a relationship to this tag\">Ohkawa G<\/a><\/p><div class=\"tp_bibtex\" id=\"tp_bibtex_57\" style=\"display:none;\"><div class=\"tp_bibtex_entry\"><pre>@article{Gao2026.02.08.704500,<br \/>\r\ntitle = {Minute-scale coupling of chromatin marks and transcriptional bursts},<br \/>\r\nauthor = {Xiaohui Gao and Chaebeen Ko and Yuanchao Dong and Takeru Fujii and Satoshi Uchino and Yoshiaki Kobayashi and Akihito Harada and Hiroaki Ohishi and Yasuyuki Ohkawa and Hiroshi Kimura and Hiroshi Ochiai},<br \/>\r\nurl = {https:\/\/www.biorxiv.org\/content\/early\/2026\/02\/10\/2026.02.08.704500},<br \/>\r\ndoi = {10.64898\/2026.02.08.704500},<br \/>\r\nyear  = {2026},<br \/>\r\ndate = {2026-02-10},<br \/>\r\nurldate = {2026-01-01},<br \/>\r\njournal = {bioRxiv},<br \/>\r\npublisher = {Cold Spring Harbor Laboratory},<br \/>\r\nabstract = {Histone modifications are often described as stable epigenetic marks that contribute to maintaining gene-expression programs during development and environmental responses. However, transcription of many genes is intermittent, switching between transcriptionally active and inactive episodes within minutes. Whether chromatin marks around individual genes change on these rapid timescales remains unclear. Here we show that local chromatin modification signals around endogenous genes in mouse embryonic stem cells fluctuate reversibly with transcriptional state, using live imaging of individual genes together with fluorescent probes that report histone modifications. Activation-associated acetylation and methylation marks increased in association with transcriptional activation and decreased with inactivation, whereas a Polycomb-associated repressive mark behaved oppositely. Transcriptional coactivators and both histone acetyltransferase and deacetylase complexes were enriched during transcriptionally active state, consistent with opposing enzymatic activities shaping local acetylation levels. Inhibiting histone deacetylases altered the durations of active and inactive events, supporting a role for deacetylation in regulating transcriptional state transitions. Thus, histone modifications undergo reversible, minute-scale changes coupled to transcriptional activity. This framework helps explain how stochastic transcriptional bursts can occur with stable gene regulation over longer timescales.},<br \/>\r\nkeywords = {Kimura G, Ochiai G, Ohkawa G},<br \/>\r\npubstate = {published},<br \/>\r\ntppubtype = {article}<br \/>\r\n}<br \/>\r\n<\/pre><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('57','tp_bibtex')\">Close<\/a><\/p><\/div><div class=\"tp_abstract\" id=\"tp_abstract_57\" style=\"display:none;\"><div class=\"tp_abstract_entry\">Histone modifications are often described as stable epigenetic marks that contribute to maintaining gene-expression programs during development and environmental responses. However, transcription of many genes is intermittent, switching between transcriptionally active and inactive episodes within minutes. Whether chromatin marks around individual genes change on these rapid timescales remains unclear. Here we show that local chromatin modification signals around endogenous genes in mouse embryonic stem cells fluctuate reversibly with transcriptional state, using live imaging of individual genes together with fluorescent probes that report histone modifications. Activation-associated acetylation and methylation marks increased in association with transcriptional activation and decreased with inactivation, whereas a Polycomb-associated repressive mark behaved oppositely. Transcriptional coactivators and both histone acetyltransferase and deacetylase complexes were enriched during transcriptionally active state, consistent with opposing enzymatic activities shaping local acetylation levels. Inhibiting histone deacetylases altered the durations of active and inactive events, supporting a role for deacetylation in regulating transcriptional state transitions. Thus, histone modifications undergo reversible, minute-scale changes coupled to transcriptional activity. This framework helps explain how stochastic transcriptional bursts can occur with stable gene regulation over longer timescales.<\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('57','tp_abstract')\">Close<\/a><\/p><\/div><div class=\"tp_links\" id=\"tp_links_57\" style=\"display:none;\"><div class=\"tp_links_entry\"><ul class=\"tp_pub_list\"><li><i class=\"fas fa-globe\"><\/i><a class=\"tp_pub_list\" href=\"https:\/\/www.biorxiv.org\/content\/early\/2026\/02\/10\/2026.02.08.704500\" title=\"https:\/\/www.biorxiv.org\/content\/early\/2026\/02\/10\/2026.02.08.704500\" target=\"_blank\">https:\/\/www.biorxiv.org\/content\/early\/2026\/02\/10\/2026.02.08.704500<\/a><\/li><li><i class=\"ai ai-doi\"><\/i><a class=\"tp_pub_list\" href=\"https:\/\/dx.doi.org\/10.64898\/2026.02.08.704500\" title=\"Follow DOI:10.64898\/2026.02.08.704500\" target=\"_blank\">doi:10.64898\/2026.02.08.704500<\/a><\/li><\/ul><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('57','tp_links')\">Close<\/a><\/p><\/div><\/div><\/div><div class=\"tp_publication tp_publication_article\"><div class=\"tp_pub_number\">56.<\/div><div class=\"tp_pub_info\"><p class=\"tp_pub_author\">Yusuke Umemura,  Takashi Fukaya<\/p><p class=\"tp_pub_title\"><a class=\"tp_title_link\" href=\"https:\/\/dx.doi.org\/10.64898\/2026.02.03.703437\" title=\"The Drosophila ZAD zinc finger protein Mulberry shapes the organization of the regulatory genome in the early embryo\" target=\"blank\">The Drosophila ZAD zinc finger protein Mulberry shapes the organization of the regulatory genome in the early embryo<\/a> <span class=\"tp_pub_type article\">Journal Article<\/span> <\/p><p class=\"tp_pub_additional\"><span class=\"tp_pub_additional_in\">In: <\/span><span class=\"tp_pub_additional_journal\">bioRxiv, <\/span><span class=\"tp_pub_additional_year\">2026<\/span>.<\/p><p class=\"tp_pub_menu\"><span class=\"tp_abstract_link\"><a id=\"tp_abstract_sh_56\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('56','tp_abstract')\" title=\"Show abstract\" style=\"cursor:pointer;\">Abstract<\/a><\/span> | <span class=\"tp_resource_link\"><a id=\"tp_links_sh_56\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('56','tp_links')\" title=\"Show links and resources\" style=\"cursor:pointer;\">Links<\/a><\/span> | <span class=\"tp_pub_tags_label\">\u30bf\u30b0: <\/span><a rel=\"nofollow\" href=\"https:\/\/www.bioreg.kyushu-u.ac.jp\/ext\/epicode\/publications?tgid=6#tppubs\" title=\"Show all publications which have a relationship to this tag\">Fukaya G<\/a><\/p><div class=\"tp_bibtex\" id=\"tp_bibtex_56\" style=\"display:none;\"><div class=\"tp_bibtex_entry\"><pre>@article{Umemura2026.02.03.703437,<br \/>\r\ntitle = {The Drosophila ZAD zinc finger protein Mulberry shapes the organization of the regulatory genome in the early embryo},<br \/>\r\nauthor = {Yusuke Umemura and Takashi Fukaya},<br \/>\r\nurl = {https:\/\/www.biorxiv.org\/content\/early\/2026\/02\/05\/2026.02.03.703437},<br \/>\r\ndoi = {10.64898\/2026.02.03.703437},<br \/>\r\nyear  = {2026},<br \/>\r\ndate = {2026-02-05},<br \/>\r\nurldate = {2026-01-01},<br \/>\r\njournal = {bioRxiv},<br \/>\r\npublisher = {Cold Spring Harbor Laboratory},<br \/>\r\nabstract = {Long-range regulatory interactions play a fundamentally important role in the control of gene activity during animal development, yet the underlying mechanisms remain largely unclear. Here, we identified a zinc finger-associated domain (ZAD)-C2H2 zinc finger protein, CG31365\/Mulberry, as a looping factor that mediates long-range tethering activity in the early Drosophila embryo. Evidence is provided that Mulberry is specifically recruited to a subset of loop anchors and topological boundaries at key developmental loci to shape genome organization and gene activity. Super-resolution imaging analysis revealed that Mulberry forms nuclear condensates that associate with its target loci through the structured N-terminal ZAD domain. Micro-C analysis further demonstrated that the formation of loops and boundaries is lost in the condensation-deficient Mulberry mutant in a locus-specific manner. We propose that Mulberry acts as a condensation-dependent structural regulator of genome topology, organizing \"multi-way regulatory hubs\" that mediate long-range gene activation during early embryogenesis.},<br \/>\r\nkeywords = {Fukaya G},<br \/>\r\npubstate = {published},<br \/>\r\ntppubtype = {article}<br \/>\r\n}<br \/>\r\n<\/pre><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('56','tp_bibtex')\">Close<\/a><\/p><\/div><div class=\"tp_abstract\" id=\"tp_abstract_56\" style=\"display:none;\"><div class=\"tp_abstract_entry\">Long-range regulatory interactions play a fundamentally important role in the control of gene activity during animal development, yet the underlying mechanisms remain largely unclear. Here, we identified a zinc finger-associated domain (ZAD)-C2H2 zinc finger protein, CG31365\/Mulberry, as a looping factor that mediates long-range tethering activity in the early Drosophila embryo. Evidence is provided that Mulberry is specifically recruited to a subset of loop anchors and topological boundaries at key developmental loci to shape genome organization and gene activity. Super-resolution imaging analysis revealed that Mulberry forms nuclear condensates that associate with its target loci through the structured N-terminal ZAD domain. Micro-C analysis further demonstrated that the formation of loops and boundaries is lost in the condensation-deficient Mulberry mutant in a locus-specific manner. We propose that Mulberry acts as a condensation-dependent structural regulator of genome topology, organizing &quot;multi-way regulatory hubs&quot; that mediate long-range gene activation during early embryogenesis.<\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('56','tp_abstract')\">Close<\/a><\/p><\/div><div class=\"tp_links\" id=\"tp_links_56\" style=\"display:none;\"><div class=\"tp_links_entry\"><ul class=\"tp_pub_list\"><li><i class=\"fas fa-globe\"><\/i><a class=\"tp_pub_list\" href=\"https:\/\/www.biorxiv.org\/content\/early\/2026\/02\/05\/2026.02.03.703437\" title=\"https:\/\/www.biorxiv.org\/content\/early\/2026\/02\/05\/2026.02.03.703437\" target=\"_blank\">https:\/\/www.biorxiv.org\/content\/early\/2026\/02\/05\/2026.02.03.703437<\/a><\/li><li><i class=\"ai ai-doi\"><\/i><a class=\"tp_pub_list\" href=\"https:\/\/dx.doi.org\/10.64898\/2026.02.03.703437\" title=\"Follow DOI:10.64898\/2026.02.03.703437\" target=\"_blank\">doi:10.64898\/2026.02.03.703437<\/a><\/li><\/ul><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('56','tp_links')\">Close<\/a><\/p><\/div><\/div><\/div><div class=\"tp_publication tp_publication_article\"><div class=\"tp_pub_number\">55.<\/div><div class=\"tp_pub_info\"><p class=\"tp_pub_author\">Yusaku Tanaka,  Akihisa Osakabe,  Wataru Shihoya,  Hisato Hirano,  Yuzuru Itoh,  Tetsuji Kakutani,  Osamu Nureki<\/p><p class=\"tp_pub_title\"><a class=\"tp_title_link\" href=\"https:\/\/dx.doi.org\/10.1266\/ggs.25-00096\" title=\"Structure and evolution of the sequence-specific anti-silencing factor VANC21 and its target DNA\" target=\"blank\">Structure and evolution of the sequence-specific anti-silencing factor VANC21 and its target DNA<\/a> <span class=\"tp_pub_type article\">Journal Article<\/span> <\/p><p class=\"tp_pub_additional\"><span class=\"tp_pub_additional_in\">In: <\/span><span class=\"tp_pub_additional_journal\">Genes Genet. Syst., <\/span><span class=\"tp_pub_additional_year\">2026<\/span>, <span class=\"tp_pub_additional_issn\">ISSN: 1880-5779<\/span>.<\/p><p class=\"tp_pub_menu\"><span class=\"tp_abstract_link\"><a id=\"tp_abstract_sh_55\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('55','tp_abstract')\" title=\"Show abstract\" style=\"cursor:pointer;\">Abstract<\/a><\/span> | <span class=\"tp_resource_link\"><a id=\"tp_links_sh_55\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('55','tp_links')\" title=\"Show links and resources\" style=\"cursor:pointer;\">Links<\/a><\/span> | <span class=\"tp_pub_tags_label\">\u30bf\u30b0: <\/span><a rel=\"nofollow\" href=\"https:\/\/www.bioreg.kyushu-u.ac.jp\/ext\/epicode\/publications?tgid=26#tppubs\" title=\"Show all publications which have a relationship to this tag\">Osakabe G<\/a><\/p><div class=\"tp_bibtex\" id=\"tp_bibtex_55\" style=\"display:none;\"><div class=\"tp_bibtex_entry\"><pre>@article{Tanaka2025,<br \/>\r\ntitle = {Structure and evolution of the sequence-specific anti-silencing factor VANC21 and its target DNA},<br \/>\r\nauthor = {Yusaku Tanaka and Akihisa Osakabe and Wataru Shihoya and Hisato Hirano and Yuzuru Itoh and Tetsuji Kakutani and Osamu Nureki},<br \/>\r\ndoi = {10.1266\/ggs.25-00096},<br \/>\r\nissn = {1880-5779},<br \/>\r\nyear  = {2026},<br \/>\r\ndate = {2026-02-03},<br \/>\r\njournal = {Genes Genet. Syst.},<br \/>\r\npublisher = {Genetics Society of Japan},<br \/>\r\nabstract = {VANDAL family DNA transposons are prevalent in Arabidopsis and related plants. A notable feature of VANDALs is that they can overcome epigenetic silencing from the host, using a VANC protein encoded in each VANDAL member: VANC21 protein encoded in VANDAL21 specifically accumulates on its target DNA motifs that are concentrated in the non-coding regions of this TE and induces loss of DNA methylation, transcriptional derepression, and mobilization of the element. In this study, to elucidate the mechanism of how VANC subtypes have diverged to bind specifically to their own target motifs in their cognate VANDAL subfamilies, we determined the crystal structure of VANC21 in complex with its target DNA at 2.0 \u00c5 resolution. The VANC structure adopts a globular novel fold with a Zn ion coordinated at the DNA-binding site. Interestingly, most DNA-interacting VANC residues are located in the loops but not in the conserved regions among VANC subtypes. This observation suggests that the high variability of DNA-interacting regions of VANC proteins brought about the co-evolution of VANCs and their target sequences. This rapid differentiation by co-evolution enabled VANDAL family TEs to proliferate while avoiding deleterious effects on host fitness. Therefore, our findings help to understand the adaptive evolutionary strategy for the survival of parasitic sequences.},<br \/>\r\nkeywords = {Osakabe G},<br \/>\r\npubstate = {published},<br \/>\r\ntppubtype = {article}<br \/>\r\n}<br \/>\r\n<\/pre><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('55','tp_bibtex')\">Close<\/a><\/p><\/div><div class=\"tp_abstract\" id=\"tp_abstract_55\" style=\"display:none;\"><div class=\"tp_abstract_entry\">VANDAL family DNA transposons are prevalent in Arabidopsis and related plants. A notable feature of VANDALs is that they can overcome epigenetic silencing from the host, using a VANC protein encoded in each VANDAL member: VANC21 protein encoded in VANDAL21 specifically accumulates on its target DNA motifs that are concentrated in the non-coding regions of this TE and induces loss of DNA methylation, transcriptional derepression, and mobilization of the element. In this study, to elucidate the mechanism of how VANC subtypes have diverged to bind specifically to their own target motifs in their cognate VANDAL subfamilies, we determined the crystal structure of VANC21 in complex with its target DNA at 2.0 \u00c5 resolution. The VANC structure adopts a globular novel fold with a Zn ion coordinated at the DNA-binding site. Interestingly, most DNA-interacting VANC residues are located in the loops but not in the conserved regions among VANC subtypes. This observation suggests that the high variability of DNA-interacting regions of VANC proteins brought about the co-evolution of VANCs and their target sequences. This rapid differentiation by co-evolution enabled VANDAL family TEs to proliferate while avoiding deleterious effects on host fitness. Therefore, our findings help to understand the adaptive evolutionary strategy for the survival of parasitic sequences.<\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('55','tp_abstract')\">Close<\/a><\/p><\/div><div class=\"tp_links\" id=\"tp_links_55\" style=\"display:none;\"><div class=\"tp_links_entry\"><ul class=\"tp_pub_list\"><li><i class=\"ai ai-doi\"><\/i><a class=\"tp_pub_list\" href=\"https:\/\/dx.doi.org\/10.1266\/ggs.25-00096\" title=\"Follow DOI:10.1266\/ggs.25-00096\" target=\"_blank\">doi:10.1266\/ggs.25-00096<\/a><\/li><\/ul><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('55','tp_links')\">Close<\/a><\/p><\/div><\/div><\/div><div class=\"tp_publication tp_publication_article\"><div class=\"tp_pub_number\">54.<\/div><div class=\"tp_pub_info\"><p class=\"tp_pub_author\">Tomoya Kujirai,  Haruhiko Ehara,  Tomoko Ito,  Masami Henmi,  Eriko Oya,  Takehiko Kobayashi,  Shun-ichi Sekine,  Hitoshi Kurumizaka<\/p><p class=\"tp_pub_title\"><a class=\"tp_title_link\" href=\"https:\/\/dx.doi.org\/10.1126\/sciadv.aed1952\" title=\"Structural basis of transcription-coupled H3K36 trimethylation by Set2 in coordination with FACT\" target=\"blank\">Structural basis of transcription-coupled H3K36 trimethylation by Set2 in coordination with FACT<\/a> <span class=\"tp_pub_type article\">Journal Article<\/span> <\/p><p class=\"tp_pub_additional\"><span class=\"tp_pub_additional_in\">In: <\/span><span class=\"tp_pub_additional_journal\">Science Advances, <\/span><span class=\"tp_pub_additional_volume\">vol. 12, <\/span><span class=\"tp_pub_additional_number\">no. 5, <\/span><span class=\"tp_pub_additional_pages\">pp. eaed1952, <\/span><span class=\"tp_pub_additional_year\">2026<\/span>.<\/p><p class=\"tp_pub_menu\"><span class=\"tp_abstract_link\"><a id=\"tp_abstract_sh_54\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('54','tp_abstract')\" title=\"Show abstract\" style=\"cursor:pointer;\">Abstract<\/a><\/span> | <span class=\"tp_resource_link\"><a id=\"tp_links_sh_54\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('54','tp_links')\" title=\"Show links and resources\" style=\"cursor:pointer;\">Links<\/a><\/span> | <span class=\"tp_pub_tags_label\">\u30bf\u30b0: <\/span><a rel=\"nofollow\" href=\"https:\/\/www.bioreg.kyushu-u.ac.jp\/ext\/epicode\/publications?tgid=4#tppubs\" title=\"Show all publications which have a relationship to this tag\">Kurumizaka G<\/a><\/p><div class=\"tp_bibtex\" id=\"tp_bibtex_54\" style=\"display:none;\"><div class=\"tp_bibtex_entry\"><pre>@article{&lt;LineBreak&gt;doi:10.1126\/sciadv.aed1952,<br \/>\r\ntitle = {Structural basis of transcription-coupled H3K36 trimethylation by Set2 in coordination with FACT},<br \/>\r\nauthor = {Tomoya Kujirai and Haruhiko Ehara and Tomoko Ito and Masami Henmi and Eriko Oya and Takehiko Kobayashi and Shun-ichi Sekine and Hitoshi Kurumizaka},<br \/>\r\nurl = {https:\/\/www.science.org\/doi\/abs\/10.1126\/sciadv.aed1952},<br \/>\r\ndoi = {10.1126\/sciadv.aed1952},<br \/>\r\nyear  = {2026},<br \/>\r\ndate = {2026-01-28},<br \/>\r\nurldate = {2026-01-01},<br \/>\r\njournal = {Science Advances},<br \/>\r\nvolume = {12},<br \/>\r\nnumber = {5},<br \/>\r\npages = {eaed1952},<br \/>\r\nabstract = {Trimethylation of the histone H3K36 residue (H3K36me3) plays an indispensable role in ensuring transcription fidelity by suppressing undesired cryptic transcription in chromatin. H3K36me3 modification is accomplished by Set2\/SETD2 during transcription elongation by the RNA polymerase II elongation complex (EC). Here, we found that Set2-mediated H3K36me3 deposition occurs on the nucleosome reassembling behind the EC. The histone chaperone FACT suppresses H3K36me3 deposition on the downstream nucleosome, thereby ensuring that Set2 targets specifically on the reassembling upstream nucleosome. Cryo\u2013electron microscopy structures of the nucleosome-transcribing EC complexed with Set2 revealed that Set2 is anchored by the Spt6 subunit of the EC to capture both of the H3 N-terminal tails in a stepwise manner during the nucleosome reassembly process. Abrogation of the Set2-EC interaction leads to defective transcription-coupled H3K36me3 deposition. These insights elucidate the structure-based mechanism of transcription-coupled H3K36me3 deposition in chromatin. Cryo-EM structures of RNAPII EC-Set2-nucleosome with FACT reveal the mechanism of transcription-coupled H3K36 trimethylation.},<br \/>\r\nkeywords = {Kurumizaka G},<br \/>\r\npubstate = {published},<br \/>\r\ntppubtype = {article}<br \/>\r\n}<br \/>\r\n<\/pre><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('54','tp_bibtex')\">Close<\/a><\/p><\/div><div class=\"tp_abstract\" id=\"tp_abstract_54\" style=\"display:none;\"><div class=\"tp_abstract_entry\">Trimethylation of the histone H3K36 residue (H3K36me3) plays an indispensable role in ensuring transcription fidelity by suppressing undesired cryptic transcription in chromatin. H3K36me3 modification is accomplished by Set2\/SETD2 during transcription elongation by the RNA polymerase II elongation complex (EC). Here, we found that Set2-mediated H3K36me3 deposition occurs on the nucleosome reassembling behind the EC. The histone chaperone FACT suppresses H3K36me3 deposition on the downstream nucleosome, thereby ensuring that Set2 targets specifically on the reassembling upstream nucleosome. Cryo\u2013electron microscopy structures of the nucleosome-transcribing EC complexed with Set2 revealed that Set2 is anchored by the Spt6 subunit of the EC to capture both of the H3 N-terminal tails in a stepwise manner during the nucleosome reassembly process. Abrogation of the Set2-EC interaction leads to defective transcription-coupled H3K36me3 deposition. These insights elucidate the structure-based mechanism of transcription-coupled H3K36me3 deposition in chromatin. Cryo-EM structures of RNAPII EC-Set2-nucleosome with FACT reveal the mechanism of transcription-coupled H3K36 trimethylation.<\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('54','tp_abstract')\">Close<\/a><\/p><\/div><div class=\"tp_links\" id=\"tp_links_54\" style=\"display:none;\"><div class=\"tp_links_entry\"><ul class=\"tp_pub_list\"><li><i class=\"fas fa-globe\"><\/i><a class=\"tp_pub_list\" href=\"https:\/\/www.science.org\/doi\/abs\/10.1126\/sciadv.aed1952\" title=\"https:\/\/www.science.org\/doi\/abs\/10.1126\/sciadv.aed1952\" target=\"_blank\">https:\/\/www.science.org\/doi\/abs\/10.1126\/sciadv.aed1952<\/a><\/li><li><i class=\"ai ai-doi\"><\/i><a class=\"tp_pub_list\" href=\"https:\/\/dx.doi.org\/10.1126\/sciadv.aed1952\" title=\"Follow DOI:10.1126\/sciadv.aed1952\" target=\"_blank\">doi:10.1126\/sciadv.aed1952<\/a><\/li><\/ul><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('54','tp_links')\">Close<\/a><\/p><\/div><\/div><\/div><div class=\"tp_publication tp_publication_article\"><div class=\"tp_pub_number\">53.<\/div><div class=\"tp_pub_info\"><p class=\"tp_pub_author\">Naoki Horikoshi,  Hitoshi Kurumizaka<\/p><p class=\"tp_pub_title\"><a class=\"tp_title_link\" href=\"https:\/\/dx.doi.org\/10.1002\/bies.70104\" title=\"Nucleosome Bundling by Barrier\u2010to\u2010Autointegration Factor: Implications for Its Diverse Functions\" target=\"blank\">Nucleosome Bundling by Barrier\u2010to\u2010Autointegration Factor: Implications for Its Diverse Functions<\/a> <span class=\"tp_pub_type article\">Journal Article<\/span> <\/p><p class=\"tp_pub_additional\"><span class=\"tp_pub_additional_in\">In: <\/span><span class=\"tp_pub_additional_journal\">BioEssays, <\/span><span class=\"tp_pub_additional_volume\">vol. 48, <\/span><span class=\"tp_pub_additional_number\">no. 1, <\/span><span class=\"tp_pub_additional_year\">2026<\/span>, <span class=\"tp_pub_additional_issn\">ISSN: 1521-1878<\/span>.<\/p><p class=\"tp_pub_menu\"><span class=\"tp_abstract_link\"><a id=\"tp_abstract_sh_53\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('53','tp_abstract')\" title=\"Show abstract\" style=\"cursor:pointer;\">Abstract<\/a><\/span> | <span class=\"tp_resource_link\"><a id=\"tp_links_sh_53\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('53','tp_links')\" title=\"Show links and resources\" style=\"cursor:pointer;\">Links<\/a><\/span> | <span class=\"tp_pub_tags_label\">\u30bf\u30b0: <\/span><a rel=\"nofollow\" href=\"https:\/\/www.bioreg.kyushu-u.ac.jp\/ext\/epicode\/publications?tgid=8#tppubs\" title=\"Show all publications which have a relationship to this tag\">Horikoshi G<\/a>, <a rel=\"nofollow\" href=\"https:\/\/www.bioreg.kyushu-u.ac.jp\/ext\/epicode\/publications?tgid=4#tppubs\" title=\"Show all publications which have a relationship to this tag\">Kurumizaka G<\/a><\/p><div class=\"tp_bibtex\" id=\"tp_bibtex_53\" style=\"display:none;\"><div class=\"tp_bibtex_entry\"><pre>@article{Horikoshi2026,<br \/>\r\ntitle = {Nucleosome Bundling by Barrier\u2010to\u2010Autointegration Factor: Implications for Its Diverse Functions},<br \/>\r\nauthor = {Naoki Horikoshi and Hitoshi Kurumizaka},<br \/>\r\ndoi = {10.1002\/bies.70104},<br \/>\r\nissn = {1521-1878},<br \/>\r\nyear  = {2026},<br \/>\r\ndate = {2026-01-22},<br \/>\r\njournal = {BioEssays},<br \/>\r\nvolume = {48},<br \/>\r\nnumber = {1},<br \/>\r\npublisher = {Wiley},<br \/>\r\nabstract = {In eukaryotic cells, genomic DNA is packaged into chromatin, restricting the access of regulatory proteins and thus regulating key processes such as transcription, replication, recombination, and the repair of DNA. Barrier-to-autointegration factor (BAF) plays key roles in organizing chromatin architecture and nuclear functions. BAF bridges DNA segments and connects them to Lamin A\/C and inner nuclear membrane proteins containing the LEM domain, ensuring proper chromatin organization and nuclear envelope assembly and repair. Over the last three decades, multiple structural studies have revealed that BAF dimerizes to bind DNA and shapes higher-order chromatin structure. In this review, we summarize the structural features of BAF in complexes with its binding partners and explore how these interactions contribute to maintaining nuclear integrity and regulating genome function.},<br \/>\r\nkeywords = {Horikoshi G, Kurumizaka G},<br \/>\r\npubstate = {published},<br \/>\r\ntppubtype = {article}<br \/>\r\n}<br \/>\r\n<\/pre><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('53','tp_bibtex')\">Close<\/a><\/p><\/div><div class=\"tp_abstract\" id=\"tp_abstract_53\" style=\"display:none;\"><div class=\"tp_abstract_entry\">In eukaryotic cells, genomic DNA is packaged into chromatin, restricting the access of regulatory proteins and thus regulating key processes such as transcription, replication, recombination, and the repair of DNA. Barrier-to-autointegration factor (BAF) plays key roles in organizing chromatin architecture and nuclear functions. BAF bridges DNA segments and connects them to Lamin A\/C and inner nuclear membrane proteins containing the LEM domain, ensuring proper chromatin organization and nuclear envelope assembly and repair. Over the last three decades, multiple structural studies have revealed that BAF dimerizes to bind DNA and shapes higher-order chromatin structure. In this review, we summarize the structural features of BAF in complexes with its binding partners and explore how these interactions contribute to maintaining nuclear integrity and regulating genome function.<\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('53','tp_abstract')\">Close<\/a><\/p><\/div><div class=\"tp_links\" id=\"tp_links_53\" style=\"display:none;\"><div class=\"tp_links_entry\"><ul class=\"tp_pub_list\"><li><i class=\"ai ai-doi\"><\/i><a class=\"tp_pub_list\" href=\"https:\/\/dx.doi.org\/10.1002\/bies.70104\" title=\"Follow DOI:10.1002\/bies.70104\" target=\"_blank\">doi:10.1002\/bies.70104<\/a><\/li><\/ul><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('53','tp_links')\">Close<\/a><\/p><\/div><\/div><\/div><div class=\"tp_publication tp_publication_unpublished\"><div class=\"tp_pub_number\">52.<\/div><div class=\"tp_pub_info\"><p class=\"tp_pub_author\">Marina Takechi,  Yezhang Zhu,  Zezhen Lu,  Ying Zeng,  Ken-Ich Mizutani,  Toru Nakano,  Li Shen,  Shinpei Yamaguchi<\/p><p class=\"tp_pub_title\"><a class=\"tp_title_link\" href=\"https:\/\/dx.doi.org\/10.64898\/2026.01.06.697935\" title=\"Parthenogenote-Derived Brain Unveils the Critical Role of Paternal Genome in Neural Development\" target=\"blank\">Parthenogenote-Derived Brain Unveils the Critical Role of Paternal Genome in Neural Development<\/a> <span class=\"tp_pub_type unpublished\">Unpublished<\/span> <\/p><p class=\"tp_pub_additional\"><span class=\"tp_pub_additional_howpublished\">bioRxiv, <\/span><span class=\"tp_pub_additional_year\">2026<\/span>.<\/p><p class=\"tp_pub_menu\"><span class=\"tp_abstract_link\"><a id=\"tp_abstract_sh_52\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('52','tp_abstract')\" title=\"Show abstract\" style=\"cursor:pointer;\">Abstract<\/a><\/span> | <span class=\"tp_resource_link\"><a id=\"tp_links_sh_52\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('52','tp_links')\" title=\"Show links and resources\" style=\"cursor:pointer;\">Links<\/a><\/span> | <span class=\"tp_pub_tags_label\">\u30bf\u30b0: <\/span><a rel=\"nofollow\" href=\"https:\/\/www.bioreg.kyushu-u.ac.jp\/ext\/epicode\/publications?tgid=25#tppubs\" title=\"Show all publications which have a relationship to this tag\">Yamaguchi G<\/a><\/p><div class=\"tp_bibtex\" id=\"tp_bibtex_52\" style=\"display:none;\"><div class=\"tp_bibtex_entry\"><pre>@unpublished{Takechi2026,<br \/>\r\ntitle = {Parthenogenote-Derived Brain Unveils the Critical Role of Paternal Genome in Neural Development},<br \/>\r\nauthor = {Marina Takechi and Yezhang Zhu and Zezhen Lu and Ying Zeng and Ken-Ich Mizutani and Toru Nakano and Li Shen and Shinpei Yamaguchi},<br \/>\r\nurl = {http:\/\/biorxiv.org\/lookup\/doi\/10.64898\/2026.01.06.697935},<br \/>\r\ndoi = {10.64898\/2026.01.06.697935},<br \/>\r\nyear  = {2026},<br \/>\r\ndate = {2026-01-06},<br \/>\r\nurldate = {2026-01-06},<br \/>\r\npublisher = {openRxiv},<br \/>\r\nabstract = {Genomic imprinting, an epigenetic mechanism that governs parent-of-origin-specific gene expression, is essential for mammalian development, yet its role in late-stage development remains unclear due to the lethality of parthenogenetic (Pg) embryos. Here, we establish cell replacement with parthenogenote-derived cells (CReP), a blastocyst complementation strategy that enables survival and tissue-specific contribution of Pg-derived cells. Brain-targeted CReP showed that Pg-derived cells can participate in neural development but fail to maintain neuronal-glial balance due to aberrant activation of Notch signaling caused by the loss of the paternally expressed gene Dlk1. Restoration of Dlk1 normalized Notch activity and rescued neuronal differentiation. These findings reveal a critical role of the paternal genome, through Dlk1-mediated regulation of Notch signaling, in ensuring neural stem cell expansion and balanced cell fate decisions. The CReP model provides a powerful platform for investigating genomic imprinting and parental genome contributions in development and disease.},<br \/>\r\nhowpublished = {bioRxiv},<br \/>\r\nkeywords = {Yamaguchi G},<br \/>\r\npubstate = {published},<br \/>\r\ntppubtype = {unpublished}<br \/>\r\n}<br \/>\r\n<\/pre><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('52','tp_bibtex')\">Close<\/a><\/p><\/div><div class=\"tp_abstract\" id=\"tp_abstract_52\" style=\"display:none;\"><div class=\"tp_abstract_entry\">Genomic imprinting, an epigenetic mechanism that governs parent-of-origin-specific gene expression, is essential for mammalian development, yet its role in late-stage development remains unclear due to the lethality of parthenogenetic (Pg) embryos. Here, we establish cell replacement with parthenogenote-derived cells (CReP), a blastocyst complementation strategy that enables survival and tissue-specific contribution of Pg-derived cells. Brain-targeted CReP showed that Pg-derived cells can participate in neural development but fail to maintain neuronal-glial balance due to aberrant activation of Notch signaling caused by the loss of the paternally expressed gene Dlk1. Restoration of Dlk1 normalized Notch activity and rescued neuronal differentiation. These findings reveal a critical role of the paternal genome, through Dlk1-mediated regulation of Notch signaling, in ensuring neural stem cell expansion and balanced cell fate decisions. The CReP model provides a powerful platform for investigating genomic imprinting and parental genome contributions in development and disease.<\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('52','tp_abstract')\">Close<\/a><\/p><\/div><div class=\"tp_links\" id=\"tp_links_52\" style=\"display:none;\"><div class=\"tp_links_entry\"><ul class=\"tp_pub_list\"><li><i class=\"fas fa-globe\"><\/i><a class=\"tp_pub_list\" href=\"http:\/\/biorxiv.org\/lookup\/doi\/10.64898\/2026.01.06.697935\" title=\"http:\/\/biorxiv.org\/lookup\/doi\/10.64898\/2026.01.06.697935\" target=\"_blank\">http:\/\/biorxiv.org\/lookup\/doi\/10.64898\/2026.01.06.697935<\/a><\/li><li><i class=\"ai ai-doi\"><\/i><a class=\"tp_pub_list\" href=\"https:\/\/dx.doi.org\/10.64898\/2026.01.06.697935\" title=\"Follow DOI:10.64898\/2026.01.06.697935\" target=\"_blank\">doi:10.64898\/2026.01.06.697935<\/a><\/li><\/ul><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('52','tp_links')\">Close<\/a><\/p><\/div><\/div><\/div><div class=\"tp_publication tp_publication_article\"><div class=\"tp_pub_number\">51.<\/div><div class=\"tp_pub_info\"><p class=\"tp_pub_author\">Gabriel Galindo,  Daiki Maejima,  Jacob DeRoo,  Scott R. Burlingham,  Gretchen Fixen,  Tatsuya Morisaki,  Hallie P. Febvre,  Ryan Hasbrook,  Ning Zhao,  Soham Ghosh,  E. Handly Mayton,  Christopher D. Snow,  Brian J. Geiss,  Yasuyuki Ohkawa,  Yuko Sato,  Hiroshi Kimura,  Timothy J. Stasevich<\/p><p class=\"tp_pub_title\"><a class=\"tp_title_link\" href=\"https:\/\/dx.doi.org\/10.1126\/sciadv.adx8352\" title=\"AI-assisted protein design to rapidly convert antibody sequences to intrabodies targeting diverse peptides and histone modifications\" target=\"blank\">AI-assisted protein design to rapidly convert antibody sequences to intrabodies targeting diverse peptides and histone modifications<\/a> <span class=\"tp_pub_type article\">Journal Article<\/span> <\/p><p class=\"tp_pub_additional\"><span class=\"tp_pub_additional_in\">In: <\/span><span class=\"tp_pub_additional_journal\">Sci. Adv., <\/span><span class=\"tp_pub_additional_volume\">vol. 12, <\/span><span class=\"tp_pub_additional_number\">no. 1, <\/span><span class=\"tp_pub_additional_year\">2026<\/span>, <span class=\"tp_pub_additional_issn\">ISSN: 2375-2548<\/span>.<\/p><p class=\"tp_pub_menu\"><span class=\"tp_abstract_link\"><a id=\"tp_abstract_sh_51\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('51','tp_abstract')\" title=\"Show abstract\" style=\"cursor:pointer;\">Abstract<\/a><\/span> | <span class=\"tp_resource_link\"><a id=\"tp_links_sh_51\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('51','tp_links')\" title=\"Show links and resources\" style=\"cursor:pointer;\">Links<\/a><\/span> | <span class=\"tp_pub_tags_label\">\u30bf\u30b0: <\/span><a rel=\"nofollow\" href=\"https:\/\/www.bioreg.kyushu-u.ac.jp\/ext\/epicode\/publications?tgid=2#tppubs\" title=\"Show all publications which have a relationship to this tag\">Kimura G<\/a>, <a rel=\"nofollow\" href=\"https:\/\/www.bioreg.kyushu-u.ac.jp\/ext\/epicode\/publications?tgid=1#tppubs\" title=\"Show all publications which have a relationship to this tag\">Ohkawa G<\/a><\/p><div class=\"tp_bibtex\" id=\"tp_bibtex_51\" style=\"display:none;\"><div class=\"tp_bibtex_entry\"><pre>@article{Galindo2026,<br \/>\r\ntitle = {AI-assisted protein design to rapidly convert antibody sequences to intrabodies targeting diverse peptides and histone modifications},<br \/>\r\nauthor = {Gabriel Galindo and Daiki Maejima and Jacob DeRoo and Scott R. Burlingham and Gretchen Fixen and Tatsuya Morisaki and Hallie P. Febvre and Ryan Hasbrook and Ning Zhao and Soham Ghosh and E. Handly Mayton and Christopher D. Snow and Brian J. Geiss and Yasuyuki Ohkawa and Yuko Sato and Hiroshi Kimura and Timothy J. Stasevich},<br \/>\r\ndoi = {10.1126\/sciadv.adx8352},<br \/>\r\nissn = {2375-2548},<br \/>\r\nyear  = {2026},<br \/>\r\ndate = {2026-01-02},<br \/>\r\nurldate = {2026-01-02},<br \/>\r\njournal = {Sci. Adv.},<br \/>\r\nvolume = {12},<br \/>\r\nnumber = {1},<br \/>\r\npublisher = {American Association for the Advancement of Science (AAAS)},<br \/>\r\nabstract = {Intrabodies are engineered antibodies that function inside living cells, enabling therapeutic, diagnostic, and imaging applications. While powerful, their development has been hindered by challenges associated with their folding, solubility, and stability in the reduced intracellular environment. Here, we present an artificial intelligence-driven pipeline integrating AlphaFold2, ProteinMPNN, and live-cell screening to optimize antibody framework regions while preserving epitope-binding complementarity-determining regions. Using this approach, we successfully converted 19 of 26 antibody sequences into functional single-chain variable fragment intrabodies, including a panel targeting diverse histone modifications for real-time imaging of chromatin dynamics and gene regulation. Notably, 18 of these 19 sequences had failed to convert using the standard approach, demonstrating the unique effectiveness of our method. As antibody sequence databases expand, our method will accelerate intrabody design, making their development easier, more cost effective, and broadly accessible for biological research.},<br \/>\r\nkeywords = {Kimura G, Ohkawa G},<br \/>\r\npubstate = {published},<br \/>\r\ntppubtype = {article}<br \/>\r\n}<br \/>\r\n<\/pre><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('51','tp_bibtex')\">Close<\/a><\/p><\/div><div class=\"tp_abstract\" id=\"tp_abstract_51\" style=\"display:none;\"><div class=\"tp_abstract_entry\">Intrabodies are engineered antibodies that function inside living cells, enabling therapeutic, diagnostic, and imaging applications. While powerful, their development has been hindered by challenges associated with their folding, solubility, and stability in the reduced intracellular environment. Here, we present an artificial intelligence-driven pipeline integrating AlphaFold2, ProteinMPNN, and live-cell screening to optimize antibody framework regions while preserving epitope-binding complementarity-determining regions. Using this approach, we successfully converted 19 of 26 antibody sequences into functional single-chain variable fragment intrabodies, including a panel targeting diverse histone modifications for real-time imaging of chromatin dynamics and gene regulation. Notably, 18 of these 19 sequences had failed to convert using the standard approach, demonstrating the unique effectiveness of our method. As antibody sequence databases expand, our method will accelerate intrabody design, making their development easier, more cost effective, and broadly accessible for biological research.<\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('51','tp_abstract')\">Close<\/a><\/p><\/div><div class=\"tp_links\" id=\"tp_links_51\" style=\"display:none;\"><div class=\"tp_links_entry\"><ul class=\"tp_pub_list\"><li><i class=\"ai ai-doi\"><\/i><a class=\"tp_pub_list\" href=\"https:\/\/dx.doi.org\/10.1126\/sciadv.adx8352\" title=\"Follow DOI:10.1126\/sciadv.adx8352\" target=\"_blank\">doi:10.1126\/sciadv.adx8352<\/a><\/li><\/ul><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('51','tp_links')\">Close<\/a><\/p><\/div><\/div><\/div><h3 class=\"tp_h3\" id=\"tp_h3_2025\">2025<\/h3><div class=\"tp_publication tp_publication_article\"><div class=\"tp_pub_number\">50.<\/div><div class=\"tp_pub_info\"><p class=\"tp_pub_author\">Kazumitsu Maehara,  Yasuyuki Ohkawa<\/p><p class=\"tp_pub_title\"><a class=\"tp_title_link\" href=\"https:\/\/dx.doi.org\/10.1038\/s41467-025-67782-6\" title=\"Geometry-preserving vector field reconstruction of high-dimensional cell-state dynamics using ddHodge\" target=\"blank\">Geometry-preserving vector field reconstruction of high-dimensional cell-state dynamics using ddHodge<\/a> <span class=\"tp_pub_type article\">Journal Article<\/span> <\/p><p class=\"tp_pub_additional\"><span class=\"tp_pub_additional_in\">In: <\/span><span class=\"tp_pub_additional_journal\">Nat Commun, <\/span><span class=\"tp_pub_additional_volume\">vol. 16, <\/span><span class=\"tp_pub_additional_number\">no. 1, <\/span><span class=\"tp_pub_additional_year\">2025<\/span>, <span class=\"tp_pub_additional_issn\">ISSN: 2041-1723<\/span>.<\/p><p class=\"tp_pub_menu\"><span class=\"tp_abstract_link\"><a id=\"tp_abstract_sh_49\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('49','tp_abstract')\" title=\"Show abstract\" style=\"cursor:pointer;\">Abstract<\/a><\/span> | <span class=\"tp_resource_link\"><a id=\"tp_links_sh_49\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('49','tp_links')\" title=\"Show links and resources\" style=\"cursor:pointer;\">Links<\/a><\/span> | <span class=\"tp_pub_tags_label\">\u30bf\u30b0: <\/span><a rel=\"nofollow\" href=\"https:\/\/www.bioreg.kyushu-u.ac.jp\/ext\/epicode\/publications?tgid=1#tppubs\" title=\"Show all publications which have a relationship to this tag\">Ohkawa G<\/a><\/p><div class=\"tp_bibtex\" id=\"tp_bibtex_49\" style=\"display:none;\"><div class=\"tp_bibtex_entry\"><pre>@article{Maehara2025,<br \/>\r\ntitle = {Geometry-preserving vector field reconstruction of high-dimensional cell-state dynamics using ddHodge},<br \/>\r\nauthor = {Kazumitsu Maehara and Yasuyuki Ohkawa},<br \/>\r\ndoi = {10.1038\/s41467-025-67782-6},<br \/>\r\nissn = {2041-1723},<br \/>\r\nyear  = {2025},<br \/>\r\ndate = {2025-12-29},<br \/>\r\njournal = {Nat Commun},<br \/>\r\nvolume = {16},<br \/>\r\nnumber = {1},<br \/>\r\npublisher = {Springer Science and Business Media LLC},<br \/>\r\nabstract = {The differentiation potency of cells is governed by dynamic changes in gene expression, which can be inferred from single-cell RNA sequencing (scRNA-seq) data. While velocity-based approaches have been used to analyze cell state changes as vector fields, extracting acceleration (change of change) information remains challenging because of the sparsity and high-dimensionality of the data. Here, we develop ddHodge, a framework based on Hodge decomposition for precise vector-field reconstruction. ddHodge accurately recovers all basic components of the vector field, namely, the gradient, curl, and divergence, including the acceleration of the cell state, as second-order derivatives, even from biased and sparse samples. Furthermore, we extend the method to approximate high-dimensional gene expression dynamics on lower-dimensional data manifolds. By applying ddHodge to scRNA-seq data from mouse embryogenesis, we reveal that the gene expression dynamics during development follow a gradient system shaped by potential landscapes, which has not previously been validated with real data. Furthermore, we quantify differentiation potency as cell state stability on the basis of the divergence and identify key genes that drive potency. Our general computational framework for analyzing complex biological systems can elucidate cell fate decisions in developmental processes.},<br \/>\r\nkeywords = {Ohkawa G},<br \/>\r\npubstate = {published},<br \/>\r\ntppubtype = {article}<br \/>\r\n}<br \/>\r\n<\/pre><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('49','tp_bibtex')\">Close<\/a><\/p><\/div><div class=\"tp_abstract\" id=\"tp_abstract_49\" style=\"display:none;\"><div class=\"tp_abstract_entry\">The differentiation potency of cells is governed by dynamic changes in gene expression, which can be inferred from single-cell RNA sequencing (scRNA-seq) data. While velocity-based approaches have been used to analyze cell state changes as vector fields, extracting acceleration (change of change) information remains challenging because of the sparsity and high-dimensionality of the data. Here, we develop ddHodge, a framework based on Hodge decomposition for precise vector-field reconstruction. ddHodge accurately recovers all basic components of the vector field, namely, the gradient, curl, and divergence, including the acceleration of the cell state, as second-order derivatives, even from biased and sparse samples. Furthermore, we extend the method to approximate high-dimensional gene expression dynamics on lower-dimensional data manifolds. By applying ddHodge to scRNA-seq data from mouse embryogenesis, we reveal that the gene expression dynamics during development follow a gradient system shaped by potential landscapes, which has not previously been validated with real data. Furthermore, we quantify differentiation potency as cell state stability on the basis of the divergence and identify key genes that drive potency. Our general computational framework for analyzing complex biological systems can elucidate cell fate decisions in developmental processes.<\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('49','tp_abstract')\">Close<\/a><\/p><\/div><div class=\"tp_links\" id=\"tp_links_49\" style=\"display:none;\"><div class=\"tp_links_entry\"><ul class=\"tp_pub_list\"><li><i class=\"ai ai-doi\"><\/i><a class=\"tp_pub_list\" href=\"https:\/\/dx.doi.org\/10.1038\/s41467-025-67782-6\" title=\"Follow DOI:10.1038\/s41467-025-67782-6\" target=\"_blank\">doi:10.1038\/s41467-025-67782-6<\/a><\/li><\/ul><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('49','tp_links')\">Close<\/a><\/p><\/div><\/div><\/div><div class=\"tp_publication tp_publication_article\"><div class=\"tp_pub_number\">49.<\/div><div class=\"tp_pub_info\"><p class=\"tp_pub_author\">Takeru Fujii,  Kosuke Tomimatsu,  Michiko Kato,  Miho Ito,  Shoko Sato,  Hitoshi Kurumizaka,  Yuko Sato,  Kazumitsu Maehara,  Hiroshi Kimura,  Akihito Harada,  Yasuyuki Ohkawa<\/p><p class=\"tp_pub_title\"><a class=\"tp_title_link\" href=\"https:\/\/dx.doi.org\/10.1038\/s41467-025-67016-9\" title=\"Reconstructing epigenomic dynamics through a single-cell multi-epigenome data integration framework\" target=\"blank\">Reconstructing epigenomic dynamics through a single-cell multi-epigenome data integration framework<\/a> <span class=\"tp_pub_type article\">Journal Article<\/span> <\/p><p class=\"tp_pub_additional\"><span class=\"tp_pub_additional_in\">In: <\/span><span class=\"tp_pub_additional_journal\">Nat Commun, <\/span><span class=\"tp_pub_additional_volume\">vol. 16, <\/span><span class=\"tp_pub_additional_number\">no. 1, <\/span><span class=\"tp_pub_additional_year\">2025<\/span>, <span class=\"tp_pub_additional_issn\">ISSN: 2041-1723<\/span>.<\/p><p class=\"tp_pub_menu\"><span class=\"tp_abstract_link\"><a id=\"tp_abstract_sh_48\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('48','tp_abstract')\" title=\"Show abstract\" style=\"cursor:pointer;\">Abstract<\/a><\/span> | <span class=\"tp_resource_link\"><a id=\"tp_links_sh_48\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('48','tp_links')\" title=\"Show links and resources\" style=\"cursor:pointer;\">Links<\/a><\/span> | <span class=\"tp_pub_tags_label\">\u30bf\u30b0: <\/span><a rel=\"nofollow\" href=\"https:\/\/www.bioreg.kyushu-u.ac.jp\/ext\/epicode\/publications?tgid=2#tppubs\" title=\"Show all publications which have a relationship to this tag\">Kimura G<\/a>, <a rel=\"nofollow\" href=\"https:\/\/www.bioreg.kyushu-u.ac.jp\/ext\/epicode\/publications?tgid=4#tppubs\" title=\"Show all publications which have a relationship to this tag\">Kurumizaka G<\/a>, <a rel=\"nofollow\" href=\"https:\/\/www.bioreg.kyushu-u.ac.jp\/ext\/epicode\/publications?tgid=1#tppubs\" title=\"Show all publications which have a relationship to this tag\">Ohkawa G<\/a><\/p><div class=\"tp_bibtex\" id=\"tp_bibtex_48\" style=\"display:none;\"><div class=\"tp_bibtex_entry\"><pre>@article{Fujii2025,<br \/>\r\ntitle = {Reconstructing epigenomic dynamics through a single-cell multi-epigenome data integration framework},<br \/>\r\nauthor = {Takeru Fujii and Kosuke Tomimatsu and Michiko Kato and Miho Ito and Shoko Sato and Hitoshi Kurumizaka and Yuko Sato and Kazumitsu Maehara and Hiroshi Kimura and Akihito Harada and Yasuyuki Ohkawa},<br \/>\r\ndoi = {10.1038\/s41467-025-67016-9},<br \/>\r\nissn = {2041-1723},<br \/>\r\nyear  = {2025},<br \/>\r\ndate = {2025-12-17},<br \/>\r\njournal = {Nat Commun},<br \/>\r\nvolume = {16},<br \/>\r\nnumber = {1},<br \/>\r\npublisher = {Springer Science and Business Media LLC},<br \/>\r\nabstract = {Transcriptional regulation arises from the dynamic and combinatorial actions of multiple regulatory factors on genomic DNA. Although many epigenomic regulators have been identified, the precise order in which these factors accumulate at individual gene loci to activate transcription remains unclear. Here we show a single-cell data integration framework that infers the binding order of multiple chromatin factors at single-cell resolution. Central to this framework is sci-mtChIL-seq, a scalable single-cell method that simultaneously profiles genome-wide binding of RNA polymerase II (RNAPII) and diverse epigenomic regulators. By defining transcriptional states through RNAPII occupancy and integrating multiple sci-mtChIL-seq datasets, we systematically link the combinatorial patterns of transcription factor binding, histone modifications and chromatin remodeling. This framework reveals the temporal coordination among chromatin factors during transcriptional activation, providing a powerful approach to uncover context-dependent epigenomic dynamics and the principles of gene regulation in complex cellular systems.},<br \/>\r\nkeywords = {Kimura G, Kurumizaka G, Ohkawa G},<br \/>\r\npubstate = {published},<br \/>\r\ntppubtype = {article}<br \/>\r\n}<br \/>\r\n<\/pre><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('48','tp_bibtex')\">Close<\/a><\/p><\/div><div class=\"tp_abstract\" id=\"tp_abstract_48\" style=\"display:none;\"><div class=\"tp_abstract_entry\">Transcriptional regulation arises from the dynamic and combinatorial actions of multiple regulatory factors on genomic DNA. Although many epigenomic regulators have been identified, the precise order in which these factors accumulate at individual gene loci to activate transcription remains unclear. Here we show a single-cell data integration framework that infers the binding order of multiple chromatin factors at single-cell resolution. Central to this framework is sci-mtChIL-seq, a scalable single-cell method that simultaneously profiles genome-wide binding of RNA polymerase II (RNAPII) and diverse epigenomic regulators. By defining transcriptional states through RNAPII occupancy and integrating multiple sci-mtChIL-seq datasets, we systematically link the combinatorial patterns of transcription factor binding, histone modifications and chromatin remodeling. This framework reveals the temporal coordination among chromatin factors during transcriptional activation, providing a powerful approach to uncover context-dependent epigenomic dynamics and the principles of gene regulation in complex cellular systems.<\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('48','tp_abstract')\">Close<\/a><\/p><\/div><div class=\"tp_links\" id=\"tp_links_48\" style=\"display:none;\"><div class=\"tp_links_entry\"><ul class=\"tp_pub_list\"><li><i class=\"ai ai-doi\"><\/i><a class=\"tp_pub_list\" href=\"https:\/\/dx.doi.org\/10.1038\/s41467-025-67016-9\" title=\"Follow DOI:10.1038\/s41467-025-67016-9\" target=\"_blank\">doi:10.1038\/s41467-025-67016-9<\/a><\/li><\/ul><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('48','tp_links')\">Close<\/a><\/p><\/div><\/div><\/div><div class=\"tp_publication tp_publication_article\"><div class=\"tp_pub_number\">48.<\/div><div class=\"tp_pub_info\"><p class=\"tp_pub_author\">Cheng-Han Ho,  Yuki Kobayashi,  Mitsuo Ogasawara,  Yoshimasa Takizawa,  Hitoshi Kurumizaka<\/p><p class=\"tp_pub_title\"><a class=\"tp_title_link\" href=\"https:\/\/dx.doi.org\/10.1016\/j.isci.2025.114453\" title=\"A method for cryo-EM analysis of eukaryotic nucleosomes reconstituted in bacterial cells\" target=\"blank\">A method for cryo-EM analysis of eukaryotic nucleosomes reconstituted in bacterial cells<\/a> <span class=\"tp_pub_type article\">Journal Article<\/span> <\/p><p class=\"tp_pub_additional\"><span class=\"tp_pub_additional_in\">In: <\/span><span class=\"tp_pub_additional_journal\">iScience, <\/span><span class=\"tp_pub_additional_volume\">vol. 29, <\/span><span class=\"tp_pub_additional_number\">no. 1, <\/span><span class=\"tp_pub_additional_year\">2025<\/span>, <span class=\"tp_pub_additional_issn\">ISSN: 2589-0042<\/span>.<\/p><p class=\"tp_pub_menu\"><span class=\"tp_abstract_link\"><a id=\"tp_abstract_sh_50\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('50','tp_abstract')\" title=\"Show abstract\" style=\"cursor:pointer;\">Abstract<\/a><\/span> | <span class=\"tp_resource_link\"><a id=\"tp_links_sh_50\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('50','tp_links')\" title=\"Show links and resources\" style=\"cursor:pointer;\">Links<\/a><\/span> | <span class=\"tp_pub_tags_label\">\u30bf\u30b0: <\/span><a rel=\"nofollow\" href=\"https:\/\/www.bioreg.kyushu-u.ac.jp\/ext\/epicode\/publications?tgid=4#tppubs\" title=\"Show all publications which have a relationship to this tag\">Kurumizaka G<\/a><\/p><div class=\"tp_bibtex\" id=\"tp_bibtex_50\" style=\"display:none;\"><div class=\"tp_bibtex_entry\"><pre>@article{Ho2026,<br \/>\r\ntitle = {A method for cryo-EM analysis of eukaryotic nucleosomes reconstituted in bacterial cells},<br \/>\r\nauthor = {Cheng-Han Ho and Yuki Kobayashi and Mitsuo Ogasawara and Yoshimasa Takizawa and Hitoshi Kurumizaka},<br \/>\r\ndoi = {10.1016\/j.isci.2025.114453},<br \/>\r\nissn = {2589-0042},<br \/>\r\nyear  = {2025},<br \/>\r\ndate = {2025-12-15},<br \/>\r\njournal = {iScience},<br \/>\r\nvolume = {29},<br \/>\r\nnumber = {1},<br \/>\r\npublisher = {Elsevier BV},<br \/>\r\nabstract = {Conventional methods for preparing nucleosomes are time-consuming and technically demanding. In the present study, we extended the approach of generating nucleosomes in E. coli by the co-expression of all four histones, allowing nucleosomes to be assembled in cells. The bacterially reconstituted nucleosomes can be readily prepared from the E. coli cells and directly subjected to cryo-EM single particle analysis. Using this method, we obtained a 2.56 \u00c5 nucleosome structure that is highly similar to a previously reported nucleosome crystal structure, validating the use of nucleosomes formed in E. coli for cryo-EM analysis. Unexpectedly, we also discovered a non-canonical nucleosome structure, in which two hexasomes are closely packed. This system provides a robust and efficient platform for structural studies of nucleosomes and nucleosome variants, and may facilitate the discovery of chromatin architectures.},<br \/>\r\nkeywords = {Kurumizaka G},<br \/>\r\npubstate = {published},<br \/>\r\ntppubtype = {article}<br \/>\r\n}<br \/>\r\n<\/pre><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('50','tp_bibtex')\">Close<\/a><\/p><\/div><div class=\"tp_abstract\" id=\"tp_abstract_50\" style=\"display:none;\"><div class=\"tp_abstract_entry\">Conventional methods for preparing nucleosomes are time-consuming and technically demanding. In the present study, we extended the approach of generating nucleosomes in E. coli by the co-expression of all four histones, allowing nucleosomes to be assembled in cells. The bacterially reconstituted nucleosomes can be readily prepared from the E. coli cells and directly subjected to cryo-EM single particle analysis. Using this method, we obtained a 2.56 \u00c5 nucleosome structure that is highly similar to a previously reported nucleosome crystal structure, validating the use of nucleosomes formed in E. coli for cryo-EM analysis. Unexpectedly, we also discovered a non-canonical nucleosome structure, in which two hexasomes are closely packed. This system provides a robust and efficient platform for structural studies of nucleosomes and nucleosome variants, and may facilitate the discovery of chromatin architectures.<\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('50','tp_abstract')\">Close<\/a><\/p><\/div><div class=\"tp_links\" id=\"tp_links_50\" style=\"display:none;\"><div class=\"tp_links_entry\"><ul class=\"tp_pub_list\"><li><i class=\"ai ai-doi\"><\/i><a class=\"tp_pub_list\" href=\"https:\/\/dx.doi.org\/10.1016\/j.isci.2025.114453\" title=\"Follow DOI:10.1016\/j.isci.2025.114453\" target=\"_blank\">doi:10.1016\/j.isci.2025.114453<\/a><\/li><\/ul><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('50','tp_links')\">Close<\/a><\/p><\/div><\/div><\/div><div class=\"tp_publication tp_publication_article\"><div class=\"tp_pub_number\">47.<\/div><div class=\"tp_pub_info\"><p class=\"tp_pub_author\">Yohsuke T. Fukai,  Tomoya Kujirai,  Masatoshi Wakamori,  Setsuko Kanamura,  Lisa Yamauchi,  Somayeh Zeraati,  Satoshi Morita,  Chiharu Tanegashima,  Mitsutaka Kadota,  Mikako Shirouzu,  Hitoshi Kurumizaka,  Takashi Umehara,  Kyogo Kawaguchi<\/p><p class=\"tp_pub_title\"><a class=\"tp_title_link\" href=\"https:\/\/dx.doi.org\/10.1126\/sciadv.adx9282\" title=\"Gene-scale in vitro reconstitution reveals histone acetylation directly controls chromatin architecture\" target=\"blank\">Gene-scale in vitro reconstitution reveals histone acetylation directly controls chromatin architecture<\/a> <span class=\"tp_pub_type article\">Journal Article<\/span> <\/p><p class=\"tp_pub_additional\"><span class=\"tp_pub_additional_in\">In: <\/span><span class=\"tp_pub_additional_journal\">Sci. Adv., <\/span><span class=\"tp_pub_additional_volume\">vol. 11, <\/span><span class=\"tp_pub_additional_number\">no. 47, <\/span><span class=\"tp_pub_additional_year\">2025<\/span>, <span class=\"tp_pub_additional_issn\">ISSN: 2375-2548<\/span>.<\/p><p class=\"tp_pub_menu\"><span class=\"tp_abstract_link\"><a id=\"tp_abstract_sh_47\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('47','tp_abstract')\" title=\"Show abstract\" style=\"cursor:pointer;\">Abstract<\/a><\/span> | <span class=\"tp_resource_link\"><a id=\"tp_links_sh_47\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('47','tp_links')\" title=\"Show links and resources\" style=\"cursor:pointer;\">Links<\/a><\/span> | <span class=\"tp_pub_tags_label\">\u30bf\u30b0: <\/span><a rel=\"nofollow\" href=\"https:\/\/www.bioreg.kyushu-u.ac.jp\/ext\/epicode\/publications?tgid=4#tppubs\" title=\"Show all publications which have a relationship to this tag\">Kurumizaka G<\/a><\/p><div class=\"tp_bibtex\" id=\"tp_bibtex_47\" style=\"display:none;\"><div class=\"tp_bibtex_entry\"><pre>@article{Fukai2025,<br \/>\r\ntitle = {Gene-scale in vitro reconstitution reveals histone acetylation directly controls chromatin architecture},<br \/>\r\nauthor = {Yohsuke T. Fukai and Tomoya Kujirai and Masatoshi Wakamori and Setsuko Kanamura and Lisa Yamauchi and Somayeh Zeraati and Satoshi Morita and Chiharu Tanegashima and Mitsutaka Kadota and Mikako Shirouzu and Hitoshi Kurumizaka and Takashi Umehara and Kyogo Kawaguchi},<br \/>\r\ndoi = {10.1126\/sciadv.adx9282},<br \/>\r\nissn = {2375-2548},<br \/>\r\nyear  = {2025},<br \/>\r\ndate = {2025-11-21},<br \/>\r\nurldate = {2025-11-21},<br \/>\r\njournal = {Sci. Adv.},<br \/>\r\nvolume = {11},<br \/>\r\nnumber = {47},<br \/>\r\npublisher = {American Association for the Advancement of Science (AAAS)},<br \/>\r\nabstract = {Understanding how epigenetic modifications intrinsically shape gene-scale chromatin architecture remains challenging due to difficulties in reconstituting and characterizing sufficiently long arrays with defined modification patterns. Here, we overcome this barrier by reconstituting 20-kilobase (96-nucleosome) chromatin arrays with modification patterns precisely controlled at 12-nucleosome resolution. Single-molecule microscopy reveals the dynamics governed by hydrodynamic interactions, demonstrating that increasing histone H4 acetylation density enhances structural fluctuations and relaxation times. In vitro Hi-C reveals power-law decay of the nucleosome contacts consistent with the Gaussian chain, which is globally reduced by acetylation. We also observe that heterogeneous modification patterns alone are sufficient to create distinct structural domains reminiscent of higher-order chromatin organization. These findings establish how histone modifications modulate chromatin architecture via changes in local stiffness and nucleosome interactions, providing a quantitative framework for genome organization.},<br \/>\r\nkeywords = {Kurumizaka G},<br \/>\r\npubstate = {published},<br \/>\r\ntppubtype = {article}<br \/>\r\n}<br \/>\r\n<\/pre><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('47','tp_bibtex')\">Close<\/a><\/p><\/div><div class=\"tp_abstract\" id=\"tp_abstract_47\" style=\"display:none;\"><div class=\"tp_abstract_entry\">Understanding how epigenetic modifications intrinsically shape gene-scale chromatin architecture remains challenging due to difficulties in reconstituting and characterizing sufficiently long arrays with defined modification patterns. Here, we overcome this barrier by reconstituting 20-kilobase (96-nucleosome) chromatin arrays with modification patterns precisely controlled at 12-nucleosome resolution. Single-molecule microscopy reveals the dynamics governed by hydrodynamic interactions, demonstrating that increasing histone H4 acetylation density enhances structural fluctuations and relaxation times. In vitro Hi-C reveals power-law decay of the nucleosome contacts consistent with the Gaussian chain, which is globally reduced by acetylation. We also observe that heterogeneous modification patterns alone are sufficient to create distinct structural domains reminiscent of higher-order chromatin organization. These findings establish how histone modifications modulate chromatin architecture via changes in local stiffness and nucleosome interactions, providing a quantitative framework for genome organization.<\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('47','tp_abstract')\">Close<\/a><\/p><\/div><div class=\"tp_links\" id=\"tp_links_47\" style=\"display:none;\"><div class=\"tp_links_entry\"><ul class=\"tp_pub_list\"><li><i class=\"ai ai-doi\"><\/i><a class=\"tp_pub_list\" href=\"https:\/\/dx.doi.org\/10.1126\/sciadv.adx9282\" title=\"Follow DOI:10.1126\/sciadv.adx9282\" target=\"_blank\">doi:10.1126\/sciadv.adx9282<\/a><\/li><\/ul><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('47','tp_links')\">Close<\/a><\/p><\/div><\/div><\/div><div class=\"tp_publication tp_publication_article\"><div class=\"tp_pub_number\">46.<\/div><div class=\"tp_pub_info\"><p class=\"tp_pub_author\">Syota Matsumoto,  Yoshimasa Takizawa,  Mitsuo Ogasawara,  Kana Hashimoto,  Lumi Negishi,  Wenjie Xu,  Haruna Tachibana,  Junpei Yamamoto,  Shigenori Iwai,  Kaoru Sugasawa,  Hitoshi Kurumizaka<\/p><p class=\"tp_pub_title\"><a class=\"tp_title_link\" href=\"https:\/\/dx.doi.org\/10.1038\/s41467-025-65486-5\" title=\"Structural basis of cyclobutane pyrimidine dimer recognition by UV-DDB in the nucleosome\" target=\"blank\">Structural basis of cyclobutane pyrimidine dimer recognition by UV-DDB in the nucleosome<\/a> <span class=\"tp_pub_type article\">Journal Article<\/span> <\/p><p class=\"tp_pub_additional\"><span class=\"tp_pub_additional_in\">In: <\/span><span class=\"tp_pub_additional_journal\">Nature Communications, <\/span><span class=\"tp_pub_additional_volume\">vol. 16, <\/span><span class=\"tp_pub_additional_number\">no. 1, <\/span><span class=\"tp_pub_additional_year\">2025<\/span>, <span class=\"tp_pub_additional_issn\">ISSN: 2041-1723<\/span>.<\/p><p class=\"tp_pub_menu\"><span class=\"tp_abstract_link\"><a id=\"tp_abstract_sh_46\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('46','tp_abstract')\" title=\"Show abstract\" style=\"cursor:pointer;\">Abstract<\/a><\/span> | <span class=\"tp_resource_link\"><a id=\"tp_links_sh_46\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('46','tp_links')\" title=\"Show links and resources\" style=\"cursor:pointer;\">Links<\/a><\/span> | <span class=\"tp_pub_tags_label\">\u30bf\u30b0: <\/span><a rel=\"nofollow\" href=\"https:\/\/www.bioreg.kyushu-u.ac.jp\/ext\/epicode\/publications?tgid=4#tppubs\" title=\"Show all publications which have a relationship to this tag\">Kurumizaka G<\/a><\/p><div class=\"tp_bibtex\" id=\"tp_bibtex_46\" style=\"display:none;\"><div class=\"tp_bibtex_entry\"><pre>@article{Matsumoto2025,<br \/>\r\ntitle = {Structural basis of cyclobutane pyrimidine dimer recognition by UV-DDB in the nucleosome},<br \/>\r\nauthor = {Syota Matsumoto and Yoshimasa Takizawa and Mitsuo Ogasawara and Kana Hashimoto and Lumi Negishi and Wenjie Xu and Haruna Tachibana and Junpei Yamamoto and Shigenori Iwai and Kaoru Sugasawa and Hitoshi Kurumizaka},<br \/>\r\ndoi = {10.1038\/s41467-025-65486-5},<br \/>\r\nissn = {2041-1723},<br \/>\r\nyear  = {2025},<br \/>\r\ndate = {2025-11-11},<br \/>\r\njournal = {Nature Communications},<br \/>\r\nvolume = {16},<br \/>\r\nnumber = {1},<br \/>\r\npublisher = {Springer Science and Business Media LLC},<br \/>\r\nabstract = {In mammalian global genomic nucleotide excision repair, UV-DDB plays a central role in recognizing DNA lesions, such as 6-4 photoproducts and cyclobutane pyrimidine dimers, within chromatin. In the present study, we perform cryo-electron microscopy analyses coupled with chromatin-immunoprecipitation to reveal that the cellular UV-DDB binds to UV-damaged DNA lesions in a chromatin unit, the nucleosome, at a position approximately 20 base-pairs from the nucleosomal dyad in human cells. An alternative analysis of the in vitro reconstituted UV-DDB-cyclobutane pyrimidine dimer nucleosome structure demonstrates that the DDB2 subunit of UV-DDB specifically recognizes the cyclobutane pyrimidine dimer lesion at this position on the nucleosome. We also determine the structures of UV-DDB bound to DNA lesions at other positions in purified cellular human nucleosomes. These cellular and reconstituted UV-DDB-nucleosome complex structures provide important evidence for understanding the mechanism by which UV lesions in chromatin are recognized and repaired in mammalian cells.},<br \/>\r\nkeywords = {Kurumizaka G},<br \/>\r\npubstate = {published},<br \/>\r\ntppubtype = {article}<br \/>\r\n}<br \/>\r\n<\/pre><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('46','tp_bibtex')\">Close<\/a><\/p><\/div><div class=\"tp_abstract\" id=\"tp_abstract_46\" style=\"display:none;\"><div class=\"tp_abstract_entry\">In mammalian global genomic nucleotide excision repair, UV-DDB plays a central role in recognizing DNA lesions, such as 6-4 photoproducts and cyclobutane pyrimidine dimers, within chromatin. In the present study, we perform cryo-electron microscopy analyses coupled with chromatin-immunoprecipitation to reveal that the cellular UV-DDB binds to UV-damaged DNA lesions in a chromatin unit, the nucleosome, at a position approximately 20 base-pairs from the nucleosomal dyad in human cells. An alternative analysis of the in vitro reconstituted UV-DDB-cyclobutane pyrimidine dimer nucleosome structure demonstrates that the DDB2 subunit of UV-DDB specifically recognizes the cyclobutane pyrimidine dimer lesion at this position on the nucleosome. We also determine the structures of UV-DDB bound to DNA lesions at other positions in purified cellular human nucleosomes. These cellular and reconstituted UV-DDB-nucleosome complex structures provide important evidence for understanding the mechanism by which UV lesions in chromatin are recognized and repaired in mammalian cells.<\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('46','tp_abstract')\">Close<\/a><\/p><\/div><div class=\"tp_links\" id=\"tp_links_46\" style=\"display:none;\"><div class=\"tp_links_entry\"><ul class=\"tp_pub_list\"><li><i class=\"ai ai-doi\"><\/i><a class=\"tp_pub_list\" href=\"https:\/\/dx.doi.org\/10.1038\/s41467-025-65486-5\" title=\"Follow DOI:10.1038\/s41467-025-65486-5\" target=\"_blank\">doi:10.1038\/s41467-025-65486-5<\/a><\/li><\/ul><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('46','tp_links')\">Close<\/a><\/p><\/div><\/div><\/div><div class=\"tp_publication tp_publication_article\"><div class=\"tp_pub_number\">45.<\/div><div class=\"tp_pub_info\"><p class=\"tp_pub_author\">Yuriko Yoshimura,  Aki Hayashi,  Mayo Tanaka,  Mieko Suzuki\u2010Matsubara,  Reiko Nakagawa,  Gohei Nishibuchi,  Hideaki Tagami,  Masaya Oki,  Jun\u2010ichi Nakayama<\/p><p class=\"tp_pub_title\"><a class=\"tp_title_link\" href=\"https:\/\/dx.doi.org\/10.1096\/fj.202500384r\" title=\"Mitotic Phosphorylation of Swi6\/HP1 Regulates Its Chromatin Binding and Chromosome Segregation\" target=\"blank\">Mitotic Phosphorylation of Swi6\/HP1 Regulates Its Chromatin Binding and Chromosome Segregation<\/a> <span class=\"tp_pub_type article\">Journal Article<\/span> <\/p><p class=\"tp_pub_additional\"><span class=\"tp_pub_additional_in\">In: <\/span><span class=\"tp_pub_additional_journal\">The FASEB Journal, <\/span><span class=\"tp_pub_additional_volume\">vol. 39, <\/span><span class=\"tp_pub_additional_number\">no. 21, <\/span><span class=\"tp_pub_additional_year\">2025<\/span>, <span class=\"tp_pub_additional_issn\">ISSN: 1530-6860<\/span>.<\/p><p class=\"tp_pub_menu\"><span class=\"tp_abstract_link\"><a id=\"tp_abstract_sh_45\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('45','tp_abstract')\" title=\"Show abstract\" style=\"cursor:pointer;\">Abstract<\/a><\/span> | <span class=\"tp_resource_link\"><a id=\"tp_links_sh_45\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('45','tp_links')\" title=\"Show links and resources\" style=\"cursor:pointer;\">Links<\/a><\/span> | <span class=\"tp_pub_tags_label\">\u30bf\u30b0: <\/span><a rel=\"nofollow\" href=\"https:\/\/www.bioreg.kyushu-u.ac.jp\/ext\/epicode\/publications?tgid=7#tppubs\" title=\"Show all publications which have a relationship to this tag\">Nakayama G<\/a><\/p><div class=\"tp_bibtex\" id=\"tp_bibtex_45\" style=\"display:none;\"><div class=\"tp_bibtex_entry\"><pre>@article{Yoshimura2025,<br \/>\r\ntitle = {Mitotic Phosphorylation of Swi6\/HP1 Regulates Its Chromatin Binding and Chromosome Segregation},<br \/>\r\nauthor = {Yuriko Yoshimura and Aki Hayashi and Mayo Tanaka and Mieko Suzuki\u2010Matsubara and Reiko Nakagawa and Gohei Nishibuchi and Hideaki Tagami and Masaya Oki and Jun\u2010ichi Nakayama},<br \/>\r\ndoi = {10.1096\/fj.202500384r},<br \/>\r\nissn = {1530-6860},<br \/>\r\nyear  = {2025},<br \/>\r\ndate = {2025-11-02},<br \/>\r\nurldate = {2025-11-15},<br \/>\r\njournal = {The FASEB Journal},<br \/>\r\nvolume = {39},<br \/>\r\nnumber = {21},<br \/>\r\npublisher = {Wiley},<br \/>\r\nabstract = {In eukaryotic cells, heterochromatin assembly is critical for chromosome segregation and transcriptional gene silencing. Heterochromatin protein 1 (HP1) is a conserved chromosomal protein that plays an important role in heterochromatin assembly. We have previously shown that mammalian HP1\u03b1 and Schizosaccharomyces pombe Swi6 are phosphorylated by casein kinase II (CK2) and that this phosphorylation is essential for their function in heterochromatin assembly. In addition to CK2-mediated phosphorylation, several studies have shown that HP1 proteins undergo additional phosphorylation during mitosis. However, functional significance of the mitotic phosphorylation of HP1 remains unclear. Here, we identified mitotic phosphorylation sites within fission yeast Swi6 and showed that this phosphorylation is involved in chromosome segregation. Using an Escherichia coli co-expression system, we showed that Swi6 is phosphorylated by Ark1, a solo Aurora kinase in S. pombe, and mutational analyses revealed that serine residues in the conserved N-terminal region of Swi6 are the primary targets of Ark1. By expressing mutant Swi6, we confirmed that these serine residues are phosphorylated during mitosis in vivo. Although non-phosphorylatable or phosphomimic mutations in Swi6 had little effect on heterochromatic silencing, they caused defects in early chromosome segregation and modulated the temperature-sensitive growth of mutant cells for chromosome passenger complex components. These results suggest that the Ark1-mediated mitotic phosphorylation of Swi6 is involved in chromosome segregation during mitosis and implicates a conserved regulatory role for the mitotic phosphorylation of HP1 proteins.},<br \/>\r\nkeywords = {Nakayama G},<br \/>\r\npubstate = {published},<br \/>\r\ntppubtype = {article}<br \/>\r\n}<br \/>\r\n<\/pre><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('45','tp_bibtex')\">Close<\/a><\/p><\/div><div class=\"tp_abstract\" id=\"tp_abstract_45\" style=\"display:none;\"><div class=\"tp_abstract_entry\">In eukaryotic cells, heterochromatin assembly is critical for chromosome segregation and transcriptional gene silencing. Heterochromatin protein 1 (HP1) is a conserved chromosomal protein that plays an important role in heterochromatin assembly. We have previously shown that mammalian HP1\u03b1 and Schizosaccharomyces pombe Swi6 are phosphorylated by casein kinase II (CK2) and that this phosphorylation is essential for their function in heterochromatin assembly. In addition to CK2-mediated phosphorylation, several studies have shown that HP1 proteins undergo additional phosphorylation during mitosis. However, functional significance of the mitotic phosphorylation of HP1 remains unclear. Here, we identified mitotic phosphorylation sites within fission yeast Swi6 and showed that this phosphorylation is involved in chromosome segregation. Using an Escherichia coli co-expression system, we showed that Swi6 is phosphorylated by Ark1, a solo Aurora kinase in S. pombe, and mutational analyses revealed that serine residues in the conserved N-terminal region of Swi6 are the primary targets of Ark1. By expressing mutant Swi6, we confirmed that these serine residues are phosphorylated during mitosis in vivo. Although non-phosphorylatable or phosphomimic mutations in Swi6 had little effect on heterochromatic silencing, they caused defects in early chromosome segregation and modulated the temperature-sensitive growth of mutant cells for chromosome passenger complex components. These results suggest that the Ark1-mediated mitotic phosphorylation of Swi6 is involved in chromosome segregation during mitosis and implicates a conserved regulatory role for the mitotic phosphorylation of HP1 proteins.<\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('45','tp_abstract')\">Close<\/a><\/p><\/div><div class=\"tp_links\" id=\"tp_links_45\" style=\"display:none;\"><div class=\"tp_links_entry\"><ul class=\"tp_pub_list\"><li><i class=\"ai ai-doi\"><\/i><a class=\"tp_pub_list\" href=\"https:\/\/dx.doi.org\/10.1096\/fj.202500384r\" title=\"Follow DOI:10.1096\/fj.202500384r\" target=\"_blank\">doi:10.1096\/fj.202500384r<\/a><\/li><\/ul><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('45','tp_links')\">Close<\/a><\/p><\/div><\/div><\/div><div class=\"tp_publication tp_publication_article\"><div class=\"tp_pub_number\">44.<\/div><div class=\"tp_pub_info\"><p class=\"tp_pub_author\">Suguru Hatazawa, Yoshimasa Takizawa, Hitoshi Kurumizaka<\/p><p class=\"tp_pub_title\"><a class=\"tp_title_link\" href=\"https:\/\/dx.doi.org\/10.21769\/BioProtoc.5472\" title=\"Preparation of Chromatin Fragments From Human Cells for Cryo\u2010EM Analysis\" target=\"blank\">Preparation of Chromatin Fragments From Human Cells for Cryo\u2010EM Analysis<\/a> <span class=\"tp_pub_type article\">Journal Article<\/span> <\/p><p class=\"tp_pub_additional\"><span class=\"tp_pub_additional_in\">In: <\/span><span class=\"tp_pub_additional_journal\">Bio-protocol, <\/span><span class=\"tp_pub_additional_volume\">vol. 15, <\/span><span class=\"tp_pub_additional_number\">no. 20, <\/span><span class=\"tp_pub_additional_pages\">pp. e5472, <\/span><span class=\"tp_pub_additional_year\">2025<\/span><span class=\"tp_pub_additional_note\">, (Available online: Sep 17, 2025)<\/span>.<\/p><p class=\"tp_pub_menu\"><span class=\"tp_abstract_link\"><a id=\"tp_abstract_sh_44\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('44','tp_abstract')\" title=\"Show abstract\" style=\"cursor:pointer;\">Abstract<\/a><\/span> | <span class=\"tp_resource_link\"><a id=\"tp_links_sh_44\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('44','tp_links')\" title=\"Show links and resources\" style=\"cursor:pointer;\">Links<\/a><\/span> | <span class=\"tp_pub_tags_label\">\u30bf\u30b0: <\/span><a rel=\"nofollow\" href=\"https:\/\/www.bioreg.kyushu-u.ac.jp\/ext\/epicode\/publications?tgid=4#tppubs\" title=\"Show all publications which have a relationship to this tag\">Kurumizaka G<\/a><\/p><div class=\"tp_bibtex\" id=\"tp_bibtex_44\" style=\"display:none;\"><div class=\"tp_bibtex_entry\"><pre>@article{Hatazawa_Takizawa_Kurumizaka_2025,<br \/>\r\ntitle = {Preparation of Chromatin Fragments From Human Cells for Cryo\u2010EM Analysis},<br \/>\r\nauthor = {Suguru Hatazawa, Yoshimasa Takizawa, Hitoshi Kurumizaka},<br \/>\r\nurl = {https:\/\/bio-protocol.org\/en\/bpdetail?id=5472&type=0},<br \/>\r\ndoi = {10.21769\/BioProtoc.5472},<br \/>\r\nyear  = {2025},<br \/>\r\ndate = {2025-09-17},<br \/>\r\nurldate = {2025-01-01},<br \/>\r\njournal = {Bio-protocol},<br \/>\r\nvolume = {15},<br \/>\r\nnumber = {20},<br \/>\r\npages = {e5472},<br \/>\r\nabstract = {Eukaryotic genomic DNA is packaged into chromatin, which plays a critical role in regulating gene expression by dynamically modulating its higher-order structure. While in vitro reconstitution approaches have offered valuable insights into chromatin organization, they often fail to fully capture the native structural context found within cells. To overcome this limitation, we present a protocol for isolating native chromatin fragments from human cells for cryo-electron microscopy (cryo-EM) analysis. In this method, chromatin from formaldehyde-crosslinked human HeLa S3 nuclei is digested with micrococcal nuclease (MNase) to generate mono- and poly-nucleosome fragments. These fragments are subsequently fractionated by sucrose-gradient ultracentrifugation and prepared for cryo-EM. The resulting chromatin fragments retain native-like nucleosome\u2013nucleosome interactions, facilitating structural analyses of chromatin organization under near-physiological conditions.},<br \/>\r\nnote = {Available online: Sep 17, 2025},<br \/>\r\nkeywords = {Kurumizaka G},<br \/>\r\npubstate = {published},<br \/>\r\ntppubtype = {article}<br \/>\r\n}<br \/>\r\n<\/pre><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('44','tp_bibtex')\">Close<\/a><\/p><\/div><div class=\"tp_abstract\" id=\"tp_abstract_44\" style=\"display:none;\"><div class=\"tp_abstract_entry\">Eukaryotic genomic DNA is packaged into chromatin, which plays a critical role in regulating gene expression by dynamically modulating its higher-order structure. While in vitro reconstitution approaches have offered valuable insights into chromatin organization, they often fail to fully capture the native structural context found within cells. To overcome this limitation, we present a protocol for isolating native chromatin fragments from human cells for cryo-electron microscopy (cryo-EM) analysis. In this method, chromatin from formaldehyde-crosslinked human HeLa S3 nuclei is digested with micrococcal nuclease (MNase) to generate mono- and poly-nucleosome fragments. These fragments are subsequently fractionated by sucrose-gradient ultracentrifugation and prepared for cryo-EM. The resulting chromatin fragments retain native-like nucleosome\u2013nucleosome interactions, facilitating structural analyses of chromatin organization under near-physiological conditions.<\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('44','tp_abstract')\">Close<\/a><\/p><\/div><div class=\"tp_links\" id=\"tp_links_44\" style=\"display:none;\"><div class=\"tp_links_entry\"><ul class=\"tp_pub_list\"><li><i class=\"fas fa-globe\"><\/i><a class=\"tp_pub_list\" href=\"https:\/\/bio-protocol.org\/en\/bpdetail?id=5472&amp;type=0\" title=\"https:\/\/bio-protocol.org\/en\/bpdetail?id=5472&amp;type=0\" target=\"_blank\">https:\/\/bio-protocol.org\/en\/bpdetail?id=5472&amp;type=0<\/a><\/li><li><i class=\"ai ai-doi\"><\/i><a class=\"tp_pub_list\" href=\"https:\/\/dx.doi.org\/10.21769\/BioProtoc.5472\" title=\"Follow DOI:10.21769\/BioProtoc.5472\" target=\"_blank\">doi:10.21769\/BioProtoc.5472<\/a><\/li><\/ul><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('44','tp_links')\">Close<\/a><\/p><\/div><\/div><\/div><div class=\"tp_publication tp_publication_article\"><div class=\"tp_pub_number\">43.<\/div><div class=\"tp_pub_info\"><p class=\"tp_pub_author\">Takuro Shioi,  Suguru Hatazawa,  Yoshimasa Takizawa,  Hitoshi Kurumizaka<\/p><p class=\"tp_pub_title\"><a class=\"tp_title_link\" href=\"https:\/\/dx.doi.org\/https:\/\/doi.org\/10.1016\/j.dnarep.2025.103891\" title=\"Mechanistic insights into RAD51-mediated nucleosome binding and remodeling in homologous recombination\" target=\"blank\">Mechanistic insights into RAD51-mediated nucleosome binding and remodeling in homologous recombination<\/a> <span class=\"tp_pub_type article\">Journal Article<\/span> <\/p><p class=\"tp_pub_additional\"><span class=\"tp_pub_additional_in\">In: <\/span><span class=\"tp_pub_additional_journal\">DNA Repair, <\/span><span class=\"tp_pub_additional_pages\">pp. 103891, <\/span><span class=\"tp_pub_additional_year\">2025<\/span>, <span class=\"tp_pub_additional_issn\">ISSN: 1568-7864<\/span>.<\/p><p class=\"tp_pub_menu\"><span class=\"tp_abstract_link\"><a id=\"tp_abstract_sh_43\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('43','tp_abstract')\" title=\"Show abstract\" style=\"cursor:pointer;\">Abstract<\/a><\/span> | <span class=\"tp_resource_link\"><a id=\"tp_links_sh_43\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('43','tp_links')\" title=\"Show links and resources\" style=\"cursor:pointer;\">Links<\/a><\/span> | <span class=\"tp_pub_tags_label\">\u30bf\u30b0: <\/span><a rel=\"nofollow\" href=\"https:\/\/www.bioreg.kyushu-u.ac.jp\/ext\/epicode\/publications?tgid=15#tppubs\" title=\"Show all publications which have a relationship to this tag\">Chromatin<\/a>, <a rel=\"nofollow\" href=\"https:\/\/www.bioreg.kyushu-u.ac.jp\/ext\/epicode\/publications?tgid=22#tppubs\" title=\"Show all publications which have a relationship to this tag\">Chromatin remodeler<\/a>, <a rel=\"nofollow\" href=\"https:\/\/www.bioreg.kyushu-u.ac.jp\/ext\/epicode\/publications?tgid=24#tppubs\" title=\"Show all publications which have a relationship to this tag\">Cryo-electron microscopy<\/a>, <a rel=\"nofollow\" href=\"https:\/\/www.bioreg.kyushu-u.ac.jp\/ext\/epicode\/publications?tgid=21#tppubs\" title=\"Show all publications which have a relationship to this tag\">Homologous recombination<\/a>, <a rel=\"nofollow\" href=\"https:\/\/www.bioreg.kyushu-u.ac.jp\/ext\/epicode\/publications?tgid=4#tppubs\" title=\"Show all publications which have a relationship to this tag\">Kurumizaka G<\/a>, <a rel=\"nofollow\" href=\"https:\/\/www.bioreg.kyushu-u.ac.jp\/ext\/epicode\/publications?tgid=14#tppubs\" title=\"Show all publications which have a relationship to this tag\">Nucleosome<\/a>, <a rel=\"nofollow\" href=\"https:\/\/www.bioreg.kyushu-u.ac.jp\/ext\/epicode\/publications?tgid=23#tppubs\" title=\"Show all publications which have a relationship to this tag\">RAD51<\/a><\/p><div class=\"tp_bibtex\" id=\"tp_bibtex_43\" style=\"display:none;\"><div class=\"tp_bibtex_entry\"><pre>@article{SHIOI2025103891,<br \/>\r\ntitle = {Mechanistic insights into RAD51-mediated nucleosome binding and remodeling in homologous recombination},<br \/>\r\nauthor = {Takuro Shioi and Suguru Hatazawa and Yoshimasa Takizawa and Hitoshi Kurumizaka},<br \/>\r\nurl = {https:\/\/www.sciencedirect.com\/science\/article\/pii\/S1568786425000874},<br \/>\r\ndoi = {https:\/\/doi.org\/10.1016\/j.dnarep.2025.103891},<br \/>\r\nissn = {1568-7864},<br \/>\r\nyear  = {2025},<br \/>\r\ndate = {2025-09-13},<br \/>\r\nurldate = {2025-01-01},<br \/>\r\njournal = {DNA Repair},<br \/>\r\npages = {103891},<br \/>\r\nabstract = {Eukaryotic cells organize their genomic DNA into chromatin to achieve both compact packaging and precise regulation of essential processes, including DNA repair. Depending on the type of damage, distinct repair pathways are activated through the targeted recruitment of repair factors to chromatin. RAD51 is the central recombinase in homologous recombination (HR) and forms nucleoprotein filaments, but its mode of chromatin engagement has remained elusive. In this review, we summarize recent progress in the structural and biochemical understanding of DNA repair within chromatin, with a particular focus on RAD51 and its role in HR. Specifically, we review newly determined cryo-electron microscopy (cryo-EM) structures of RAD51 bound to nucleosomes, revealing how RAD51 assembles on chromatin, recognizes DNA damage sites, and remodels nucleosomes into filamentous intermediates. We summarize current insights into how HR-associated proteins regulate RAD51 activity on chromatin, ensuring the fidelity of each step in HR. We conclude by outlining future directions for elucidating the downstream mechanisms of RAD51-mediated HR in the chromatin context.},<br \/>\r\nkeywords = {Chromatin, Chromatin remodeler, Cryo-electron microscopy, Homologous recombination, Kurumizaka G, Nucleosome, RAD51},<br \/>\r\npubstate = {published},<br \/>\r\ntppubtype = {article}<br \/>\r\n}<br \/>\r\n<\/pre><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('43','tp_bibtex')\">Close<\/a><\/p><\/div><div class=\"tp_abstract\" id=\"tp_abstract_43\" style=\"display:none;\"><div class=\"tp_abstract_entry\">Eukaryotic cells organize their genomic DNA into chromatin to achieve both compact packaging and precise regulation of essential processes, including DNA repair. Depending on the type of damage, distinct repair pathways are activated through the targeted recruitment of repair factors to chromatin. RAD51 is the central recombinase in homologous recombination (HR) and forms nucleoprotein filaments, but its mode of chromatin engagement has remained elusive. In this review, we summarize recent progress in the structural and biochemical understanding of DNA repair within chromatin, with a particular focus on RAD51 and its role in HR. Specifically, we review newly determined cryo-electron microscopy (cryo-EM) structures of RAD51 bound to nucleosomes, revealing how RAD51 assembles on chromatin, recognizes DNA damage sites, and remodels nucleosomes into filamentous intermediates. We summarize current insights into how HR-associated proteins regulate RAD51 activity on chromatin, ensuring the fidelity of each step in HR. We conclude by outlining future directions for elucidating the downstream mechanisms of RAD51-mediated HR in the chromatin context.<\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('43','tp_abstract')\">Close<\/a><\/p><\/div><div class=\"tp_links\" id=\"tp_links_43\" style=\"display:none;\"><div class=\"tp_links_entry\"><ul class=\"tp_pub_list\"><li><i class=\"fas fa-globe\"><\/i><a class=\"tp_pub_list\" href=\"https:\/\/www.sciencedirect.com\/science\/article\/pii\/S1568786425000874\" title=\"https:\/\/www.sciencedirect.com\/science\/article\/pii\/S1568786425000874\" target=\"_blank\">https:\/\/www.sciencedirect.com\/science\/article\/pii\/S1568786425000874<\/a><\/li><li><i class=\"ai ai-doi\"><\/i><a class=\"tp_pub_list\" href=\"https:\/\/dx.doi.org\/https:\/\/doi.org\/10.1016\/j.dnarep.2025.103891\" title=\"Follow DOI:https:\/\/doi.org\/10.1016\/j.dnarep.2025.103891\" target=\"_blank\">doi:https:\/\/doi.org\/10.1016\/j.dnarep.2025.103891<\/a><\/li><\/ul><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('43','tp_links')\">Close<\/a><\/p><\/div><\/div><\/div><div class=\"tp_publication tp_publication_article\"><div class=\"tp_pub_number\">42.<\/div><div class=\"tp_pub_info\"><p class=\"tp_pub_author\">Rinko Nakamura,  Aki Hayashi,  Reiko Nakagawa,  Yuriko Yoshimura,  Naoki Horikoshi,  Hitoshi Kurumizaka,  Jun-ichi Nakayama<\/p><p class=\"tp_pub_title\"><a class=\"tp_title_link\" href=\"https:\/\/dx.doi.org\/10.1093\/nar\/gkaf878\" title=\"Intrinsically disordered region of Clr4\/Suv39 regulates its enzymatic activity and ensures heterochromatin spreading\" target=\"blank\">Intrinsically disordered region of Clr4\/Suv39 regulates its enzymatic activity and ensures heterochromatin spreading<\/a> <span class=\"tp_pub_type article\">Journal Article<\/span> <\/p><p class=\"tp_pub_additional\"><span class=\"tp_pub_additional_in\">In: <\/span><span class=\"tp_pub_additional_journal\">Nucleic Acids Research, <\/span><span class=\"tp_pub_additional_volume\">vol. 53, <\/span><span class=\"tp_pub_additional_number\">no. 17, <\/span><span class=\"tp_pub_additional_pages\">pp. gkaf878, <\/span><span class=\"tp_pub_additional_year\">2025<\/span>, <span class=\"tp_pub_additional_issn\">ISSN: 1362-4962<\/span>.<\/p><p class=\"tp_pub_menu\"><span class=\"tp_abstract_link\"><a id=\"tp_abstract_sh_42\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('42','tp_abstract')\" title=\"Show abstract\" style=\"cursor:pointer;\">Abstract<\/a><\/span> | <span class=\"tp_resource_link\"><a id=\"tp_links_sh_42\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('42','tp_links')\" title=\"Show links and resources\" style=\"cursor:pointer;\">Links<\/a><\/span> | <span class=\"tp_pub_tags_label\">\u30bf\u30b0: <\/span><a rel=\"nofollow\" href=\"https:\/\/www.bioreg.kyushu-u.ac.jp\/ext\/epicode\/publications?tgid=4#tppubs\" title=\"Show all publications which have a relationship to this tag\">Kurumizaka G<\/a>, <a rel=\"nofollow\" href=\"https:\/\/www.bioreg.kyushu-u.ac.jp\/ext\/epicode\/publications?tgid=7#tppubs\" title=\"Show all publications which have a relationship to this tag\">Nakayama G<\/a><\/p><div class=\"tp_bibtex\" id=\"tp_bibtex_42\" style=\"display:none;\"><div class=\"tp_bibtex_entry\"><pre>@article{10.1093\/nar\/gkaf878,<br \/>\r\ntitle = {Intrinsically disordered region of Clr4\/Suv39 regulates its enzymatic activity and ensures heterochromatin spreading},<br \/>\r\nauthor = {Rinko Nakamura and Aki Hayashi and Reiko Nakagawa and Yuriko Yoshimura and Naoki Horikoshi and Hitoshi Kurumizaka and Jun-ichi Nakayama},<br \/>\r\nurl = {https:\/\/doi.org\/10.1093\/nar\/gkaf878},<br \/>\r\ndoi = {10.1093\/nar\/gkaf878},<br \/>\r\nissn = {1362-4962},<br \/>\r\nyear  = {2025},<br \/>\r\ndate = {2025-09-09},<br \/>\r\nurldate = {2025-01-01},<br \/>\r\njournal = {Nucleic Acids Research},<br \/>\r\nvolume = {53},<br \/>\r\nnumber = {17},<br \/>\r\npages = {gkaf878},<br \/>\r\nabstract = {Methylation of histone H3 at lysine 9 (H3K9me), a hallmark of heterochromatin, is catalyzed by Clr4\/Suv39. Clr4\/Suv39 contains two conserved domains\u2014an N-terminal chromodomain and a C-terminal catalytic domain\u2014connected by an intrinsically disordered region (IDR). Several mechanisms have been proposed to regulate Clr4\/Suv39 activity, but how it is regulated under physiological conditions remains largely unknown. We found that the N-terminus of Clr4 interacts with its C-terminal catalytic domain and represses its enzymatic activity. Detailed biochemical analyses revealed that basic amino acid residues in the IDR are involved in this interaction. Amino acid substitutions of these residues weakened this interaction, thereby promoting Clr4 activity in vitro. Interestingly, cells expressing mutant Clr4 with these substitutions showed a silencing defect, which suggested additional roles of the IDR in vivo. Genetic analysis revealed that the IDR functions in H3K9me spreading and that this activity is functionally linked to the RNAi pathway. We also showed that Clr4 binds to RNAs via the IDR and that RNA attenuates Clr4 autoinhibition in vitro. Furthermore, the IDR was found to contribute to the targeting of nucleosomal substrates in vitro. These results reveal a novel function of the Clr4\/Suv39 IDR in regulating its enzymatic activity and heterochromatin spreading.},<br \/>\r\nkeywords = {Kurumizaka G, Nakayama G},<br \/>\r\npubstate = {published},<br \/>\r\ntppubtype = {article}<br \/>\r\n}<br \/>\r\n<\/pre><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('42','tp_bibtex')\">Close<\/a><\/p><\/div><div class=\"tp_abstract\" id=\"tp_abstract_42\" style=\"display:none;\"><div class=\"tp_abstract_entry\">Methylation of histone H3 at lysine 9 (H3K9me), a hallmark of heterochromatin, is catalyzed by Clr4\/Suv39. Clr4\/Suv39 contains two conserved domains\u2014an N-terminal chromodomain and a C-terminal catalytic domain\u2014connected by an intrinsically disordered region (IDR). Several mechanisms have been proposed to regulate Clr4\/Suv39 activity, but how it is regulated under physiological conditions remains largely unknown. We found that the N-terminus of Clr4 interacts with its C-terminal catalytic domain and represses its enzymatic activity. Detailed biochemical analyses revealed that basic amino acid residues in the IDR are involved in this interaction. Amino acid substitutions of these residues weakened this interaction, thereby promoting Clr4 activity in vitro. Interestingly, cells expressing mutant Clr4 with these substitutions showed a silencing defect, which suggested additional roles of the IDR in vivo. Genetic analysis revealed that the IDR functions in H3K9me spreading and that this activity is functionally linked to the RNAi pathway. We also showed that Clr4 binds to RNAs via the IDR and that RNA attenuates Clr4 autoinhibition in vitro. Furthermore, the IDR was found to contribute to the targeting of nucleosomal substrates in vitro. These results reveal a novel function of the Clr4\/Suv39 IDR in regulating its enzymatic activity and heterochromatin spreading.<\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('42','tp_abstract')\">Close<\/a><\/p><\/div><div class=\"tp_links\" id=\"tp_links_42\" style=\"display:none;\"><div class=\"tp_links_entry\"><ul class=\"tp_pub_list\"><li><i class=\"fas fa-globe\"><\/i><a class=\"tp_pub_list\" href=\"https:\/\/doi.org\/10.1093\/nar\/gkaf878\" title=\"https:\/\/doi.org\/10.1093\/nar\/gkaf878\" target=\"_blank\">https:\/\/doi.org\/10.1093\/nar\/gkaf878<\/a><\/li><li><i class=\"ai ai-doi\"><\/i><a class=\"tp_pub_list\" href=\"https:\/\/dx.doi.org\/10.1093\/nar\/gkaf878\" title=\"Follow DOI:10.1093\/nar\/gkaf878\" target=\"_blank\">doi:10.1093\/nar\/gkaf878<\/a><\/li><\/ul><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('42','tp_links')\">Close<\/a><\/p><\/div><\/div><\/div><div class=\"tp_publication tp_publication_inbook\"><div class=\"tp_pub_number\">41.<\/div><div class=\"tp_pub_info\"><p class=\"tp_pub_author\">Daichi Nishiguchi,  Kensuke Tatsukawa,  Tatsuro S. Takahashi<\/p><p class=\"tp_pub_title\"><a class=\"tp_title_link\" href=\"https:\/\/dx.doi.org\/10.1007\/978-1-0716-4714-1_14\" title=\"Preparation of Nucleoplasmic Extract and Its Application in DNA End Processing\" target=\"blank\">Preparation of Nucleoplasmic Extract and Its Application in DNA End Processing<\/a> <span class=\"tp_pub_type inbook\">Book Chapter<\/span> <\/p><p class=\"tp_pub_additional\"><span class=\"tp_pub_additional_in\">In: <\/span><span class=\"tp_pub_additional_booktitle\">Methods in Molecular Biology, <\/span><span class=\"tp_pub_additional_pages\">pp. 201\u2013223, <\/span><span class=\"tp_pub_additional_publisher\">Springer US, <\/span><span class=\"tp_pub_additional_year\">2025<\/span>, <span class=\"tp_pub_additional_isbn\">ISBN: 9781071647141<\/span>.<\/p><p class=\"tp_pub_menu\"><span class=\"tp_abstract_link\"><a id=\"tp_abstract_sh_40\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('40','tp_abstract')\" title=\"Show abstract\" style=\"cursor:pointer;\">Abstract<\/a><\/span> | <span class=\"tp_resource_link\"><a id=\"tp_links_sh_40\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('40','tp_links')\" title=\"Show links and resources\" style=\"cursor:pointer;\">Links<\/a><\/span> | <span class=\"tp_pub_tags_label\">\u30bf\u30b0: <\/span><a rel=\"nofollow\" href=\"https:\/\/www.bioreg.kyushu-u.ac.jp\/ext\/epicode\/publications?tgid=10#tppubs\" title=\"Show all publications which have a relationship to this tag\">Takahashi G<\/a><\/p><div class=\"tp_bibtex\" id=\"tp_bibtex_40\" style=\"display:none;\"><div class=\"tp_bibtex_entry\"><pre>@inbook{Nishiguchi2025,<br \/>\r\ntitle = {Preparation of Nucleoplasmic Extract and Its Application in DNA End Processing},<br \/>\r\nauthor = {Daichi Nishiguchi and Kensuke Tatsukawa and Tatsuro S. Takahashi},<br \/>\r\ndoi = {10.1007\/978-1-0716-4714-1_14},<br \/>\r\nisbn = {9781071647141},<br \/>\r\nyear  = {2025},<br \/>\r\ndate = {2025-08-21},<br \/>\r\nurldate = {2025-08-21},<br \/>\r\nbooktitle = {Methods in Molecular Biology},<br \/>\r\npages = {201--223},<br \/>\r\npublisher = {Springer US},<br \/>\r\nabstract = {The nucleoplasmic extract (NPE) of Xenopus laevis eggs contains a physiological concentration of nuclear proteins that recapitulate a functional nuclear environment. This system has been widely used to study key nuclear processes, including DNA replication, repair, transcription, and chromatin assembly. Its soluble nature, free from membrane fractions and insoluble structures, enables direct analysis of nuclear responses to specific DNA structures and lesions. Here, we describe an NPE preparation protocol with our modifications and its application in the processing of DNA double-strand breaks, a critical step in homology-directed repair.},<br \/>\r\nkeywords = {Takahashi G},<br \/>\r\npubstate = {published},<br \/>\r\ntppubtype = {inbook}<br \/>\r\n}<br \/>\r\n<\/pre><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('40','tp_bibtex')\">Close<\/a><\/p><\/div><div class=\"tp_abstract\" id=\"tp_abstract_40\" style=\"display:none;\"><div class=\"tp_abstract_entry\">The nucleoplasmic extract (NPE) of Xenopus laevis eggs contains a physiological concentration of nuclear proteins that recapitulate a functional nuclear environment. This system has been widely used to study key nuclear processes, including DNA replication, repair, transcription, and chromatin assembly. Its soluble nature, free from membrane fractions and insoluble structures, enables direct analysis of nuclear responses to specific DNA structures and lesions. Here, we describe an NPE preparation protocol with our modifications and its application in the processing of DNA double-strand breaks, a critical step in homology-directed repair.<\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('40','tp_abstract')\">Close<\/a><\/p><\/div><div class=\"tp_links\" id=\"tp_links_40\" style=\"display:none;\"><div class=\"tp_links_entry\"><ul class=\"tp_pub_list\"><li><i class=\"ai ai-doi\"><\/i><a class=\"tp_pub_list\" href=\"https:\/\/dx.doi.org\/10.1007\/978-1-0716-4714-1_14\" title=\"Follow DOI:10.1007\/978-1-0716-4714-1_14\" target=\"_blank\">doi:10.1007\/978-1-0716-4714-1_14<\/a><\/li><\/ul><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('40','tp_links')\">Close<\/a><\/p><\/div><\/div><\/div><div class=\"tp_publication tp_publication_inbook\"><div class=\"tp_pub_number\">40.<\/div><div class=\"tp_pub_info\"><p class=\"tp_pub_author\">Nao Yonezawa,  Yasushi Hiraoka,  Tokuko Haraguchi,  Kazuo Yamagata<\/p><p class=\"tp_pub_title\"><a class=\"tp_title_link\" href=\"https:\/\/dx.doi.org\/10.1007\/978-1-0716-4714-1_13\" title=\"T4 DNA-Induced Reconstruction of Artificial Nuclei in Living Mouse Oocytes\" target=\"blank\">T4 DNA-Induced Reconstruction of Artificial Nuclei in Living Mouse Oocytes<\/a> <span class=\"tp_pub_type inbook\">Book Chapter<\/span> <\/p><p class=\"tp_pub_additional\"><span class=\"tp_pub_additional_in\">In: <\/span><span class=\"tp_pub_additional_booktitle\">Methods in Molecular Biology, <\/span><span class=\"tp_pub_additional_pages\">pp. 183\u2013199, <\/span><span class=\"tp_pub_additional_publisher\">Springer US, <\/span><span class=\"tp_pub_additional_year\">2025<\/span>, <span class=\"tp_pub_additional_isbn\">ISBN: 9781071647141<\/span>.<\/p><p class=\"tp_pub_menu\"><span class=\"tp_abstract_link\"><a id=\"tp_abstract_sh_39\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('39','tp_abstract')\" title=\"Show abstract\" style=\"cursor:pointer;\">Abstract<\/a><\/span> | <span class=\"tp_resource_link\"><a id=\"tp_links_sh_39\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('39','tp_links')\" title=\"Show links and resources\" style=\"cursor:pointer;\">Links<\/a><\/span> | <span class=\"tp_pub_tags_label\">\u30bf\u30b0: <\/span><a rel=\"nofollow\" href=\"https:\/\/www.bioreg.kyushu-u.ac.jp\/ext\/epicode\/publications?tgid=5#tppubs\" title=\"Show all publications which have a relationship to this tag\">Yamagata G<\/a><\/p><div class=\"tp_bibtex\" id=\"tp_bibtex_39\" style=\"display:none;\"><div class=\"tp_bibtex_entry\"><pre>@inbook{Yonezawa2025,<br \/>\r\ntitle = {T4 DNA-Induced Reconstruction of Artificial Nuclei in Living Mouse Oocytes},<br \/>\r\nauthor = {Nao Yonezawa and Yasushi Hiraoka and Tokuko Haraguchi and Kazuo Yamagata},<br \/>\r\ndoi = {10.1007\/978-1-0716-4714-1_13},<br \/>\r\nisbn = {9781071647141},<br \/>\r\nyear  = {2025},<br \/>\r\ndate = {2025-08-21},<br \/>\r\nbooktitle = {Methods in Molecular Biology},<br \/>\r\npages = {183--199},<br \/>\r\npublisher = {Springer US},<br \/>\r\nabstract = {Fertilization involves a specialized nuclear formation process distinct from that of somatic cells, and reconstitution methods are useful for understanding its underlying mechanisms. Recently, we successfully reconstructed a nuclear-like structure, termed an \u201cartificial nucleus,\u201d in living mouse oocytes by microinjecting solutions of T4 DNA (~166 kbp). This achievement allowed us to identify the physicochemical properties necessary for nuclear formation. In this paper, we describe a method for constructing artificial nuclei using T4 DNA solutions, which will contribute to future studies on the mechanisms of nuclear formation.},<br \/>\r\nkeywords = {Yamagata G},<br \/>\r\npubstate = {published},<br \/>\r\ntppubtype = {inbook}<br \/>\r\n}<br \/>\r\n<\/pre><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('39','tp_bibtex')\">Close<\/a><\/p><\/div><div class=\"tp_abstract\" id=\"tp_abstract_39\" style=\"display:none;\"><div class=\"tp_abstract_entry\">Fertilization involves a specialized nuclear formation process distinct from that of somatic cells, and reconstitution methods are useful for understanding its underlying mechanisms. Recently, we successfully reconstructed a nuclear-like structure, termed an \u201cartificial nucleus,\u201d in living mouse oocytes by microinjecting solutions of T4 DNA (~166 kbp). This achievement allowed us to identify the physicochemical properties necessary for nuclear formation. In this paper, we describe a method for constructing artificial nuclei using T4 DNA solutions, which will contribute to future studies on the mechanisms of nuclear formation.<\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('39','tp_abstract')\">Close<\/a><\/p><\/div><div class=\"tp_links\" id=\"tp_links_39\" style=\"display:none;\"><div class=\"tp_links_entry\"><ul class=\"tp_pub_list\"><li><i class=\"ai ai-doi\"><\/i><a class=\"tp_pub_list\" href=\"https:\/\/dx.doi.org\/10.1007\/978-1-0716-4714-1_13\" title=\"Follow DOI:10.1007\/978-1-0716-4714-1_13\" target=\"_blank\">doi:10.1007\/978-1-0716-4714-1_13<\/a><\/li><\/ul><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('39','tp_links')\">Close<\/a><\/p><\/div><\/div><\/div><div class=\"tp_publication tp_publication_article\"><div class=\"tp_pub_number\">39.<\/div><div class=\"tp_pub_info\"><p class=\"tp_pub_author\">Chihiro Matsuda,  Akane Ichiki,  Yuko Sato,  Yukino Kudo,  Mika Saotome,  Chihiro Takayama,  Khoa Minh Le,  Satoshi Uchino,  Ryota Higuchi,  Kazuhiko Kawata,  Kosuke Tomimatsu,  Manabu Ozawa,  Masahito Ikawa,  Yasuyuki Ohkawa,  Yoshihiro Baba,  Hiroshi Kimura<\/p><p class=\"tp_pub_title\"><a class=\"tp_title_link\" href=\"https:\/\/dx.doi.org\/10.1016\/j.jmb.2025.169395\" title=\"Organization and Dynamics of Transcription Elongation Foci in Mouse Tissues\" target=\"blank\">Organization and Dynamics of Transcription Elongation Foci in Mouse Tissues<\/a> <span class=\"tp_pub_type article\">Journal Article<\/span> <\/p><p class=\"tp_pub_additional\"><span class=\"tp_pub_additional_in\">In: <\/span><span class=\"tp_pub_additional_journal\">Journal of Molecular Biology, <\/span><span class=\"tp_pub_additional_year\">2025<\/span>, <span class=\"tp_pub_additional_issn\">ISSN: 0022-2836<\/span>.<\/p><p class=\"tp_pub_menu\"><span class=\"tp_abstract_link\"><a id=\"tp_abstract_sh_41\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('41','tp_abstract')\" title=\"Show abstract\" style=\"cursor:pointer;\">Abstract<\/a><\/span> | <span class=\"tp_resource_link\"><a id=\"tp_links_sh_41\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('41','tp_links')\" title=\"Show links and resources\" style=\"cursor:pointer;\">Links<\/a><\/span> | <span class=\"tp_pub_tags_label\">\u30bf\u30b0: <\/span><a rel=\"nofollow\" href=\"https:\/\/www.bioreg.kyushu-u.ac.jp\/ext\/epicode\/publications?tgid=2#tppubs\" title=\"Show all publications which have a relationship to this tag\">Kimura G<\/a>, <a rel=\"nofollow\" href=\"https:\/\/www.bioreg.kyushu-u.ac.jp\/ext\/epicode\/publications?tgid=1#tppubs\" title=\"Show all publications which have a relationship to this tag\">Ohkawa G<\/a><\/p><div class=\"tp_bibtex\" id=\"tp_bibtex_41\" style=\"display:none;\"><div class=\"tp_bibtex_entry\"><pre>@article{Matsuda2025,<br \/>\r\ntitle = {Organization and Dynamics of Transcription Elongation Foci in Mouse Tissues},<br \/>\r\nauthor = {Chihiro Matsuda and Akane Ichiki and Yuko Sato and Yukino Kudo and Mika Saotome and Chihiro Takayama and Khoa Minh Le and Satoshi Uchino and Ryota Higuchi and Kazuhiko Kawata and Kosuke Tomimatsu and Manabu Ozawa and Masahito Ikawa and Yasuyuki Ohkawa and Yoshihiro Baba and Hiroshi Kimura},<br \/>\r\ndoi = {10.1016\/j.jmb.2025.169395},<br \/>\r\nissn = {0022-2836},<br \/>\r\nyear  = {2025},<br \/>\r\ndate = {2025-08-13},<br \/>\r\njournal = {Journal of Molecular Biology},<br \/>\r\npublisher = {Elsevier BV},<br \/>\r\nabstract = {RNA polymerase II (RNAP2) transcribes most genes in eukaryotic nuclei. During the transition from transcription initiation to productive elongation, and throughout the elongation phase, RNAP2 becomes phosphorylated at the Ser2 residue within the heptapeptide repeats of the carboxyl-terminal domain of its largest subunit. Antibodies specific to RNAP2 Ser2 phosphorylation (Ser2ph) have enabled visualization of active transcription sites in fixed cells and tissues. Here, we report the generation and characterization of knock-in mice ubiquitously expressing a fluorescent protein-tagged, modification-specific intracellular antibody (mintbody) targeting RNAP2 Ser2ph. Using these mice, we successfully visualized transcription elongation foci in mouse tissues and characterized their distribution and dynamics across diverse cell types. RNAP2 Ser2ph-mintbody formed hundreds to thousands of nuclear foci, which were excluded from heterochromatin and transcriptionally repressed domains, such as the XY body in pachytene spermatocytes. Quantitative analysis revealed tissue- and cell type-specific variation in both the number and mobility of transcription elongation foci. The mobility of transcription foci was more restricted in differentiated cells compared to differentiating and proliferating cells, likely reflecting a reduced number of actively transcribed genes and more limited open chromatin regions upon differentiation. These findings suggest that the spatial organization and dynamics of transcription elongation are closely associated with cell identity and differentiation status. The RNAP2 Ser2ph-mintbody knock-in mice provide a valuable tool for future studies of transcription organization and dynamics at the tissue level.},<br \/>\r\nkeywords = {Kimura G, Ohkawa G},<br \/>\r\npubstate = {published},<br \/>\r\ntppubtype = {article}<br \/>\r\n}<br \/>\r\n<\/pre><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('41','tp_bibtex')\">Close<\/a><\/p><\/div><div class=\"tp_abstract\" id=\"tp_abstract_41\" style=\"display:none;\"><div class=\"tp_abstract_entry\">RNA polymerase II (RNAP2) transcribes most genes in eukaryotic nuclei. During the transition from transcription initiation to productive elongation, and throughout the elongation phase, RNAP2 becomes phosphorylated at the Ser2 residue within the heptapeptide repeats of the carboxyl-terminal domain of its largest subunit. Antibodies specific to RNAP2 Ser2 phosphorylation (Ser2ph) have enabled visualization of active transcription sites in fixed cells and tissues. Here, we report the generation and characterization of knock-in mice ubiquitously expressing a fluorescent protein-tagged, modification-specific intracellular antibody (mintbody) targeting RNAP2 Ser2ph. Using these mice, we successfully visualized transcription elongation foci in mouse tissues and characterized their distribution and dynamics across diverse cell types. RNAP2 Ser2ph-mintbody formed hundreds to thousands of nuclear foci, which were excluded from heterochromatin and transcriptionally repressed domains, such as the XY body in pachytene spermatocytes. Quantitative analysis revealed tissue- and cell type-specific variation in both the number and mobility of transcription elongation foci. The mobility of transcription foci was more restricted in differentiated cells compared to differentiating and proliferating cells, likely reflecting a reduced number of actively transcribed genes and more limited open chromatin regions upon differentiation. These findings suggest that the spatial organization and dynamics of transcription elongation are closely associated with cell identity and differentiation status. The RNAP2 Ser2ph-mintbody knock-in mice provide a valuable tool for future studies of transcription organization and dynamics at the tissue level.<\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('41','tp_abstract')\">Close<\/a><\/p><\/div><div class=\"tp_links\" id=\"tp_links_41\" style=\"display:none;\"><div class=\"tp_links_entry\"><ul class=\"tp_pub_list\"><li><i class=\"ai ai-doi\"><\/i><a class=\"tp_pub_list\" href=\"https:\/\/dx.doi.org\/10.1016\/j.jmb.2025.169395\" title=\"Follow DOI:10.1016\/j.jmb.2025.169395\" target=\"_blank\">doi:10.1016\/j.jmb.2025.169395<\/a><\/li><\/ul><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('41','tp_links')\">Close<\/a><\/p><\/div><\/div><\/div><div class=\"tp_publication tp_publication_article\"><div class=\"tp_pub_number\">38.<\/div><div class=\"tp_pub_info\"><p class=\"tp_pub_author\">Shoko Mizutani,  Kanji Furuya,  Ayumi Mure,  Yuuki Takahashi,  Akihiro Mori,  Nozomu Sakurai,  Takuto Suito,  Kohjiro Nagao,  Masato Umeda,  Kaori Watanabe,  Yukako Hattori,  Tadashi Uemura<\/p><p class=\"tp_pub_title\"><a class=\"tp_title_link\" href=\"https:\/\/dx.doi.org\/10.1038\/s44319-025-00503-8\" title=\"Growth phase diets diminish histone acetyltransferase Gcn5 function and shorten lifespan of Drosophila males\" target=\"blank\">Growth phase diets diminish histone acetyltransferase Gcn5 function and shorten lifespan of Drosophila males<\/a> <span class=\"tp_pub_type article\">Journal Article<\/span> <\/p><p class=\"tp_pub_additional\"><span class=\"tp_pub_additional_in\">In: <\/span><span class=\"tp_pub_additional_journal\">EMBO Rep, <\/span><span class=\"tp_pub_additional_year\">2025<\/span>, <span class=\"tp_pub_additional_issn\">ISSN: 1469-3178<\/span>.<\/p><p class=\"tp_pub_menu\"><span class=\"tp_abstract_link\"><a id=\"tp_abstract_sh_38\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('38','tp_abstract')\" title=\"Show abstract\" style=\"cursor:pointer;\">Abstract<\/a><\/span> | <span class=\"tp_resource_link\"><a id=\"tp_links_sh_38\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('38','tp_links')\" title=\"Show links and resources\" style=\"cursor:pointer;\">Links<\/a><\/span> | <span class=\"tp_pub_tags_label\">\u30bf\u30b0: <\/span><\/p><div class=\"tp_bibtex\" id=\"tp_bibtex_38\" style=\"display:none;\"><div class=\"tp_bibtex_entry\"><pre>@article{Mizutani2025,<br \/>\r\ntitle = {Growth phase diets diminish histone acetyltransferase Gcn5 function and shorten lifespan of Drosophila males},<br \/>\r\nauthor = {Shoko Mizutani and Kanji Furuya and Ayumi Mure and Yuuki Takahashi and Akihiro Mori and Nozomu Sakurai and Takuto Suito and Kohjiro Nagao and Masato Umeda and Kaori Watanabe and Yukako Hattori and Tadashi Uemura},<br \/>\r\ndoi = {10.1038\/s44319-025-00503-8},<br \/>\r\nissn = {1469-3178},<br \/>\r\nyear  = {2025},<br \/>\r\ndate = {2025-07-10},<br \/>\r\njournal = {EMBO Rep},<br \/>\r\npublisher = {Springer Science and Business Media LLC},<br \/>\r\nabstract = {<jats:title>Abstract<\/jats:title><br \/>\n          <jats:p>The nutritional environment in early life, referred to as the nutrition history, exerts far-reaching health effects beyond the developmental stage. Here, with <jats:italic>Drosophila melanogaster<\/jats:italic> as a model, we fed larvae on diets consisting of a variety of yeast mutants and explored the resulting histories that impacted adult lifespan. A larval diet comprised of yeast <jats:italic>nat3<\/jats:italic> KO shortened the lifespan of male adults; and remarkably, this diet diminished the function of histone acetyltransferase Gcn5 in larvae. Concordantly, perturbation of <jats:italic>Gcn5<\/jats:italic>-mediated gene regulation in the larval whole body or neurons significantly contributed to the earlier death of adults. The <jats:italic>nat3<\/jats:italic> KO diet is much more abundant in long-chain fatty acids and branched-chain amino acids (BCAAs) than the control yeast diet. Supplementing the control diet with a combination of oleic acid, valine, and acetic acid recapitulated the effects of the <jats:italic>nat3<\/jats:italic> KO diet on the larval transcriptome and the lifespan of males. Our findings strongly suggest a causal link between a fatty acids- and BCAA-rich diet in developmental stages and lifespan reduction via the adverse effect on the Gcn5 function.<\/jats:p>},<br \/>\r\nkeywords = {},<br \/>\r\npubstate = {published},<br \/>\r\ntppubtype = {article}<br \/>\r\n}<br \/>\r\n<\/pre><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('38','tp_bibtex')\">Close<\/a><\/p><\/div><div class=\"tp_abstract\" id=\"tp_abstract_38\" style=\"display:none;\"><div class=\"tp_abstract_entry\"><jats:title>Abstract<\/jats:title><br \/>\n          <jats:p>The nutritional environment in early life, referred to as the nutrition history, exerts far-reaching health effects beyond the developmental stage. Here, with <jats:italic>Drosophila melanogaster<\/jats:italic> as a model, we fed larvae on diets consisting of a variety of yeast mutants and explored the resulting histories that impacted adult lifespan. A larval diet comprised of yeast <jats:italic>nat3<\/jats:italic> KO shortened the lifespan of male adults; and remarkably, this diet diminished the function of histone acetyltransferase Gcn5 in larvae. Concordantly, perturbation of <jats:italic>Gcn5<\/jats:italic>-mediated gene regulation in the larval whole body or neurons significantly contributed to the earlier death of adults. The <jats:italic>nat3<\/jats:italic> KO diet is much more abundant in long-chain fatty acids and branched-chain amino acids (BCAAs) than the control yeast diet. Supplementing the control diet with a combination of oleic acid, valine, and acetic acid recapitulated the effects of the <jats:italic>nat3<\/jats:italic> KO diet on the larval transcriptome and the lifespan of males. Our findings strongly suggest a causal link between a fatty acids- and BCAA-rich diet in developmental stages and lifespan reduction via the adverse effect on the Gcn5 function.<\/jats:p><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('38','tp_abstract')\">Close<\/a><\/p><\/div><div class=\"tp_links\" id=\"tp_links_38\" style=\"display:none;\"><div class=\"tp_links_entry\"><ul class=\"tp_pub_list\"><li><i class=\"ai ai-doi\"><\/i><a class=\"tp_pub_list\" href=\"https:\/\/dx.doi.org\/10.1038\/s44319-025-00503-8\" title=\"Follow DOI:10.1038\/s44319-025-00503-8\" target=\"_blank\">doi:10.1038\/s44319-025-00503-8<\/a><\/li><\/ul><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('38','tp_links')\">Close<\/a><\/p><\/div><\/div><\/div><div class=\"tp_publication tp_publication_article\"><div class=\"tp_pub_number\">37.<\/div><div class=\"tp_pub_info\"><p class=\"tp_pub_author\">Takashi Fukaya<\/p><p class=\"tp_pub_title\"><a class=\"tp_title_link\" href=\"https:\/\/dx.doi.org\/10.1016\/j.jmb.2025.169311\" title=\"Multilayered mechanisms for long-range regulatory interactions in eukaryotic transcription\" target=\"blank\">Multilayered mechanisms for long-range regulatory interactions in eukaryotic transcription<\/a> <span class=\"tp_pub_type article\">Journal Article<\/span> <\/p><p class=\"tp_pub_additional\"><span class=\"tp_pub_additional_in\">In: <\/span><span class=\"tp_pub_additional_journal\">Journal of Molecular Biology, <\/span><span class=\"tp_pub_additional_year\">2025<\/span>, <span class=\"tp_pub_additional_issn\">ISSN: 0022-2836<\/span>.<\/p><p class=\"tp_pub_menu\"><span class=\"tp_abstract_link\"><a id=\"tp_abstract_sh_37\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('37','tp_abstract')\" title=\"Show abstract\" style=\"cursor:pointer;\">Abstract<\/a><\/span> | <span class=\"tp_resource_link\"><a id=\"tp_links_sh_37\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('37','tp_links')\" title=\"Show links and resources\" style=\"cursor:pointer;\">Links<\/a><\/span> | <span class=\"tp_pub_tags_label\">\u30bf\u30b0: <\/span><a rel=\"nofollow\" href=\"https:\/\/www.bioreg.kyushu-u.ac.jp\/ext\/epicode\/publications?tgid=6#tppubs\" title=\"Show all publications which have a relationship to this tag\">Fukaya G<\/a><\/p><div class=\"tp_bibtex\" id=\"tp_bibtex_37\" style=\"display:none;\"><div class=\"tp_bibtex_entry\"><pre>@article{Fukaya2025,<br \/>\r\ntitle = {Multilayered mechanisms for long-range regulatory interactions in eukaryotic transcription},<br \/>\r\nauthor = {Takashi Fukaya},<br \/>\r\ndoi = {10.1016\/j.jmb.2025.169311},<br \/>\r\nissn = {0022-2836},<br \/>\r\nyear  = {2025},<br \/>\r\ndate = {2025-06-26},<br \/>\r\njournal = {Journal of Molecular Biology},<br \/>\r\npublisher = {Elsevier BV},<br \/>\r\nabstract = {Transcription is a fundamental biological reaction that underlies essentially all developmental and physiological processes across species. While substantial efforts have been made to decipher the basic mechanisms of transcriptional regulation over the decades, we are still far from a comprehensive understanding of this highly intricate biological reaction including the temporal and spatial dynamics of the process. In recent years, new concepts and models have been proposed based on novel insights obtained from the use of cutting-edge technologies such as genome editing, whole-genome assays, structural analysis, and quantitative live-imaging approaches. In this review, I summarize emerging models and concepts for the dynamic modulation of long-range regulatory interactions in the context of animal development. I suggest that the multilayered actions of enhancers and associating regulatory DNAs such as \u201dFacilitators\u201d and \u201cRange Extenders\u201d dynamically modulate clustering of transcription machineries at specific genomic loci to flexibly control the temporal and spatial dynamics of gene expression during development.},<br \/>\r\nkeywords = {Fukaya G},<br \/>\r\npubstate = {published},<br \/>\r\ntppubtype = {article}<br \/>\r\n}<br \/>\r\n<\/pre><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('37','tp_bibtex')\">Close<\/a><\/p><\/div><div class=\"tp_abstract\" id=\"tp_abstract_37\" style=\"display:none;\"><div class=\"tp_abstract_entry\">Transcription is a fundamental biological reaction that underlies essentially all developmental and physiological processes across species. While substantial efforts have been made to decipher the basic mechanisms of transcriptional regulation over the decades, we are still far from a comprehensive understanding of this highly intricate biological reaction including the temporal and spatial dynamics of the process. In recent years, new concepts and models have been proposed based on novel insights obtained from the use of cutting-edge technologies such as genome editing, whole-genome assays, structural analysis, and quantitative live-imaging approaches. In this review, I summarize emerging models and concepts for the dynamic modulation of long-range regulatory interactions in the context of animal development. I suggest that the multilayered actions of enhancers and associating regulatory DNAs such as \u201dFacilitators\u201d and \u201cRange Extenders\u201d dynamically modulate clustering of transcription machineries at specific genomic loci to flexibly control the temporal and spatial dynamics of gene expression during development.<\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('37','tp_abstract')\">Close<\/a><\/p><\/div><div class=\"tp_links\" id=\"tp_links_37\" style=\"display:none;\"><div class=\"tp_links_entry\"><ul class=\"tp_pub_list\"><li><i class=\"ai ai-doi\"><\/i><a class=\"tp_pub_list\" href=\"https:\/\/dx.doi.org\/10.1016\/j.jmb.2025.169311\" title=\"Follow DOI:10.1016\/j.jmb.2025.169311\" target=\"_blank\">doi:10.1016\/j.jmb.2025.169311<\/a><\/li><\/ul><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('37','tp_links')\">Close<\/a><\/p><\/div><\/div><\/div><div class=\"tp_publication tp_publication_article\"><div class=\"tp_pub_number\">36.<\/div><div class=\"tp_pub_info\"><p class=\"tp_pub_author\">Naoki Okashita,  Ryo Maeda,  Shunsuke Kuroki,  Kyona Sasaki,  Yoko Uno,  Peter Koopman,  Makoto Tachibana<\/p><p class=\"tp_pub_title\"><a class=\"tp_title_link\" href=\"https:\/\/dx.doi.org\/10.1038\/s41586-025-09063-2\" title=\"Maternal iron deficiency causes male-to-female sex reversal in mouse embryos\" target=\"blank\">Maternal iron deficiency causes male-to-female sex reversal in mouse embryos<\/a> <span class=\"tp_pub_type article\">Journal Article<\/span> <\/p><p class=\"tp_pub_additional\"><span class=\"tp_pub_additional_in\">In: <\/span><span class=\"tp_pub_additional_journal\">Nature, <\/span><span class=\"tp_pub_additional_year\">2025<\/span>, <span class=\"tp_pub_additional_issn\">ISSN: 0028-0836<\/span>.<\/p><p class=\"tp_pub_menu\"><span class=\"tp_abstract_link\"><a id=\"tp_abstract_sh_34\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('34','tp_abstract')\" title=\"Show abstract\" style=\"cursor:pointer;\">Abstract<\/a><\/span> | <span class=\"tp_resource_link\"><a id=\"tp_links_sh_34\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('34','tp_links')\" title=\"Show links and resources\" style=\"cursor:pointer;\">Links<\/a><\/span> | <span class=\"tp_pub_tags_label\">\u30bf\u30b0: <\/span><a rel=\"nofollow\" href=\"https:\/\/www.bioreg.kyushu-u.ac.jp\/ext\/epicode\/publications?tgid=19#tppubs\" title=\"Show all publications which have a relationship to this tag\">Tachibana G<\/a><\/p><div class=\"tp_bibtex\" id=\"tp_bibtex_34\" style=\"display:none;\"><div class=\"tp_bibtex_entry\"><pre>@article{10.1038\/s41586-025-09063-2,<br \/>\r\ntitle = {Maternal iron deficiency causes male-to-female sex reversal in mouse embryos},<br \/>\r\nauthor = {Naoki Okashita and Ryo Maeda and Shunsuke Kuroki and Kyona Sasaki and Yoko Uno and Peter Koopman and Makoto Tachibana},<br \/>\r\ndoi = {10.1038\/s41586-025-09063-2},<br \/>\r\nissn = {0028-0836},<br \/>\r\nyear  = {2025},<br \/>\r\ndate = {2025-06-04},<br \/>\r\nurldate = {2025-01-01},<br \/>\r\njournal = {Nature},<br \/>\r\nabstract = {Ferrous iron (Fe2+) is essential in all eukaryotic cells for various oxidoreductase reactions, including the demethylation of DNA and proteins. Histone demethylation is required for normal epigenetic regulation of the Y-chromosomal sex-determining gene Sry in developing gonads during male sex determination1,2. Here we investigate the potential connection between iron metabolism, histone demethylation and sex determination in mammals. We found that Fe2+-producing pathways are substantially activated in mouse embryonic gonads during the sex-determining period. Chelation of iron in cultured XY gonads reduced the level of KDM3A-mediated H3K9 demethylation of Sry, mostly abolished Sry expression and caused the gonads to express ovarian markers. In vivo, conditional deletion of the gene Tfrc\u2014which is required for iron incorporation\u2014in fetal XY gonadal somatic cells, or acute pharmaceutical suppression of available iron in pregnant mice, resulted in male-to-female gonadal sex reversal in a proportion of offspring, highlighting the pivotal role of iron metabolism in male sex determination. Finally, long-term feeding of pregnant mice with a low-iron diet, when combined with a heterozygous variant of Kdm3a that by itself has no observable effect, suppressed Sry expression and caused male-to-female sex reversal in some of the progeny, revealing a connection between maternal dietary iron and fetal developmental outcomes.},<br \/>\r\nkeywords = {Tachibana G},<br \/>\r\npubstate = {published},<br \/>\r\ntppubtype = {article}<br \/>\r\n}<br \/>\r\n<\/pre><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('34','tp_bibtex')\">Close<\/a><\/p><\/div><div class=\"tp_abstract\" id=\"tp_abstract_34\" style=\"display:none;\"><div class=\"tp_abstract_entry\">Ferrous iron (Fe2+) is essential in all eukaryotic cells for various oxidoreductase reactions, including the demethylation of DNA and proteins. Histone demethylation is required for normal epigenetic regulation of the Y-chromosomal sex-determining gene Sry in developing gonads during male sex determination1,2. Here we investigate the potential connection between iron metabolism, histone demethylation and sex determination in mammals. We found that Fe2+-producing pathways are substantially activated in mouse embryonic gonads during the sex-determining period. Chelation of iron in cultured XY gonads reduced the level of KDM3A-mediated H3K9 demethylation of Sry, mostly abolished Sry expression and caused the gonads to express ovarian markers. In vivo, conditional deletion of the gene Tfrc\u2014which is required for iron incorporation\u2014in fetal XY gonadal somatic cells, or acute pharmaceutical suppression of available iron in pregnant mice, resulted in male-to-female gonadal sex reversal in a proportion of offspring, highlighting the pivotal role of iron metabolism in male sex determination. Finally, long-term feeding of pregnant mice with a low-iron diet, when combined with a heterozygous variant of Kdm3a that by itself has no observable effect, suppressed Sry expression and caused male-to-female sex reversal in some of the progeny, revealing a connection between maternal dietary iron and fetal developmental outcomes.<\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('34','tp_abstract')\">Close<\/a><\/p><\/div><div class=\"tp_links\" id=\"tp_links_34\" style=\"display:none;\"><div class=\"tp_links_entry\"><ul class=\"tp_pub_list\"><li><i class=\"ai ai-doi\"><\/i><a class=\"tp_pub_list\" href=\"https:\/\/dx.doi.org\/10.1038\/s41586-025-09063-2\" title=\"Follow DOI:10.1038\/s41586-025-09063-2\" target=\"_blank\">doi:10.1038\/s41586-025-09063-2<\/a><\/li><\/ul><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('34','tp_links')\">Close<\/a><\/p><\/div><\/div><\/div><div class=\"tp_publication tp_publication_article\"><div class=\"tp_pub_number\">35.<\/div><div class=\"tp_pub_info\"><p class=\"tp_pub_author\">Munetaka Akatsu,  Rina Hirano,  Tomoya Kujirai,  Mitsuo Ogasawara,  Haruhiko Ehara,  Shun-ichi Sekine,  Yoshimasa Takizawa,  Hitoshi Kurumizaka<\/p><p class=\"tp_pub_title\"><a class=\"tp_title_link\" href=\"https:\/\/dx.doi.org\/https:\/\/doi.org\/10.1038\/s44318-025-00473-6\" title=\"Structural basis of RNAPII transcription on the nucleosome containing histone variant H2A.B\" target=\"blank\">Structural basis of RNAPII transcription on the nucleosome containing histone variant H2A.B<\/a> <span class=\"tp_pub_type article\">Journal Article<\/span> <\/p><p class=\"tp_pub_additional\"><span class=\"tp_pub_additional_in\">In: <\/span><span class=\"tp_pub_additional_journal\">The EMBO Journal, <\/span><span class=\"tp_pub_additional_year\">2025<\/span>.<\/p><p class=\"tp_pub_menu\"><span class=\"tp_abstract_link\"><a id=\"tp_abstract_sh_33\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('33','tp_abstract')\" title=\"Show abstract\" style=\"cursor:pointer;\">Abstract<\/a><\/span> | <span class=\"tp_resource_link\"><a id=\"tp_links_sh_33\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('33','tp_links')\" title=\"Show links and resources\" style=\"cursor:pointer;\">Links<\/a><\/span> | <span class=\"tp_pub_tags_label\">\u30bf\u30b0: <\/span><a rel=\"nofollow\" href=\"https:\/\/www.bioreg.kyushu-u.ac.jp\/ext\/epicode\/publications?tgid=15#tppubs\" title=\"Show all publications which have a relationship to this tag\">Chromatin<\/a>, <a rel=\"nofollow\" href=\"https:\/\/www.bioreg.kyushu-u.ac.jp\/ext\/epicode\/publications?tgid=18#tppubs\" title=\"Show all publications which have a relationship to this tag\">H2A.B<\/a>, <a rel=\"nofollow\" href=\"https:\/\/www.bioreg.kyushu-u.ac.jp\/ext\/epicode\/publications?tgid=17#tppubs\" title=\"Show all publications which have a relationship to this tag\">Histone Variant<\/a>, <a rel=\"nofollow\" href=\"https:\/\/www.bioreg.kyushu-u.ac.jp\/ext\/epicode\/publications?tgid=4#tppubs\" title=\"Show all publications which have a relationship to this tag\">Kurumizaka G<\/a>, <a rel=\"nofollow\" href=\"https:\/\/www.bioreg.kyushu-u.ac.jp\/ext\/epicode\/publications?tgid=14#tppubs\" title=\"Show all publications which have a relationship to this tag\">Nucleosome<\/a>, <a rel=\"nofollow\" href=\"https:\/\/www.bioreg.kyushu-u.ac.jp\/ext\/epicode\/publications?tgid=16#tppubs\" title=\"Show all publications which have a relationship to this tag\">Transcription<\/a><\/p><div class=\"tp_bibtex\" id=\"tp_bibtex_33\" style=\"display:none;\"><div class=\"tp_bibtex_entry\"><pre>@article{https:\/\/doi.org\/10.1038\/s44318-025-00473-6,<br \/>\r\ntitle = {Structural basis of RNAPII transcription on the nucleosome containing histone variant H2A.B},<br \/>\r\nauthor = {Munetaka Akatsu and Rina Hirano and Tomoya Kujirai and Mitsuo Ogasawara and Haruhiko Ehara and Shun-ichi Sekine and Yoshimasa Takizawa and Hitoshi Kurumizaka},<br \/>\r\nurl = {https:\/\/www.embopress.org\/doi\/abs\/10.1038\/s44318-025-00473-6},<br \/>\r\ndoi = {https:\/\/doi.org\/10.1038\/s44318-025-00473-6},<br \/>\r\nyear  = {2025},<br \/>\r\ndate = {2025-05-30},<br \/>\r\njournal = {The EMBO Journal},<br \/>\r\nabstract = {AbstractH2A.B is a distant histone H2A variant associated with actively transcribed regions of the genome, suggesting its positive role in promoting transcription. In the present study, we demonstrate that the RNA polymerase II elongation complex (EC) transcribes the nucleosome containing H2A.B more efficiently than that with canonical H2A in vitro. Our cryo-electron microscopy analysis of the H2A.B nucleosome during transcription revealed that the proximal H2A.B-H2B dimer is released from the nucleosome as the EC transcribes the proximal half of the nucleosomal DNA. This dissociation, which is not observed in the canonical H2A nucleosome, likely enhances the EC elongation efficiency in the H2A.B nucleosome. Mutational analyses suggested that the unique short C-terminal region of H2A.B alone enhances EC elongation efficiency when substituted for its counterpart in canonical H2A. Additionally, other regions of H2A.B contribute to this enhancement. These structural and biochemical findings provide new insights into the role of H2A.B in regulating gene expression.},<br \/>\r\nkeywords = {Chromatin, H2A.B, Histone Variant, Kurumizaka G, Nucleosome, Transcription},<br \/>\r\npubstate = {published},<br \/>\r\ntppubtype = {article}<br \/>\r\n}<br \/>\r\n<\/pre><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('33','tp_bibtex')\">Close<\/a><\/p><\/div><div class=\"tp_abstract\" id=\"tp_abstract_33\" style=\"display:none;\"><div class=\"tp_abstract_entry\">AbstractH2A.B is a distant histone H2A variant associated with actively transcribed regions of the genome, suggesting its positive role in promoting transcription. In the present study, we demonstrate that the RNA polymerase II elongation complex (EC) transcribes the nucleosome containing H2A.B more efficiently than that with canonical H2A in vitro. Our cryo-electron microscopy analysis of the H2A.B nucleosome during transcription revealed that the proximal H2A.B-H2B dimer is released from the nucleosome as the EC transcribes the proximal half of the nucleosomal DNA. This dissociation, which is not observed in the canonical H2A nucleosome, likely enhances the EC elongation efficiency in the H2A.B nucleosome. Mutational analyses suggested that the unique short C-terminal region of H2A.B alone enhances EC elongation efficiency when substituted for its counterpart in canonical H2A. Additionally, other regions of H2A.B contribute to this enhancement. These structural and biochemical findings provide new insights into the role of H2A.B in regulating gene expression.<\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('33','tp_abstract')\">Close<\/a><\/p><\/div><div class=\"tp_links\" id=\"tp_links_33\" style=\"display:none;\"><div class=\"tp_links_entry\"><ul class=\"tp_pub_list\"><li><i class=\"fas fa-globe\"><\/i><a class=\"tp_pub_list\" href=\"https:\/\/www.embopress.org\/doi\/abs\/10.1038\/s44318-025-00473-6\" title=\"https:\/\/www.embopress.org\/doi\/abs\/10.1038\/s44318-025-00473-6\" target=\"_blank\">https:\/\/www.embopress.org\/doi\/abs\/10.1038\/s44318-025-00473-6<\/a><\/li><li><i class=\"ai ai-doi\"><\/i><a class=\"tp_pub_list\" href=\"https:\/\/dx.doi.org\/https:\/\/doi.org\/10.1038\/s44318-025-00473-6\" title=\"Follow DOI:https:\/\/doi.org\/10.1038\/s44318-025-00473-6\" target=\"_blank\">doi:https:\/\/doi.org\/10.1038\/s44318-025-00473-6<\/a><\/li><\/ul><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('33','tp_links')\">Close<\/a><\/p><\/div><\/div><\/div><div class=\"tp_publication tp_publication_article\"><div class=\"tp_pub_number\">34.<\/div><div class=\"tp_pub_info\"><p class=\"tp_pub_author\">Atsushi Takasu,  Toshiaki Hino,  Osamu Takenouchi,  Yasuki Miyagawa,  Zhihua Liang,  Shota Tanaka,  Tomoya Mimura,  Chisato Ida,  Yuki Matsuo,  Yuna Lee,  Haruka Ikegami,  Miho Ohsugi,  Shogo Matoba,  Atsuo Ogura,  Kazuo Yamagata,  Kazuya Matsumoto,  Tomoya S Kitajima,  Kei Miyamoto<\/p><p class=\"tp_pub_title\"><a class=\"tp_title_link\" href=\"https:\/\/dx.doi.org\/10.1016\/j.jbc.2025.110308\" title=\"Characterization of H3K4me3 in mouse oocytes at the metaphase II stage\" target=\"blank\">Characterization of H3K4me3 in mouse oocytes at the metaphase II stage<\/a> <span class=\"tp_pub_type article\">Journal Article<\/span> <\/p><p class=\"tp_pub_additional\"><span class=\"tp_pub_additional_in\">In: <\/span><span class=\"tp_pub_additional_journal\">J Biol Chem, <\/span><span class=\"tp_pub_additional_pages\">pp. 110308, <\/span><span class=\"tp_pub_additional_year\">2025<\/span>, <span class=\"tp_pub_additional_issn\">ISSN: 1083-351X<\/span>.<\/p><p class=\"tp_pub_menu\"><span class=\"tp_abstract_link\"><a id=\"tp_abstract_sh_35\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('35','tp_abstract')\" title=\"Show abstract\" style=\"cursor:pointer;\">Abstract<\/a><\/span> | <span class=\"tp_resource_link\"><a id=\"tp_links_sh_35\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('35','tp_links')\" title=\"Show links and resources\" style=\"cursor:pointer;\">Links<\/a><\/span> | <span class=\"tp_pub_tags_label\">\u30bf\u30b0: <\/span><a rel=\"nofollow\" href=\"https:\/\/www.bioreg.kyushu-u.ac.jp\/ext\/epicode\/publications?tgid=20#tppubs\" title=\"Show all publications which have a relationship to this tag\">Miyamoto G<\/a>, <a rel=\"nofollow\" href=\"https:\/\/www.bioreg.kyushu-u.ac.jp\/ext\/epicode\/publications?tgid=5#tppubs\" title=\"Show all publications which have a relationship to this tag\">Yamagata G<\/a><\/p><div class=\"tp_bibtex\" id=\"tp_bibtex_35\" style=\"display:none;\"><div class=\"tp_bibtex_entry\"><pre>@article{pmid40449591,<br \/>\r\ntitle = {Characterization of H3K4me3 in mouse oocytes at the metaphase II stage},<br \/>\r\nauthor = {Atsushi Takasu and Toshiaki Hino and Osamu Takenouchi and Yasuki Miyagawa and Zhihua Liang and Shota Tanaka and Tomoya Mimura and Chisato Ida and Yuki Matsuo and Yuna Lee and Haruka Ikegami and Miho Ohsugi and Shogo Matoba and Atsuo Ogura and Kazuo Yamagata and Kazuya Matsumoto and Tomoya S Kitajima and Kei Miyamoto},<br \/>\r\ndoi = {10.1016\/j.jbc.2025.110308},<br \/>\r\nissn = {1083-351X},<br \/>\r\nyear  = {2025},<br \/>\r\ndate = {2025-05-29},<br \/>\r\nurldate = {2025-05-01},<br \/>\r\njournal = {J Biol Chem},<br \/>\r\npages = {110308},<br \/>\r\nabstract = {Central functions of histone modifications in germ cell and embryonic development have been documented. Accumulating evidence suggests that oocytes possess unique profiles of histone modifications, among which histone H3 lysine 4 trimethylation (H3K4me3) is broadly spread on the mouse oocyte chromosomes at the metaphase II (MII) stage, unlike later embryonic stages. However, the characteristics and developmental roles of H3K4me3 on MII chromosomes are unclear. Here, we discovered that H3K4me3 was abundantly localized on some of the MII oocyte chromosomes facing the cortical side. Using multicolor FISH and CRISPR-Sirius-based labeling of chromosomes, we revealed that the X chromosome tended to be localized at the cortical side with strong H3K4me3 signals. Anchoring oocyte chromosomes to the cortex may play a role in the asymmetric H3K4me3 distribution. Furthermore, we found that the forced removal of H3K4me3 through the overexpression of a specific lysine demethylase in MII oocytes resulted in abnormal chromosome-spindle structure and impaired preimplantation development after in vitro fertilization. These findings highlight the developmental function of H3K4me3 in transcriptionally-silent MII oocytes.},<br \/>\r\nkeywords = {Miyamoto G, Yamagata G},<br \/>\r\npubstate = {published},<br \/>\r\ntppubtype = {article}<br \/>\r\n}<br \/>\r\n<\/pre><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('35','tp_bibtex')\">Close<\/a><\/p><\/div><div class=\"tp_abstract\" id=\"tp_abstract_35\" style=\"display:none;\"><div class=\"tp_abstract_entry\">Central functions of histone modifications in germ cell and embryonic development have been documented. Accumulating evidence suggests that oocytes possess unique profiles of histone modifications, among which histone H3 lysine 4 trimethylation (H3K4me3) is broadly spread on the mouse oocyte chromosomes at the metaphase II (MII) stage, unlike later embryonic stages. However, the characteristics and developmental roles of H3K4me3 on MII chromosomes are unclear. Here, we discovered that H3K4me3 was abundantly localized on some of the MII oocyte chromosomes facing the cortical side. Using multicolor FISH and CRISPR-Sirius-based labeling of chromosomes, we revealed that the X chromosome tended to be localized at the cortical side with strong H3K4me3 signals. Anchoring oocyte chromosomes to the cortex may play a role in the asymmetric H3K4me3 distribution. Furthermore, we found that the forced removal of H3K4me3 through the overexpression of a specific lysine demethylase in MII oocytes resulted in abnormal chromosome-spindle structure and impaired preimplantation development after in vitro fertilization. These findings highlight the developmental function of H3K4me3 in transcriptionally-silent MII oocytes.<\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('35','tp_abstract')\">Close<\/a><\/p><\/div><div class=\"tp_links\" id=\"tp_links_35\" style=\"display:none;\"><div class=\"tp_links_entry\"><ul class=\"tp_pub_list\"><li><i class=\"ai ai-doi\"><\/i><a class=\"tp_pub_list\" href=\"https:\/\/dx.doi.org\/10.1016\/j.jbc.2025.110308\" title=\"Follow DOI:10.1016\/j.jbc.2025.110308\" target=\"_blank\">doi:10.1016\/j.jbc.2025.110308<\/a><\/li><\/ul><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('35','tp_links')\">Close<\/a><\/p><\/div><\/div><\/div><div class=\"tp_publication tp_publication_article\"><div class=\"tp_pub_number\">33.<\/div><div class=\"tp_pub_info\"><p class=\"tp_pub_author\">Tomoya Kujirai,  Junko Kato,  Kyoka Yamamoto,  Seiya Hirai,  Takeru Fujii,  Kazumitsu Maehara,  Akihito Harada,  Lumi Negishi,  Mitsuo Ogasawara,  Yuki Yamaguchi,  Yasuyuki Ohkawa,  Yoshimasa Takizawa,  Hitoshi Kurumizaka<\/p><p class=\"tp_pub_title\"><a class=\"tp_title_link\" href=\"https:\/\/dx.doi.org\/10.1038\/s41467-025-59580-x\" title=\"Multiple structures of RNA polymerase II isolated from human nuclei by ChIP-CryoEM analysis\" target=\"blank\">Multiple structures of RNA polymerase II isolated from human nuclei by ChIP-CryoEM analysis<\/a> <span class=\"tp_pub_type article\">Journal Article<\/span> <\/p><p class=\"tp_pub_additional\"><span class=\"tp_pub_additional_in\">In: <\/span><span class=\"tp_pub_additional_journal\">Nature Communications, <\/span><span class=\"tp_pub_additional_volume\">vol. 16, <\/span><span class=\"tp_pub_additional_number\">no. 1, <\/span><span class=\"tp_pub_additional_pages\">pp. 4724, <\/span><span class=\"tp_pub_additional_year\">2025<\/span>.<\/p><p class=\"tp_pub_menu\"><span class=\"tp_abstract_link\"><a id=\"tp_abstract_sh_32\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('32','tp_abstract')\" title=\"Show abstract\" style=\"cursor:pointer;\">Abstract<\/a><\/span> | <span class=\"tp_resource_link\"><a id=\"tp_links_sh_32\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('32','tp_links')\" title=\"Show links and resources\" style=\"cursor:pointer;\">Links<\/a><\/span> | <span class=\"tp_pub_tags_label\">\u30bf\u30b0: <\/span><a rel=\"nofollow\" href=\"https:\/\/www.bioreg.kyushu-u.ac.jp\/ext\/epicode\/publications?tgid=4#tppubs\" title=\"Show all publications which have a relationship to this tag\">Kurumizaka G<\/a><\/p><div class=\"tp_bibtex\" id=\"tp_bibtex_32\" style=\"display:none;\"><div class=\"tp_bibtex_entry\"><pre>@article{10.1038\/s41467-025-59580-x,<br \/>\r\ntitle = {Multiple structures of RNA polymerase II isolated from human nuclei by ChIP-CryoEM analysis},<br \/>\r\nauthor = {Tomoya Kujirai and Junko Kato and Kyoka Yamamoto and Seiya Hirai and Takeru Fujii and Kazumitsu Maehara and Akihito Harada and Lumi Negishi and Mitsuo Ogasawara and Yuki Yamaguchi and Yasuyuki Ohkawa and Yoshimasa Takizawa and Hitoshi Kurumizaka},<br \/>\r\ndoi = {10.1038\/s41467-025-59580-x},<br \/>\r\nyear  = {2025},<br \/>\r\ndate = {2025-05-28},<br \/>\r\nurldate = {2025-01-01},<br \/>\r\njournal = {Nature Communications},<br \/>\r\nvolume = {16},<br \/>\r\nnumber = {1},<br \/>\r\npages = {4724},<br \/>\r\nabstract = {RNA polymerase II (RNAPII) is a central transcription enzyme that exists as multiple forms with or without accessory factors, and transcribes the genomic DNA packaged in chromatin. To understand how RNAPII functions in the human genome, we isolate transcribing RNAPII complexes from human nuclei by chromatin immunopurification, and determine the cryo-electron microscopy structures of RNAPII elongation complexes (ECs) associated with genomic DNA in distinct forms, without or with the elongation factors SPT4\/5, ELOF1, and SPT6. This ChIP-cryoEM method also reveals the two EC-nucleosome complexes corresponding nucleosome disassembly\/reassembly processes. In the structure of EC-downstream nucleosome, EC paused at superhelical location (SHL) \u22125 in the nucleosome, suggesting that SHL(\u22125) pausing occurs in a sequence-independent manner during nucleosome disassembly. In the structure of the EC-upstream nucleosome, EC directly contacts the nucleosome through the nucleosomal DNA-RPB4\/7 stalk and the H2A-H2B dimer-RPB2 wall interactions, suggesting that EC may be paused during nucleosome reassembly. These representative EC structures transcribing the human genome provide mechanistic insights into understanding RNAPII transcription on chromatin.},<br \/>\r\nkeywords = {Kurumizaka G},<br \/>\r\npubstate = {published},<br \/>\r\ntppubtype = {article}<br \/>\r\n}<br \/>\r\n<\/pre><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('32','tp_bibtex')\">Close<\/a><\/p><\/div><div class=\"tp_abstract\" id=\"tp_abstract_32\" style=\"display:none;\"><div class=\"tp_abstract_entry\">RNA polymerase II (RNAPII) is a central transcription enzyme that exists as multiple forms with or without accessory factors, and transcribes the genomic DNA packaged in chromatin. To understand how RNAPII functions in the human genome, we isolate transcribing RNAPII complexes from human nuclei by chromatin immunopurification, and determine the cryo-electron microscopy structures of RNAPII elongation complexes (ECs) associated with genomic DNA in distinct forms, without or with the elongation factors SPT4\/5, ELOF1, and SPT6. This ChIP-cryoEM method also reveals the two EC-nucleosome complexes corresponding nucleosome disassembly\/reassembly processes. In the structure of EC-downstream nucleosome, EC paused at superhelical location (SHL) \u22125 in the nucleosome, suggesting that SHL(\u22125) pausing occurs in a sequence-independent manner during nucleosome disassembly. In the structure of the EC-upstream nucleosome, EC directly contacts the nucleosome through the nucleosomal DNA-RPB4\/7 stalk and the H2A-H2B dimer-RPB2 wall interactions, suggesting that EC may be paused during nucleosome reassembly. These representative EC structures transcribing the human genome provide mechanistic insights into understanding RNAPII transcription on chromatin.<\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('32','tp_abstract')\">Close<\/a><\/p><\/div><div class=\"tp_links\" id=\"tp_links_32\" style=\"display:none;\"><div class=\"tp_links_entry\"><ul class=\"tp_pub_list\"><li><i class=\"ai ai-doi\"><\/i><a class=\"tp_pub_list\" href=\"https:\/\/dx.doi.org\/10.1038\/s41467-025-59580-x\" title=\"Follow DOI:10.1038\/s41467-025-59580-x\" target=\"_blank\">doi:10.1038\/s41467-025-59580-x<\/a><\/li><\/ul><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('32','tp_links')\">Close<\/a><\/p><\/div><\/div><\/div><div class=\"tp_publication tp_publication_unpublished\"><div class=\"tp_pub_number\">32.<\/div><div class=\"tp_pub_info\"><p class=\"tp_pub_author\">Raku Saito,  Yusuke Umemura,  Shiho Makino,  Takashi Fukaya<\/p><p class=\"tp_pub_title\"><a class=\"tp_title_link\" href=\"https:\/\/dx.doi.org\/10.1101\/2025.05.21.655257\" title=\"Decoding the molecular logic of rapidly evolving ZAD zinc-finger proteins in<i>Drosophila<\/i>\" target=\"blank\">Decoding the molecular logic of rapidly evolving ZAD zinc-finger proteins in<i>Drosophila<\/i><\/a> <span class=\"tp_pub_type unpublished\">Unpublished<\/span> <\/p><p class=\"tp_pub_additional\"><span class=\"tp_pub_additional_howpublished\">bioRxiv, <\/span><span class=\"tp_pub_additional_year\">2025<\/span>.<\/p><p class=\"tp_pub_menu\"><span class=\"tp_abstract_link\"><a id=\"tp_abstract_sh_36\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('36','tp_abstract')\" title=\"Show abstract\" style=\"cursor:pointer;\">Abstract<\/a><\/span> | <span class=\"tp_resource_link\"><a id=\"tp_links_sh_36\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('36','tp_links')\" title=\"Show links and resources\" style=\"cursor:pointer;\">Links<\/a><\/span> | <span class=\"tp_pub_tags_label\">\u30bf\u30b0: <\/span><a rel=\"nofollow\" href=\"https:\/\/www.bioreg.kyushu-u.ac.jp\/ext\/epicode\/publications?tgid=6#tppubs\" title=\"Show all publications which have a relationship to this tag\">Fukaya G<\/a><\/p><div class=\"tp_bibtex\" id=\"tp_bibtex_36\" style=\"display:none;\"><div class=\"tp_bibtex_entry\"><pre>@unpublished{Saito2025,<br \/>\r\ntitle = {Decoding the molecular logic of rapidly evolving ZAD zinc-finger proteins in\\textit{Drosophila}},<br \/>\r\nauthor = {Raku Saito and Yusuke Umemura and Shiho Makino and Takashi Fukaya},<br \/>\r\nurl = {http:\/\/biorxiv.org\/lookup\/doi\/10.1101\/2025.05.21.655257},<br \/>\r\ndoi = {10.1101\/2025.05.21.655257},<br \/>\r\nyear  = {2025},<br \/>\r\ndate = {2025-05-21},<br \/>\r\nurldate = {2025-05-21},<br \/>\r\npublisher = {Cold Spring Harbor Laboratory},<br \/>\r\nabstract = {&lt;jats:title&gt;Summary&lt;\/jats:title&gt;&lt;jats:p&gt;The zinc-finger associated domain (ZAD)-containing C2H2 zinc-finger proteins (ZAD-ZnFs) represent the most abundant class of transcription factors that emerged during insect evolution, yet their molecular diversity and biological functions remain largely unclear. Here, we established a systematic CRISPR-based protein-tagging approach that enables direct, unambiguous comparison of nuclear localization and genome-wide binding profiles of endogenous ZAD-ZnFs in developing&lt;jats:italic&gt;Drosophila&lt;\/jats:italic&gt;embryos. Evidence is provided that a subset of ZAD-ZnFs forms nuclear condensates through the stacking of the N-terminal ZAD dimerization surface. Disruption of condensation activity leads to misregulation of genome-wide binding profiles and lethality, underscoring its functional and physiological significance in development. Importantly, integrative ChIP-seq and Micro-C data analyses reveal that many ZAD-ZnFs colocalize with core insulator proteins such as CTCF and CP190 to strengthen the formation of topological boundaries. We suggest that the diverse molecular functions of ZAD-ZnFs have evolutionally arisen from their ancestral role as insulator-binding proteins.&lt;\/jats:p&gt;},<br \/>\r\nhowpublished = {bioRxiv},<br \/>\r\nkeywords = {Fukaya G},<br \/>\r\npubstate = {published},<br \/>\r\ntppubtype = {unpublished}<br \/>\r\n}<br \/>\r\n<\/pre><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('36','tp_bibtex')\">Close<\/a><\/p><\/div><div class=\"tp_abstract\" id=\"tp_abstract_36\" style=\"display:none;\"><div class=\"tp_abstract_entry\">&lt;jats:title&gt;Summary&lt;\/jats:title&gt;&lt;jats:p&gt;The zinc-finger associated domain (ZAD)-containing C2H2 zinc-finger proteins (ZAD-ZnFs) represent the most abundant class of transcription factors that emerged during insect evolution, yet their molecular diversity and biological functions remain largely unclear. Here, we established a systematic CRISPR-based protein-tagging approach that enables direct, unambiguous comparison of nuclear localization and genome-wide binding profiles of endogenous ZAD-ZnFs in developing&lt;jats:italic&gt;Drosophila&lt;\/jats:italic&gt;embryos. Evidence is provided that a subset of ZAD-ZnFs forms nuclear condensates through the stacking of the N-terminal ZAD dimerization surface. Disruption of condensation activity leads to misregulation of genome-wide binding profiles and lethality, underscoring its functional and physiological significance in development. Importantly, integrative ChIP-seq and Micro-C data analyses reveal that many ZAD-ZnFs colocalize with core insulator proteins such as CTCF and CP190 to strengthen the formation of topological boundaries. We suggest that the diverse molecular functions of ZAD-ZnFs have evolutionally arisen from their ancestral role as insulator-binding proteins.&lt;\/jats:p&gt;<\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('36','tp_abstract')\">Close<\/a><\/p><\/div><div class=\"tp_links\" id=\"tp_links_36\" style=\"display:none;\"><div class=\"tp_links_entry\"><ul class=\"tp_pub_list\"><li><i class=\"fas fa-globe\"><\/i><a class=\"tp_pub_list\" href=\"http:\/\/biorxiv.org\/lookup\/doi\/10.1101\/2025.05.21.655257\" title=\"http:\/\/biorxiv.org\/lookup\/doi\/10.1101\/2025.05.21.655257\" target=\"_blank\">http:\/\/biorxiv.org\/lookup\/doi\/10.1101\/2025.05.21.655257<\/a><\/li><li><i class=\"ai ai-doi\"><\/i><a class=\"tp_pub_list\" href=\"https:\/\/dx.doi.org\/10.1101\/2025.05.21.655257\" title=\"Follow DOI:10.1101\/2025.05.21.655257\" target=\"_blank\">doi:10.1101\/2025.05.21.655257<\/a><\/li><\/ul><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('36','tp_links')\">Close<\/a><\/p><\/div><\/div><\/div><div class=\"tp_publication tp_publication_article\"><div class=\"tp_pub_number\">31.<\/div><div class=\"tp_pub_info\"><p class=\"tp_pub_author\">Ting Cheng,  Jiachen Zhang,  Haicheng Li,  Jinghan Diao,  Wenxin Zhang,  Junhua Niu,  Takayuki Kawaguchi,  Jun-ichi Nakayama,  Kensuke Kataoka,  Shan Gao<\/p><p class=\"tp_pub_title\"><a class=\"tp_title_link\" href=\"https:\/\/dx.doi.org\/10.1126\/sciadv.adq4623\" title=\"Identification and characterization of the de novo methyltransferases for eukaryotic            <i>N<\/i>            <sup>6<\/sup>            -methyladenine (6mA)\" target=\"blank\">Identification and characterization of the de novo methyltransferases for eukaryotic            <i>N<\/i>            <sup>6<\/sup>            -methyladenine (6mA)<\/a> <span class=\"tp_pub_type article\">Journal Article<\/span> <\/p><p class=\"tp_pub_additional\"><span class=\"tp_pub_additional_in\">In: <\/span><span class=\"tp_pub_additional_journal\">Sci. Adv., <\/span><span class=\"tp_pub_additional_volume\">vol. 11, <\/span><span class=\"tp_pub_additional_number\">no. 20, <\/span><span class=\"tp_pub_additional_year\">2025<\/span>, <span class=\"tp_pub_additional_issn\">ISSN: 2375-2548<\/span>.<\/p><p class=\"tp_pub_menu\"><span class=\"tp_abstract_link\"><a id=\"tp_abstract_sh_31\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('31','tp_abstract')\" title=\"Show abstract\" style=\"cursor:pointer;\">Abstract<\/a><\/span> | <span class=\"tp_resource_link\"><a id=\"tp_links_sh_31\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('31','tp_links')\" title=\"Show links and resources\" style=\"cursor:pointer;\">Links<\/a><\/span> | <span class=\"tp_pub_tags_label\">\u30bf\u30b0: <\/span><a rel=\"nofollow\" href=\"https:\/\/www.bioreg.kyushu-u.ac.jp\/ext\/epicode\/publications?tgid=7#tppubs\" title=\"Show all publications which have a relationship to this tag\">Nakayama G<\/a><\/p><div class=\"tp_bibtex\" id=\"tp_bibtex_31\" style=\"display:none;\"><div class=\"tp_bibtex_entry\"><pre>@article{Cheng2025,<br \/>\r\ntitle = {Identification and characterization of the de novo methyltransferases for eukaryotic            \\textit{N}            ^{6}            -methyladenine (6mA)},<br \/>\r\nauthor = {Ting Cheng and Jiachen Zhang and Haicheng Li and Jinghan Diao and Wenxin Zhang and Junhua Niu and Takayuki Kawaguchi and Jun-ichi Nakayama and Kensuke Kataoka and Shan Gao},<br \/>\r\ndoi = {10.1126\/sciadv.adq4623},<br \/>\r\nissn = {2375-2548},<br \/>\r\nyear  = {2025},<br \/>\r\ndate = {2025-05-16},<br \/>\r\nurldate = {2025-05-16},<br \/>\r\njournal = {Sci. Adv.},<br \/>\r\nvolume = {11},<br \/>\r\nnumber = {20},<br \/>\r\npublisher = {American Association for the Advancement of Science (AAAS)},<br \/>\r\nabstract = {N6-methyladenine (6mA) is an intensively investigated epigenetic modification in eukaryotes. 6mA is maintained through semiconservative transmission during DNA replication, but the identity of de novo methyltransferase (MTase) catalyzing its establishment remains unknown. Here, we identified MT-A70 family proteins AMT2 and AMT5 as the de novo MTases responsible for 6mA establishment, using the unique sexual reproduction process of the unicellular eukaryote Tetrahymena thermophila. Deletion of AMT2 and AMT5 led to a substantial decrease in 6mA levels in the progeny macronucleus, resulting in an altered gene expression pattern and a substantial decline in the survival rate of sexual progenies. Additionally, the maintenance MTase AMT1 could exhibit a much diminished de novo methylation activity in cells lacking AMT2 and AMT5. Our study delineated the establishment-maintenance pathway of 6mA and underscored the biological importance of de novo methylation, revealing a notable parallel between 6mA and the classical 5-methylcytosine in eukaryotes.},<br \/>\r\nkeywords = {Nakayama G},<br \/>\r\npubstate = {published},<br \/>\r\ntppubtype = {article}<br \/>\r\n}<br \/>\r\n<\/pre><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('31','tp_bibtex')\">Close<\/a><\/p><\/div><div class=\"tp_abstract\" id=\"tp_abstract_31\" style=\"display:none;\"><div class=\"tp_abstract_entry\">N6-methyladenine (6mA) is an intensively investigated epigenetic modification in eukaryotes. 6mA is maintained through semiconservative transmission during DNA replication, but the identity of de novo methyltransferase (MTase) catalyzing its establishment remains unknown. Here, we identified MT-A70 family proteins AMT2 and AMT5 as the de novo MTases responsible for 6mA establishment, using the unique sexual reproduction process of the unicellular eukaryote Tetrahymena thermophila. Deletion of AMT2 and AMT5 led to a substantial decrease in 6mA levels in the progeny macronucleus, resulting in an altered gene expression pattern and a substantial decline in the survival rate of sexual progenies. Additionally, the maintenance MTase AMT1 could exhibit a much diminished de novo methylation activity in cells lacking AMT2 and AMT5. Our study delineated the establishment-maintenance pathway of 6mA and underscored the biological importance of de novo methylation, revealing a notable parallel between 6mA and the classical 5-methylcytosine in eukaryotes.<\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('31','tp_abstract')\">Close<\/a><\/p><\/div><div class=\"tp_links\" id=\"tp_links_31\" style=\"display:none;\"><div class=\"tp_links_entry\"><ul class=\"tp_pub_list\"><li><i class=\"ai ai-doi\"><\/i><a class=\"tp_pub_list\" href=\"https:\/\/dx.doi.org\/10.1126\/sciadv.adq4623\" title=\"Follow DOI:10.1126\/sciadv.adq4623\" target=\"_blank\">doi:10.1126\/sciadv.adq4623<\/a><\/li><\/ul><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('31','tp_links')\">Close<\/a><\/p><\/div><\/div><\/div><div class=\"tp_publication tp_publication_article\"><div class=\"tp_pub_number\">30.<\/div><div class=\"tp_pub_info\"><p class=\"tp_pub_author\">Suguru Hatazawa,  Naoki Horikoshi,  Hitoshi Kurumizaka<\/p><p class=\"tp_pub_title\"><a class=\"tp_title_link\" href=\"https:\/\/dx.doi.org\/https:\/\/doi.org\/10.1016\/j.sbi.2025.103054\" title=\"Structural diversity of noncanonical nucleosomes: Functions in chromatin\" target=\"blank\">Structural diversity of noncanonical nucleosomes: Functions in chromatin<\/a> <span class=\"tp_pub_type article\">Journal Article<\/span> <\/p><p class=\"tp_pub_additional\"><span class=\"tp_pub_additional_in\">In: <\/span><span class=\"tp_pub_additional_journal\">Current Opinion in Structural Biology, <\/span><span class=\"tp_pub_additional_volume\">vol. 92, <\/span><span class=\"tp_pub_additional_pages\">pp. 103054, <\/span><span class=\"tp_pub_additional_year\">2025<\/span>, <span class=\"tp_pub_additional_issn\">ISSN: 0959-440X<\/span>.<\/p><p class=\"tp_pub_menu\"><span class=\"tp_abstract_link\"><a id=\"tp_abstract_sh_29\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('29','tp_abstract')\" title=\"Show abstract\" style=\"cursor:pointer;\">Abstract<\/a><\/span> | <span class=\"tp_resource_link\"><a id=\"tp_links_sh_29\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('29','tp_links')\" title=\"Show links and resources\" style=\"cursor:pointer;\">Links<\/a><\/span> | <span class=\"tp_pub_tags_label\">\u30bf\u30b0: <\/span><a rel=\"nofollow\" href=\"https:\/\/www.bioreg.kyushu-u.ac.jp\/ext\/epicode\/publications?tgid=8#tppubs\" title=\"Show all publications which have a relationship to this tag\">Horikoshi G<\/a>, <a rel=\"nofollow\" href=\"https:\/\/www.bioreg.kyushu-u.ac.jp\/ext\/epicode\/publications?tgid=4#tppubs\" title=\"Show all publications which have a relationship to this tag\">Kurumizaka G<\/a><\/p><div class=\"tp_bibtex\" id=\"tp_bibtex_29\" style=\"display:none;\"><div class=\"tp_bibtex_entry\"><pre>@article{HATAZAWA2025103054,<br \/>\r\ntitle = {Structural diversity of noncanonical nucleosomes: Functions in chromatin},<br \/>\r\nauthor = {Suguru Hatazawa and Naoki Horikoshi and Hitoshi Kurumizaka},<br \/>\r\nurl = {https:\/\/www.sciencedirect.com\/science\/article\/pii\/S0959440X25000727},<br \/>\r\ndoi = {https:\/\/doi.org\/10.1016\/j.sbi.2025.103054},<br \/>\r\nissn = {0959-440X},<br \/>\r\nyear  = {2025},<br \/>\r\ndate = {2025-04-30},<br \/>\r\nurldate = {2025-01-01},<br \/>\r\njournal = {Current Opinion in Structural Biology},<br \/>\r\nvolume = {92},<br \/>\r\npages = {103054},<br \/>\r\nabstract = {In eukaryotes, genomic DNA is compacted into chromatin, with nucleosomes acting as its basic structural units. In addition to canonical nucleosomes, noncanonical nucleosomes, such as hexasomes, H3\u2013H4 octasomes, and overlapping dinucleosomes, exhibit alternative histone compositions and play key roles in chromatin remodeling, transcription, and replication. Recent cryo-electron microscopy (cryo-EM) studies have elucidated the structural details of these noncanonical nucleosomes and their interactions with histone chaperones and chromatin remodelers. This review highlights recent advances in the structural and functional understanding of noncanonical nucleosomes and their roles in maintaining chromatin integrity and facilitating transcriptional dynamics.},<br \/>\r\nkeywords = {Horikoshi G, Kurumizaka G},<br \/>\r\npubstate = {published},<br \/>\r\ntppubtype = {article}<br \/>\r\n}<br \/>\r\n<\/pre><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('29','tp_bibtex')\">Close<\/a><\/p><\/div><div class=\"tp_abstract\" id=\"tp_abstract_29\" style=\"display:none;\"><div class=\"tp_abstract_entry\">In eukaryotes, genomic DNA is compacted into chromatin, with nucleosomes acting as its basic structural units. In addition to canonical nucleosomes, noncanonical nucleosomes, such as hexasomes, H3\u2013H4 octasomes, and overlapping dinucleosomes, exhibit alternative histone compositions and play key roles in chromatin remodeling, transcription, and replication. Recent cryo-electron microscopy (cryo-EM) studies have elucidated the structural details of these noncanonical nucleosomes and their interactions with histone chaperones and chromatin remodelers. This review highlights recent advances in the structural and functional understanding of noncanonical nucleosomes and their roles in maintaining chromatin integrity and facilitating transcriptional dynamics.<\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('29','tp_abstract')\">Close<\/a><\/p><\/div><div class=\"tp_links\" id=\"tp_links_29\" style=\"display:none;\"><div class=\"tp_links_entry\"><ul class=\"tp_pub_list\"><li><i class=\"fas fa-globe\"><\/i><a class=\"tp_pub_list\" href=\"https:\/\/www.sciencedirect.com\/science\/article\/pii\/S0959440X25000727\" title=\"https:\/\/www.sciencedirect.com\/science\/article\/pii\/S0959440X25000727\" target=\"_blank\">https:\/\/www.sciencedirect.com\/science\/article\/pii\/S0959440X25000727<\/a><\/li><li><i class=\"ai ai-doi\"><\/i><a class=\"tp_pub_list\" href=\"https:\/\/dx.doi.org\/https:\/\/doi.org\/10.1016\/j.sbi.2025.103054\" title=\"Follow DOI:https:\/\/doi.org\/10.1016\/j.sbi.2025.103054\" target=\"_blank\">doi:https:\/\/doi.org\/10.1016\/j.sbi.2025.103054<\/a><\/li><\/ul><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('29','tp_links')\">Close<\/a><\/p><\/div><\/div><\/div><div class=\"tp_publication tp_publication_inbook\"><div class=\"tp_pub_number\">29.<\/div><div class=\"tp_pub_info\"><p class=\"tp_pub_author\">Yoshimasa Takizawa,  Cheng-Han Ho,  Shoko Sato,  Radostin Danev,  Hitoshi Kurumizaka<\/p><p class=\"tp_pub_title\"><a class=\"tp_title_link\" href=\"https:\/\/dx.doi.org\/10.1007\/978-1-0716-4486-7_6\" title=\"High-Resolution Cryo-EM Analyses of Nucleosomes\" target=\"blank\">High-Resolution Cryo-EM Analyses of Nucleosomes<\/a> <span class=\"tp_pub_type inbook\">Book Chapter<\/span> <\/p><p class=\"tp_pub_additional\"><span class=\"tp_pub_additional_in\">In: <\/span> Gaudreau, Luc;  Guillemette, Benoit (Ed.): <span class=\"tp_pub_additional_booktitle\">Histones: Methods and Protocols, <\/span><span class=\"tp_pub_additional_volume\">vol. 2919, <\/span><span class=\"tp_pub_additional_pages\">pp. 91\u2013107, <\/span><span class=\"tp_pub_additional_publisher\">Springer US, <\/span><span class=\"tp_pub_additional_address\">New York, NY, <\/span><span class=\"tp_pub_additional_year\">2025<\/span>, <span class=\"tp_pub_additional_isbn\">ISBN: 978-1-0716-4486-7<\/span>.<\/p><p class=\"tp_pub_menu\"><span class=\"tp_abstract_link\"><a id=\"tp_abstract_sh_30\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('30','tp_abstract')\" title=\"Show abstract\" style=\"cursor:pointer;\">Abstract<\/a><\/span> | <span class=\"tp_resource_link\"><a id=\"tp_links_sh_30\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('30','tp_links')\" title=\"Show links and resources\" style=\"cursor:pointer;\">Links<\/a><\/span> | <span class=\"tp_pub_tags_label\">\u30bf\u30b0: <\/span><a rel=\"nofollow\" href=\"https:\/\/www.bioreg.kyushu-u.ac.jp\/ext\/epicode\/publications?tgid=4#tppubs\" title=\"Show all publications which have a relationship to this tag\">Kurumizaka G<\/a><\/p><div class=\"tp_bibtex\" id=\"tp_bibtex_30\" style=\"display:none;\"><div class=\"tp_bibtex_entry\"><pre>@inbook{Takizawa2025,<br \/>\r\ntitle = {High-Resolution Cryo-EM Analyses of Nucleosomes},<br \/>\r\nauthor = {Yoshimasa Takizawa and Cheng-Han Ho and Shoko Sato and Radostin Danev and Hitoshi Kurumizaka},<br \/>\r\neditor = {Luc Gaudreau and Benoit Guillemette},<br \/>\r\nurl = {https:\/\/doi.org\/10.1007\/978-1-0716-4486-7_6},<br \/>\r\ndoi = {10.1007\/978-1-0716-4486-7_6},<br \/>\r\nisbn = {978-1-0716-4486-7},<br \/>\r\nyear  = {2025},<br \/>\r\ndate = {2025-04-22},<br \/>\r\nurldate = {2025-01-01},<br \/>\r\nbooktitle = {Histones: Methods and Protocols},<br \/>\r\nvolume = {2919},<br \/>\r\npages = {91\u2013107},<br \/>\r\npublisher = {Springer US},<br \/>\r\naddress = {New York, NY},<br \/>\r\nabstract = {The fundamental chromatin unit is the nucleosome, in which approximately 150 base pairs of DNA are bound to the surface of a symmetric histone octamer containing 2 copies each of histones H2A, H2B, H3, and H4. Over the years, numerous structures of nucleosomes have been determined by X-ray crystallography. However, their structural and functional versatility may not have been fully revealed, due to crystal packing effects. Various structures of nucleosomes and their complexes with nucleosome-binding proteins are now being determined by cryo-electron microscopy (cryo-EM) single-particle analysis, allowing the visualization of their structural diversity. In this report, we present a method for high-resolution structural analyses of nucleosomes by cryo-EM and describe the detailed procedures for nucleosome purification, cryo-EM grid preparation, data collection, and data processing. This method can serve as a good starting point for cryo-EM investigations of nucleosomes and their wide range of complexes.},<br \/>\r\nkeywords = {Kurumizaka G},<br \/>\r\npubstate = {published},<br \/>\r\ntppubtype = {inbook}<br \/>\r\n}<br \/>\r\n<\/pre><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('30','tp_bibtex')\">Close<\/a><\/p><\/div><div class=\"tp_abstract\" id=\"tp_abstract_30\" style=\"display:none;\"><div class=\"tp_abstract_entry\">The fundamental chromatin unit is the nucleosome, in which approximately 150 base pairs of DNA are bound to the surface of a symmetric histone octamer containing 2 copies each of histones H2A, H2B, H3, and H4. Over the years, numerous structures of nucleosomes have been determined by X-ray crystallography. However, their structural and functional versatility may not have been fully revealed, due to crystal packing effects. Various structures of nucleosomes and their complexes with nucleosome-binding proteins are now being determined by cryo-electron microscopy (cryo-EM) single-particle analysis, allowing the visualization of their structural diversity. In this report, we present a method for high-resolution structural analyses of nucleosomes by cryo-EM and describe the detailed procedures for nucleosome purification, cryo-EM grid preparation, data collection, and data processing. This method can serve as a good starting point for cryo-EM investigations of nucleosomes and their wide range of complexes.<\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('30','tp_abstract')\">Close<\/a><\/p><\/div><div class=\"tp_links\" id=\"tp_links_30\" style=\"display:none;\"><div class=\"tp_links_entry\"><ul class=\"tp_pub_list\"><li><i class=\"fas fa-globe\"><\/i><a class=\"tp_pub_list\" href=\"https:\/\/doi.org\/10.1007\/978-1-0716-4486-7_6\" title=\"https:\/\/doi.org\/10.1007\/978-1-0716-4486-7_6\" target=\"_blank\">https:\/\/doi.org\/10.1007\/978-1-0716-4486-7_6<\/a><\/li><li><i class=\"ai ai-doi\"><\/i><a class=\"tp_pub_list\" href=\"https:\/\/dx.doi.org\/10.1007\/978-1-0716-4486-7_6\" title=\"Follow DOI:10.1007\/978-1-0716-4486-7_6\" target=\"_blank\">doi:10.1007\/978-1-0716-4486-7_6<\/a><\/li><\/ul><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('30','tp_links')\">Close<\/a><\/p><\/div><\/div><\/div><div class=\"tp_publication tp_publication_article\"><div class=\"tp_pub_number\">28.<\/div><div class=\"tp_pub_info\"><p class=\"tp_pub_author\">Suguru Hatazawa,  Yoshiyuki Fukuda,  Yuki Kobayashi,  Lumi Negishi,  Masahide Kikkawa,  Yoshimasa Takizawa,  Hitoshi Kurumizaka<\/p><p class=\"tp_pub_title\"><a class=\"tp_title_link\" href=\"https:\/\/dx.doi.org\/10.1111\/gtc.70019\" title=\"Cryo\u2010EM Structures of Native Chromatin Units From Human Cells\" target=\"blank\">Cryo\u2010EM Structures of Native Chromatin Units From Human Cells<\/a> <span class=\"tp_pub_type article\">Journal Article<\/span> <\/p><p class=\"tp_pub_additional\"><span class=\"tp_pub_additional_in\">In: <\/span><span class=\"tp_pub_additional_journal\">Genes to Cells, <\/span><span class=\"tp_pub_additional_volume\">vol. 30, <\/span><span class=\"tp_pub_additional_number\">no. 3, <\/span><span class=\"tp_pub_additional_year\">2025<\/span>, <span class=\"tp_pub_additional_issn\">ISSN: 1365-2443<\/span>.<\/p><p class=\"tp_pub_menu\"><span class=\"tp_abstract_link\"><a id=\"tp_abstract_sh_27\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('27','tp_abstract')\" title=\"Show abstract\" style=\"cursor:pointer;\">Abstract<\/a><\/span> | <span class=\"tp_resource_link\"><a id=\"tp_links_sh_27\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('27','tp_links')\" title=\"Show links and resources\" style=\"cursor:pointer;\">Links<\/a><\/span> | <span class=\"tp_pub_tags_label\">\u30bf\u30b0: <\/span><a rel=\"nofollow\" href=\"https:\/\/www.bioreg.kyushu-u.ac.jp\/ext\/epicode\/publications?tgid=4#tppubs\" title=\"Show all publications which have a relationship to this tag\">Kurumizaka G<\/a><\/p><div class=\"tp_bibtex\" id=\"tp_bibtex_27\" style=\"display:none;\"><div class=\"tp_bibtex_entry\"><pre>@article{Hatazawa2025,<br \/>\r\ntitle = {Cryo\u2010EM Structures of Native Chromatin Units From Human Cells},<br \/>\r\nauthor = {Suguru Hatazawa and Yoshiyuki Fukuda and Yuki Kobayashi and Lumi Negishi and Masahide Kikkawa and Yoshimasa Takizawa and Hitoshi Kurumizaka},<br \/>\r\nurl = {https:\/\/onlinelibrary.wiley.com\/doi\/10.1111\/gtc.70019},<br \/>\r\ndoi = {10.1111\/gtc.70019},<br \/>\r\nissn = {1365-2443},<br \/>\r\nyear  = {2025},<br \/>\r\ndate = {2025-04-14},<br \/>\r\nurldate = {2025-04-14},<br \/>\r\njournal = {Genes to Cells},<br \/>\r\nvolume = {30},<br \/>\r\nnumber = {3},<br \/>\r\npublisher = {Wiley},<br \/>\r\nabstract = {In eukaryotic cells, genomic DNA is compacted by nucleosomes, as basic repeating units, into chromatin. The nucleosome arrangement in chromatin fibers could be an important determinant for chromatin folding, by which genomic DNA is regulated in the nucleus. To study the structures of chromatin units in cells, we have established a method for the structural analysis of native mono\u2010 and poly\u2010nucleosomes prepared from HeLa cells. In this method, the chromatin in isolated nuclei was crosslinked to preserve the proximity information between nucleosomes, followed by chromatin fragmentation by micrococcal nuclease treatment. The mono\u2010 and poly\u2010nucleosomes were then fractionated by sucrose gradient ultracentrifugation, and their structures were analyzed by cryo\u2010electron microscopy. Cryo\u2010electron microscopy single particle analysis and cryo\u2010electron tomography visualized a native nucleosome structure and secondary nucleosome arrangements in cellular chromatin. This method provides a complementary strategy to fill the gap between in\u00a0vitro and in\u00a0situ analyses of chromatin structure.},<br \/>\r\nkeywords = {Kurumizaka G},<br \/>\r\npubstate = {published},<br \/>\r\ntppubtype = {article}<br \/>\r\n}<br \/>\r\n<\/pre><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('27','tp_bibtex')\">Close<\/a><\/p><\/div><div class=\"tp_abstract\" id=\"tp_abstract_27\" style=\"display:none;\"><div class=\"tp_abstract_entry\">In eukaryotic cells, genomic DNA is compacted by nucleosomes, as basic repeating units, into chromatin. The nucleosome arrangement in chromatin fibers could be an important determinant for chromatin folding, by which genomic DNA is regulated in the nucleus. To study the structures of chromatin units in cells, we have established a method for the structural analysis of native mono\u2010 and poly\u2010nucleosomes prepared from HeLa cells. In this method, the chromatin in isolated nuclei was crosslinked to preserve the proximity information between nucleosomes, followed by chromatin fragmentation by micrococcal nuclease treatment. The mono\u2010 and poly\u2010nucleosomes were then fractionated by sucrose gradient ultracentrifugation, and their structures were analyzed by cryo\u2010electron microscopy. Cryo\u2010electron microscopy single particle analysis and cryo\u2010electron tomography visualized a native nucleosome structure and secondary nucleosome arrangements in cellular chromatin. This method provides a complementary strategy to fill the gap between in\u00a0vitro and in\u00a0situ analyses of chromatin structure.<\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('27','tp_abstract')\">Close<\/a><\/p><\/div><div class=\"tp_links\" id=\"tp_links_27\" style=\"display:none;\"><div class=\"tp_links_entry\"><ul class=\"tp_pub_list\"><li><i class=\"fas fa-globe\"><\/i><a class=\"tp_pub_list\" href=\"https:\/\/onlinelibrary.wiley.com\/doi\/10.1111\/gtc.70019\" title=\"https:\/\/onlinelibrary.wiley.com\/doi\/10.1111\/gtc.70019\" target=\"_blank\">https:\/\/onlinelibrary.wiley.com\/doi\/10.1111\/gtc.70019<\/a><\/li><li><i class=\"ai ai-doi\"><\/i><a class=\"tp_pub_list\" href=\"https:\/\/dx.doi.org\/10.1111\/gtc.70019\" title=\"Follow DOI:10.1111\/gtc.70019\" target=\"_blank\">doi:10.1111\/gtc.70019<\/a><\/li><\/ul><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('27','tp_links')\">Close<\/a><\/p><\/div><\/div><\/div><div class=\"tp_publication tp_publication_article\"><div class=\"tp_pub_number\">27.<\/div><div class=\"tp_pub_info\"><p class=\"tp_pub_author\">Tamiko Nozaki,  Mayu Onoda,  Misuzu Habazaki,  Yuma Takeuchi,  Hisashi Ishida,  Yuko Sato,  Tomoya Kujirai,  Kayo Hanada,  Kenzo Yamatsugu,  Hitoshi Kurumizaka,  Hiroshi Kimura,  Hidetoshi Kono,  Shigehiro A. Kawashima,  Motomu Kanai<\/p><p class=\"tp_pub_title\"><a class=\"tp_title_link\" href=\"https:\/\/dx.doi.org\/10.1021\/jacs.5c01699\" title=\"Designer Catalyst-Enabled Regiodivergent Histone Acetylation\" target=\"blank\">Designer Catalyst-Enabled Regiodivergent Histone Acetylation<\/a> <span class=\"tp_pub_type article\">Journal Article<\/span> <\/p><p class=\"tp_pub_additional\"><span class=\"tp_pub_additional_in\">In: <\/span><span class=\"tp_pub_additional_journal\">J. Am. Chem. Soc., <\/span><span class=\"tp_pub_additional_year\">2025<\/span>, <span class=\"tp_pub_additional_issn\">ISSN: 1520-5126<\/span>.<\/p><p class=\"tp_pub_menu\"><span class=\"tp_abstract_link\"><a id=\"tp_abstract_sh_26\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('26','tp_abstract')\" title=\"Show abstract\" style=\"cursor:pointer;\">Abstract<\/a><\/span> | <span class=\"tp_resource_link\"><a id=\"tp_links_sh_26\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('26','tp_links')\" title=\"Show links and resources\" style=\"cursor:pointer;\">Links<\/a><\/span> | <span class=\"tp_pub_tags_label\">\u30bf\u30b0: <\/span><a rel=\"nofollow\" href=\"https:\/\/www.bioreg.kyushu-u.ac.jp\/ext\/epicode\/publications?tgid=13#tppubs\" title=\"Show all publications which have a relationship to this tag\">Kawashima G<\/a>, <a rel=\"nofollow\" href=\"https:\/\/www.bioreg.kyushu-u.ac.jp\/ext\/epicode\/publications?tgid=2#tppubs\" title=\"Show all publications which have a relationship to this tag\">Kimura G<\/a>, <a rel=\"nofollow\" href=\"https:\/\/www.bioreg.kyushu-u.ac.jp\/ext\/epicode\/publications?tgid=4#tppubs\" title=\"Show all publications which have a relationship to this tag\">Kurumizaka G<\/a><\/p><div class=\"tp_bibtex\" id=\"tp_bibtex_26\" style=\"display:none;\"><div class=\"tp_bibtex_entry\"><pre>@article{Nozaki2025,<br \/>\r\ntitle = {Designer Catalyst-Enabled Regiodivergent Histone Acetylation},<br \/>\r\nauthor = {Tamiko Nozaki and Mayu Onoda and Misuzu Habazaki and Yuma Takeuchi and Hisashi Ishida and Yuko Sato and Tomoya Kujirai and Kayo Hanada and Kenzo Yamatsugu and Hitoshi Kurumizaka and Hiroshi Kimura and Hidetoshi Kono and Shigehiro A. Kawashima and Motomu Kanai},<br \/>\r\nurl = {https:\/\/pubs.acs.org\/doi\/full\/10.1021\/jacs.5c01699},<br \/>\r\ndoi = {10.1021\/jacs.5c01699},<br \/>\r\nissn = {1520-5126},<br \/>\r\nyear  = {2025},<br \/>\r\ndate = {2025-04-13},<br \/>\r\nurldate = {2025-04-13},<br \/>\r\njournal = {J. Am. Chem. Soc.},<br \/>\r\npublisher = {American Chemical Society (ACS)},<br \/>\r\nabstract = {The \u201chistone code,\u201d defined by the combinatorial patterns of post-translational modifications (PTMs) on histones, plays a pivotal role in chromatin structure and gene expression. Tools for the regioselective introduction of histone PTMs in living cells are critical for dissecting the functions of these epigenetic marks. Here, we report the design and development of three regioselective catalysts that acetylate distinct lysine residues (K43, K108, and K120) on histone H2B. Using a combination of molecular dynamics simulations of catalyst-nucleosome complexes and systematic experimental optimization of catalyst structures, we identified key design principles for achieving regioselectivity. Specifically, excluding highly reactive off-target lysine residues from the catalyst effective region (CER) while maintaining proximity to a target lysine residue proved crucial. Biochemical and cellular analyses of the catalytic histone acetylation revealed that each lysine acetylation elicited unique effects on the binding affinity and activity of nucleosome-interacting molecules, as well as on transcriptional programs and cellular phenotypes. These findings establish a framework for designing regioselective histone acetylation catalysts and advance our understanding of the regulatory mechanisms underlying histone PTMs.},<br \/>\r\nkeywords = {Kawashima G, Kimura G, Kurumizaka G},<br \/>\r\npubstate = {published},<br \/>\r\ntppubtype = {article}<br \/>\r\n}<br \/>\r\n<\/pre><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('26','tp_bibtex')\">Close<\/a><\/p><\/div><div class=\"tp_abstract\" id=\"tp_abstract_26\" style=\"display:none;\"><div class=\"tp_abstract_entry\">The \u201chistone code,\u201d defined by the combinatorial patterns of post-translational modifications (PTMs) on histones, plays a pivotal role in chromatin structure and gene expression. Tools for the regioselective introduction of histone PTMs in living cells are critical for dissecting the functions of these epigenetic marks. Here, we report the design and development of three regioselective catalysts that acetylate distinct lysine residues (K43, K108, and K120) on histone H2B. Using a combination of molecular dynamics simulations of catalyst-nucleosome complexes and systematic experimental optimization of catalyst structures, we identified key design principles for achieving regioselectivity. Specifically, excluding highly reactive off-target lysine residues from the catalyst effective region (CER) while maintaining proximity to a target lysine residue proved crucial. Biochemical and cellular analyses of the catalytic histone acetylation revealed that each lysine acetylation elicited unique effects on the binding affinity and activity of nucleosome-interacting molecules, as well as on transcriptional programs and cellular phenotypes. These findings establish a framework for designing regioselective histone acetylation catalysts and advance our understanding of the regulatory mechanisms underlying histone PTMs.<\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('26','tp_abstract')\">Close<\/a><\/p><\/div><div class=\"tp_links\" id=\"tp_links_26\" style=\"display:none;\"><div class=\"tp_links_entry\"><ul class=\"tp_pub_list\"><li><i class=\"fas fa-globe\"><\/i><a class=\"tp_pub_list\" href=\"https:\/\/pubs.acs.org\/doi\/full\/10.1021\/jacs.5c01699\" title=\"https:\/\/pubs.acs.org\/doi\/full\/10.1021\/jacs.5c01699\" target=\"_blank\">https:\/\/pubs.acs.org\/doi\/full\/10.1021\/jacs.5c01699<\/a><\/li><li><i class=\"ai ai-doi\"><\/i><a class=\"tp_pub_list\" href=\"https:\/\/dx.doi.org\/10.1021\/jacs.5c01699\" title=\"Follow DOI:10.1021\/jacs.5c01699\" target=\"_blank\">doi:10.1021\/jacs.5c01699<\/a><\/li><\/ul><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('26','tp_links')\">Close<\/a><\/p><\/div><\/div><\/div><div class=\"tp_publication tp_publication_unpublished\"><div class=\"tp_pub_number\">26.<\/div><div class=\"tp_pub_info\"><p class=\"tp_pub_author\">Konrad Chudzik,  Yuko Sato,  Xingchi Yan,  Simon Ullrich,  Watanya Trakarnphornsombat,  Lothar Schermelleh,  Geoffrey Fudenberg,  Hiroshi Kimura,  Michael I. Robson,  Irina Solovei<\/p><p class=\"tp_pub_title\"><a class=\"tp_title_link\" href=\"https:\/\/dx.doi.org\/10.1101\/2025.04.09.648027\" title=\"Ab-trapping - a peripheral staining artifact in antibody-based microscopy and genomics\" target=\"blank\">Ab-trapping - a peripheral staining artifact in antibody-based microscopy and genomics<\/a> <span class=\"tp_pub_type unpublished\">Unpublished<\/span> <\/p><p class=\"tp_pub_additional\"><span class=\"tp_pub_additional_howpublished\">bioRxiv, <\/span><span class=\"tp_pub_additional_year\">2025<\/span>.<\/p><p class=\"tp_pub_menu\"><span class=\"tp_abstract_link\"><a id=\"tp_abstract_sh_28\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('28','tp_abstract')\" title=\"Show abstract\" style=\"cursor:pointer;\">Abstract<\/a><\/span> | <span class=\"tp_resource_link\"><a id=\"tp_links_sh_28\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('28','tp_links')\" title=\"Show links and resources\" style=\"cursor:pointer;\">Links<\/a><\/span> | <span class=\"tp_pub_tags_label\">\u30bf\u30b0: <\/span><a rel=\"nofollow\" href=\"https:\/\/www.bioreg.kyushu-u.ac.jp\/ext\/epicode\/publications?tgid=2#tppubs\" title=\"Show all publications which have a relationship to this tag\">Kimura G<\/a><\/p><div class=\"tp_bibtex\" id=\"tp_bibtex_28\" style=\"display:none;\"><div class=\"tp_bibtex_entry\"><pre>@unpublished{Chudzik2025,<br \/>\r\ntitle = {Ab-trapping - a peripheral staining artifact in antibody-based microscopy and genomics},<br \/>\r\nauthor = {Konrad Chudzik and Yuko Sato and Xingchi Yan and Simon Ullrich and Watanya Trakarnphornsombat and Lothar Schermelleh and Geoffrey Fudenberg and Hiroshi Kimura and Michael I. Robson and Irina Solovei},<br \/>\r\nurl = {http:\/\/biorxiv.org\/lookup\/doi\/10.1101\/2025.04.09.648027},<br \/>\r\ndoi = {10.1101\/2025.04.09.648027},<br \/>\r\nyear  = {2025},<br \/>\r\ndate = {2025-04-10},<br \/>\r\nurldate = {2025-04-10},<br \/>\r\npublisher = {Cold Spring Harbor Laboratory},<br \/>\r\nabstract = {Antibodies (Ab) are essential for detecting specific epitopes in microscopy and genomics, but can produce artifacts leading to erroneous interpretations. Here, we characterize a novel artifact, Ab-trapping, in which antibodies bind at the periphery of a cellular structure and do not diffuse further into its interior. This causes anomalous peripheral staining for multiple critical targets, including endogenous or ectopically expressed nuclear proteins like nucleolar proteins, histone variants and their modifications like H3K9me2. Ab-trapping can affect any assay relying on Ab diffusion, including immunofluorescence microscopy and recent genomics approaches like CUT&Tag. Critically, computational modeling and experimental validation reveal that Ab-trapping is caused by high epitope abundance, high Ab affinity, and low diffusion rates. Consequently, its effects can be mitigated by using alternative Abs and optimizing incubation conditions. Ab-trapping is therefore a considerable artifact that should be considered when designing experiments and interpreting results.},<br \/>\r\nhowpublished = {bioRxiv},<br \/>\r\nkeywords = {Kimura G},<br \/>\r\npubstate = {published},<br \/>\r\ntppubtype = {unpublished}<br \/>\r\n}<br \/>\r\n<\/pre><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('28','tp_bibtex')\">Close<\/a><\/p><\/div><div class=\"tp_abstract\" id=\"tp_abstract_28\" style=\"display:none;\"><div class=\"tp_abstract_entry\">Antibodies (Ab) are essential for detecting specific epitopes in microscopy and genomics, but can produce artifacts leading to erroneous interpretations. Here, we characterize a novel artifact, Ab-trapping, in which antibodies bind at the periphery of a cellular structure and do not diffuse further into its interior. This causes anomalous peripheral staining for multiple critical targets, including endogenous or ectopically expressed nuclear proteins like nucleolar proteins, histone variants and their modifications like H3K9me2. Ab-trapping can affect any assay relying on Ab diffusion, including immunofluorescence microscopy and recent genomics approaches like CUT&amp;Tag. Critically, computational modeling and experimental validation reveal that Ab-trapping is caused by high epitope abundance, high Ab affinity, and low diffusion rates. Consequently, its effects can be mitigated by using alternative Abs and optimizing incubation conditions. Ab-trapping is therefore a considerable artifact that should be considered when designing experiments and interpreting results.<\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('28','tp_abstract')\">Close<\/a><\/p><\/div><div class=\"tp_links\" id=\"tp_links_28\" style=\"display:none;\"><div class=\"tp_links_entry\"><ul class=\"tp_pub_list\"><li><i class=\"fas fa-globe\"><\/i><a class=\"tp_pub_list\" href=\"http:\/\/biorxiv.org\/lookup\/doi\/10.1101\/2025.04.09.648027\" title=\"http:\/\/biorxiv.org\/lookup\/doi\/10.1101\/2025.04.09.648027\" target=\"_blank\">http:\/\/biorxiv.org\/lookup\/doi\/10.1101\/2025.04.09.648027<\/a><\/li><li><i class=\"ai ai-doi\"><\/i><a class=\"tp_pub_list\" href=\"https:\/\/dx.doi.org\/10.1101\/2025.04.09.648027\" title=\"Follow DOI:10.1101\/2025.04.09.648027\" target=\"_blank\">doi:10.1101\/2025.04.09.648027<\/a><\/li><\/ul><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('28','tp_links')\">Close<\/a><\/p><\/div><\/div><\/div><div class=\"tp_publication tp_publication_article\"><div class=\"tp_pub_number\">25.<\/div><div class=\"tp_pub_info\"><p class=\"tp_pub_author\">Tatsuma Yao,  Hisato Kobayashi,  Tatsuki Hirai,  Yuta Tokuoka,  Mikiko Tokoro,  Yuta Asayama,  Yuka Suzuki,  Yu Hatano,  Hiroki Ikeda,  Satoshi Sugimura,  Takuya Yamamoto,  Takahiro G Yamada,  Yoshihiko Hosoi,  Akira Funahashi,  Noritaka Fukunaga,  Yoshimasa Asada,  Kazuki Kurimoto,  Kazuo Yamagata<\/p><p class=\"tp_pub_title\"><a class=\"tp_title_link\" href=\"https:\/\/dx.doi.org\/10.1093\/biolre\/ioaf050\" title=\"Zinc eluted from glassware is a risk factor for embryo development in human and animal assisted reproduction\" target=\"blank\">Zinc eluted from glassware is a risk factor for embryo development in human and animal assisted reproduction<\/a> <span class=\"tp_pub_type article\">Journal Article<\/span> <\/p><p class=\"tp_pub_additional\"><span class=\"tp_pub_additional_in\">In: <\/span><span class=\"tp_pub_additional_journal\">Biology of Reproduction, <\/span><span class=\"tp_pub_additional_year\">2025<\/span>, <span class=\"tp_pub_additional_issn\">ISSN: 1529-7268<\/span>.<\/p><p class=\"tp_pub_menu\"><span class=\"tp_abstract_link\"><a id=\"tp_abstract_sh_25\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('25','tp_abstract')\" title=\"Show abstract\" style=\"cursor:pointer;\">Abstract<\/a><\/span> | <span class=\"tp_resource_link\"><a id=\"tp_links_sh_25\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('25','tp_links')\" title=\"Show links and resources\" style=\"cursor:pointer;\">Links<\/a><\/span> | <span class=\"tp_pub_tags_label\">\u30bf\u30b0: <\/span><a rel=\"nofollow\" href=\"https:\/\/www.bioreg.kyushu-u.ac.jp\/ext\/epicode\/publications?tgid=5#tppubs\" title=\"Show all publications which have a relationship to this tag\">Yamagata G<\/a><\/p><div class=\"tp_bibtex\" id=\"tp_bibtex_25\" style=\"display:none;\"><div class=\"tp_bibtex_entry\"><pre>@article{Yao2025,<br \/>\r\ntitle = {Zinc eluted from glassware is a risk factor for embryo development in human and animal assisted reproduction},<br \/>\r\nauthor = {Tatsuma Yao and Hisato Kobayashi and Tatsuki Hirai and Yuta Tokuoka and Mikiko Tokoro and Yuta Asayama and Yuka Suzuki and Yu Hatano and Hiroki Ikeda and Satoshi Sugimura and Takuya Yamamoto and Takahiro G Yamada and Yoshihiko Hosoi and Akira Funahashi and Noritaka Fukunaga and Yoshimasa Asada and Kazuki Kurimoto and Kazuo Yamagata},<br \/>\r\ndoi = {10.1093\/biolre\/ioaf050},<br \/>\r\nissn = {1529-7268},<br \/>\r\nyear  = {2025},<br \/>\r\ndate = {2025-04-02},<br \/>\r\nurldate = {2025-04-02},<br \/>\r\njournal = {Biology of Reproduction},<br \/>\r\npublisher = {Oxford University Press (OUP)},<br \/>\r\nabstract = {In assisted reproduction, many factors in the culture environment, including light, temperature, pH, and culture media, can reduce preimplantation embryo viability. Laboratory glassware is also a known risk factor for in vitro embryos; however, the underlying mechanisms that disrupt embryonic development remain unclear. We identified Zn eluted from glassware as an embryotoxic substance. In mouse embryos, Zn induced delayed development, abnormalities in chromosome segregation, cytokinesis, zygotic gene activation (e.g. Zscan4a and murine endogenous retrovirus with leucine, also known as MERVL), and aberrantly upregulated developmental gene expression (e.g. Hoxa1, Hoxb9, T, and Fgf8) that could be mediated through metal regulatory transcription factors (e.g. Mtf1). Subsequently, Zn exposure led to significantly reduced blastocyst formation. Post-implantation, Zn-exposed embryos were associated with normal birth rates, however, the birth weight increased by an average of 18% compared with embryos cultured without Zn. Furthermore, Zn exposure affected the development of bovine and human embryos, with species-based variation in the strength and timing of these effects. To mitigate these embryotoxic effects, we identified a method to prevent glass toxicity using chelating agents. This research not only highlights the importance of risk control in embryo culture but also facilitates the development of safe and effective methods for assisted reproduction.},<br \/>\r\nkeywords = {Yamagata G},<br \/>\r\npubstate = {published},<br \/>\r\ntppubtype = {article}<br \/>\r\n}<br \/>\r\n<\/pre><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('25','tp_bibtex')\">Close<\/a><\/p><\/div><div class=\"tp_abstract\" id=\"tp_abstract_25\" style=\"display:none;\"><div class=\"tp_abstract_entry\">In assisted reproduction, many factors in the culture environment, including light, temperature, pH, and culture media, can reduce preimplantation embryo viability. Laboratory glassware is also a known risk factor for in vitro embryos; however, the underlying mechanisms that disrupt embryonic development remain unclear. We identified Zn eluted from glassware as an embryotoxic substance. In mouse embryos, Zn induced delayed development, abnormalities in chromosome segregation, cytokinesis, zygotic gene activation (e.g. Zscan4a and murine endogenous retrovirus with leucine, also known as MERVL), and aberrantly upregulated developmental gene expression (e.g. Hoxa1, Hoxb9, T, and Fgf8) that could be mediated through metal regulatory transcription factors (e.g. Mtf1). Subsequently, Zn exposure led to significantly reduced blastocyst formation. Post-implantation, Zn-exposed embryos were associated with normal birth rates, however, the birth weight increased by an average of 18% compared with embryos cultured without Zn. Furthermore, Zn exposure affected the development of bovine and human embryos, with species-based variation in the strength and timing of these effects. To mitigate these embryotoxic effects, we identified a method to prevent glass toxicity using chelating agents. This research not only highlights the importance of risk control in embryo culture but also facilitates the development of safe and effective methods for assisted reproduction.<\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('25','tp_abstract')\">Close<\/a><\/p><\/div><div class=\"tp_links\" id=\"tp_links_25\" style=\"display:none;\"><div class=\"tp_links_entry\"><ul class=\"tp_pub_list\"><li><i class=\"ai ai-doi\"><\/i><a class=\"tp_pub_list\" href=\"https:\/\/dx.doi.org\/10.1093\/biolre\/ioaf050\" title=\"Follow DOI:10.1093\/biolre\/ioaf050\" target=\"_blank\">doi:10.1093\/biolre\/ioaf050<\/a><\/li><\/ul><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('25','tp_links')\">Close<\/a><\/p><\/div><\/div><\/div><div class=\"tp_publication tp_publication_article\"><div class=\"tp_pub_number\">24.<\/div><div class=\"tp_pub_info\"><p class=\"tp_pub_author\">Shinichi Hayashi,  Hitomi Suzuki,  Shinji Takada,  Tatsuya Takemoto<\/p><p class=\"tp_pub_title\"><a class=\"tp_title_link\" href=\"https:\/\/dx.doi.org\/10.1016\/j.ydbio.2025.03.015\" title=\"Wnt3a is an early regulator of the Wolffian duct directionality via the regulation of apicobasal cell polarity\" target=\"blank\">Wnt3a is an early regulator of the Wolffian duct directionality via the regulation of apicobasal cell polarity<\/a> <span class=\"tp_pub_type article\">Journal Article<\/span> <\/p><p class=\"tp_pub_additional\"><span class=\"tp_pub_additional_in\">In: <\/span><span class=\"tp_pub_additional_journal\">Developmental Biology, <\/span><span class=\"tp_pub_additional_volume\">vol. 511, <\/span><span class=\"tp_pub_additional_pages\">pp. 136-142, <\/span><span class=\"tp_pub_additional_year\">2025<\/span>, <span class=\"tp_pub_additional_issn\">ISSN: 0012-1606<\/span>.<\/p><p class=\"tp_pub_menu\"><span class=\"tp_abstract_link\"><a id=\"tp_abstract_sh_24\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('24','tp_abstract')\" title=\"Show abstract\" style=\"cursor:pointer;\">Abstract<\/a><\/span> | <span class=\"tp_resource_link\"><a id=\"tp_links_sh_24\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('24','tp_links')\" title=\"Show links and resources\" style=\"cursor:pointer;\">Links<\/a><\/span> | <span class=\"tp_pub_tags_label\">\u30bf\u30b0: <\/span><a rel=\"nofollow\" href=\"https:\/\/www.bioreg.kyushu-u.ac.jp\/ext\/epicode\/publications?tgid=12#tppubs\" title=\"Show all publications which have a relationship to this tag\">Takemoto G<\/a><\/p><div class=\"tp_bibtex\" id=\"tp_bibtex_24\" style=\"display:none;\"><div class=\"tp_bibtex_entry\"><pre>@article{Hayashi2025,<br \/>\r\ntitle = {Wnt3a is an early regulator of the Wolffian duct directionality via the regulation of apicobasal cell polarity},<br \/>\r\nauthor = {Shinichi Hayashi and Hitomi Suzuki and Shinji Takada and Tatsuya Takemoto},<br \/>\r\nurl = {https:\/\/www.sciencedirect.com\/science\/article\/pii\/S0012160625000776},<br \/>\r\ndoi = {10.1016\/j.ydbio.2025.03.015},<br \/>\r\nissn = {0012-1606},<br \/>\r\nyear  = {2025},<br \/>\r\ndate = {2025-03-27},<br \/>\r\njournal = {Developmental Biology},<br \/>\r\nvolume = {511},<br \/>\r\npages = {136-142},<br \/>\r\npublisher = {Elsevier BV},<br \/>\r\nabstract = {The Wolffian duct is a pair of epithelial ductal structures along the body axis that induces nephron development by interaction with the metanephric mesenchyme. The interaction between the mesenchyme and the ureteric bud derived from the Wolffian duct is mediated by Wnt ligands, the loss of which results in kidney agenesis. Nonetheless, the early contribution of Wnt signaling to Wolffian duct formation remains unclear. We therefore examined these dynamics in knockout and transgenic mouse embryos. The Wnt signal reporter was active in the extending Wolffian duct, and Wnt3a-knockout embryos exhibited a fragmented and misdirectional Wolffian duct. Apicobasal polarity was disrupted under Wnt3a-deficiency. These findings suggest that Wnt3a plays an important role in Wolffian duct development by regulating apicobasal polarity.},<br \/>\r\nkeywords = {Takemoto G},<br \/>\r\npubstate = {published},<br \/>\r\ntppubtype = {article}<br \/>\r\n}<br \/>\r\n<\/pre><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('24','tp_bibtex')\">Close<\/a><\/p><\/div><div class=\"tp_abstract\" id=\"tp_abstract_24\" style=\"display:none;\"><div class=\"tp_abstract_entry\">The Wolffian duct is a pair of epithelial ductal structures along the body axis that induces nephron development by interaction with the metanephric mesenchyme. The interaction between the mesenchyme and the ureteric bud derived from the Wolffian duct is mediated by Wnt ligands, the loss of which results in kidney agenesis. Nonetheless, the early contribution of Wnt signaling to Wolffian duct formation remains unclear. We therefore examined these dynamics in knockout and transgenic mouse embryos. The Wnt signal reporter was active in the extending Wolffian duct, and Wnt3a-knockout embryos exhibited a fragmented and misdirectional Wolffian duct. Apicobasal polarity was disrupted under Wnt3a-deficiency. These findings suggest that Wnt3a plays an important role in Wolffian duct development by regulating apicobasal polarity.<\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('24','tp_abstract')\">Close<\/a><\/p><\/div><div class=\"tp_links\" id=\"tp_links_24\" style=\"display:none;\"><div class=\"tp_links_entry\"><ul class=\"tp_pub_list\"><li><i class=\"fas fa-globe\"><\/i><a class=\"tp_pub_list\" href=\"https:\/\/www.sciencedirect.com\/science\/article\/pii\/S0012160625000776\" title=\"https:\/\/www.sciencedirect.com\/science\/article\/pii\/S0012160625000776\" target=\"_blank\">https:\/\/www.sciencedirect.com\/science\/article\/pii\/S0012160625000776<\/a><\/li><li><i class=\"ai ai-doi\"><\/i><a class=\"tp_pub_list\" href=\"https:\/\/dx.doi.org\/10.1016\/j.ydbio.2025.03.015\" title=\"Follow DOI:10.1016\/j.ydbio.2025.03.015\" target=\"_blank\">doi:10.1016\/j.ydbio.2025.03.015<\/a><\/li><\/ul><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('24','tp_links')\">Close<\/a><\/p><\/div><\/div><\/div><div class=\"tp_publication tp_publication_article\"><div class=\"tp_pub_number\">23.<\/div><div class=\"tp_pub_info\"><p class=\"tp_pub_author\">Osamu Kawasaki,  Yoshimasa Takizawa,  Iori Kiyokawa,  Hitoshi Kurumizaka,  Kayo Nozawa<\/p><p class=\"tp_pub_title\"><a class=\"tp_title_link\" href=\"https:\/\/dx.doi.org\/10.1111\/gtc.70016\" title=\"Cryo-EM Analysis of a Unique Subnucleosome Containing Centromere-Specific Histone Variant CENP-A\" target=\"blank\">Cryo-EM Analysis of a Unique Subnucleosome Containing Centromere-Specific Histone Variant CENP-A<\/a> <span class=\"tp_pub_type article\">Journal Article<\/span> <\/p><p class=\"tp_pub_additional\"><span class=\"tp_pub_additional_in\">In: <\/span><span class=\"tp_pub_additional_journal\">Genes Cells, <\/span><span class=\"tp_pub_additional_volume\">vol. 30, <\/span><span class=\"tp_pub_additional_number\">no. 2, <\/span><span class=\"tp_pub_additional_pages\">pp. e70016, <\/span><span class=\"tp_pub_additional_year\">2025<\/span>, <span class=\"tp_pub_additional_issn\">ISSN: 1365-2443<\/span>.<\/p><p class=\"tp_pub_menu\"><span class=\"tp_abstract_link\"><a id=\"tp_abstract_sh_22\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('22','tp_abstract')\" title=\"Show abstract\" style=\"cursor:pointer;\">Abstract<\/a><\/span> | <span class=\"tp_resource_link\"><a id=\"tp_links_sh_22\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('22','tp_links')\" title=\"Show links and resources\" style=\"cursor:pointer;\">Links<\/a><\/span> | <span class=\"tp_pub_tags_label\">\u30bf\u30b0: <\/span><a rel=\"nofollow\" href=\"https:\/\/www.bioreg.kyushu-u.ac.jp\/ext\/epicode\/publications?tgid=4#tppubs\" title=\"Show all publications which have a relationship to this tag\">Kurumizaka G<\/a><\/p><div class=\"tp_bibtex\" id=\"tp_bibtex_22\" style=\"display:none;\"><div class=\"tp_bibtex_entry\"><pre>@article{pmid40129080,<br \/>\r\ntitle = {Cryo-EM Analysis of a Unique Subnucleosome Containing Centromere-Specific Histone Variant CENP-A},<br \/>\r\nauthor = {Osamu Kawasaki and Yoshimasa Takizawa and Iori Kiyokawa and Hitoshi Kurumizaka and Kayo Nozawa},<br \/>\r\ndoi = {10.1111\/gtc.70016},<br \/>\r\nissn = {1365-2443},<br \/>\r\nyear  = {2025},<br \/>\r\ndate = {2025-03-24},<br \/>\r\nurldate = {2025-03-01},<br \/>\r\njournal = {Genes Cells},<br \/>\r\nvolume = {30},<br \/>\r\nnumber = {2},<br \/>\r\npages = {e70016},<br \/>\r\nabstract = {In eukaryotes, genomic DNA is stored in the nucleus as nucleosomes, in which a DNA segment is wrapped around a protein octamer consisting of two each of the four histones, H2A, H2B, H3, and H4. The core histones can be replaced by histone variants or altered with covalent modifications, contributing to the regulation of chromosome structure and nuclear activities. The formation of an octameric histone core in nucleosomes is widely accepted. Recently, the H3-H4 octasome, a novel nucleosome-like structure with a histone octamer consisting solely of H3 and H4, has been reported. CENP-A is the centromere-specific histone H3 variant and determines the position of kinetochore assembly during mitosis. CENP-A is a distant H3 variant sharing approximately 50% amino acid sequence with H3. In this study, we found that CENP-A and H4 also formed an octamer without H2A and H2B in\u00a0vitro. We determined the structure of the CENP-A-H4 octasome at 3.66 \u00c5 resolution. In the CENP-A-H4 octasome, an approximately 120-base pair DNA segment was wrapped around the CENP-A-H4 octameric core and displayed the four CENP-A RG-loops, which are the direct binding sites for another centromeric protein, CENP-N.},<br \/>\r\nkeywords = {Kurumizaka G},<br \/>\r\npubstate = {published},<br \/>\r\ntppubtype = {article}<br \/>\r\n}<br \/>\r\n<\/pre><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('22','tp_bibtex')\">Close<\/a><\/p><\/div><div class=\"tp_abstract\" id=\"tp_abstract_22\" style=\"display:none;\"><div class=\"tp_abstract_entry\">In eukaryotes, genomic DNA is stored in the nucleus as nucleosomes, in which a DNA segment is wrapped around a protein octamer consisting of two each of the four histones, H2A, H2B, H3, and H4. The core histones can be replaced by histone variants or altered with covalent modifications, contributing to the regulation of chromosome structure and nuclear activities. The formation of an octameric histone core in nucleosomes is widely accepted. Recently, the H3-H4 octasome, a novel nucleosome-like structure with a histone octamer consisting solely of H3 and H4, has been reported. CENP-A is the centromere-specific histone H3 variant and determines the position of kinetochore assembly during mitosis. CENP-A is a distant H3 variant sharing approximately 50% amino acid sequence with H3. In this study, we found that CENP-A and H4 also formed an octamer without H2A and H2B in\u00a0vitro. We determined the structure of the CENP-A-H4 octasome at 3.66 \u00c5 resolution. In the CENP-A-H4 octasome, an approximately 120-base pair DNA segment was wrapped around the CENP-A-H4 octameric core and displayed the four CENP-A RG-loops, which are the direct binding sites for another centromeric protein, CENP-N.<\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('22','tp_abstract')\">Close<\/a><\/p><\/div><div class=\"tp_links\" id=\"tp_links_22\" style=\"display:none;\"><div class=\"tp_links_entry\"><ul class=\"tp_pub_list\"><li><i class=\"ai ai-doi\"><\/i><a class=\"tp_pub_list\" href=\"https:\/\/dx.doi.org\/10.1111\/gtc.70016\" title=\"Follow DOI:10.1111\/gtc.70016\" target=\"_blank\">doi:10.1111\/gtc.70016<\/a><\/li><\/ul><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('22','tp_links')\">Close<\/a><\/p><\/div><\/div><\/div><div class=\"tp_publication tp_publication_article\"><div class=\"tp_pub_number\">22.<\/div><div class=\"tp_pub_info\"><p class=\"tp_pub_author\">Ayako Furukawa,  Kento Yonezawa,  Tatsuki Negami,  Yuriko Yoshimura,  Aki Hayashi,  Jun-ichi Nakayama,  Naruhiko Adachi,  Toshiya Senda,  Kentaro Shimizu,  Tohru Terada,  Nobutaka Shimizu,  Yoshifumi Nishimura<\/p><p class=\"tp_pub_title\"><a class=\"tp_title_link\" href=\"https:\/\/dx.doi.org\/10.1093\/nar\/gkaf154\" title=\"A dynamic structural unit of phase-separated heterochromatin protein 1\u03b1 as revealed by integrative structural analyses\" target=\"blank\">A dynamic structural unit of phase-separated heterochromatin protein 1\u03b1 as revealed by integrative structural analyses<\/a> <span class=\"tp_pub_type article\">Journal Article<\/span> <\/p><p class=\"tp_pub_additional\"><span class=\"tp_pub_additional_in\">In: <\/span><span class=\"tp_pub_additional_volume\">vol. 53, <\/span><span class=\"tp_pub_additional_number\">no. 6, <\/span><span class=\"tp_pub_additional_year\">2025<\/span>, <span class=\"tp_pub_additional_issn\">ISSN: 1362-4962<\/span>.<\/p><p class=\"tp_pub_menu\"><span class=\"tp_abstract_link\"><a id=\"tp_abstract_sh_21\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('21','tp_abstract')\" title=\"Show abstract\" style=\"cursor:pointer;\">Abstract<\/a><\/span> | <span class=\"tp_resource_link\"><a id=\"tp_links_sh_21\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('21','tp_links')\" title=\"Show links and resources\" style=\"cursor:pointer;\">Links<\/a><\/span> | <span class=\"tp_pub_tags_label\">\u30bf\u30b0: <\/span><a rel=\"nofollow\" href=\"https:\/\/www.bioreg.kyushu-u.ac.jp\/ext\/epicode\/publications?tgid=7#tppubs\" title=\"Show all publications which have a relationship to this tag\">Nakayama G<\/a><\/p><div class=\"tp_bibtex\" id=\"tp_bibtex_21\" style=\"display:none;\"><div class=\"tp_bibtex_entry\"><pre>@article{Furukawa2025,<br \/>\r\ntitle = {A dynamic structural unit of phase-separated heterochromatin protein 1\u03b1 as revealed by integrative structural analyses},<br \/>\r\nauthor = {Ayako Furukawa and Kento Yonezawa and Tatsuki Negami and Yuriko Yoshimura and Aki Hayashi and Jun-ichi Nakayama and Naruhiko Adachi and Toshiya Senda and Kentaro Shimizu and Tohru Terada and Nobutaka Shimizu and Yoshifumi Nishimura},<br \/>\r\ndoi = {10.1093\/nar\/gkaf154},<br \/>\r\nissn = {1362-4962},<br \/>\r\nyear  = {2025},<br \/>\r\ndate = {2025-03-20},<br \/>\r\nurldate = {2025-03-20},<br \/>\r\nvolume = {53},<br \/>\r\nnumber = {6},<br \/>\r\npublisher = {Oxford University Press (OUP)},<br \/>\r\nabstract = {&lt;jats:title&gt;Abstract&lt;\/jats:title&gt;<br \/>\r\n               &lt;jats:p&gt;The heterochromatin protein HP1\u03b1 consists of an N-terminal disordered tail (N-tail), chromodomain (CD), hinge region (HR), and C-terminal chromo shadow domain (CSD). While CD binds to the lysine9-trimethylated histone H3 (H3K9me3) tail in nucleosomes, CSD forms a dimer bridging two nucleosomes with H3K9me3. Phosphorylation of serine residues in the N-tail enhances both H3K9me3 binding and liquid\u2013liquid phase separation (LLPS) by HP1\u03b1. We have used integrative structural methods, including nuclear magnetic resonance, small-angle X-ray scattering (SAXS), and multi-angle-light scattering combined with size-exclusion chromatography, and coarse-grained molecular dynamics simulation with SAXS, to probe the HP1\u03b1 dimer and its CSD deletion monomer. We show that dynamic intra- and intermolecular interactions between the N-tails and basic segments in CD and HR depend on N-tail phosphorylation. While the phosphorylated HP1\u03b1 dimer undergoes LLPS via the formation of aggregated multimers, the N-tail phosphorylated mutant without CSD still undergoes LLPS, but its structural unit is a dynamic intermolecular dimer formed via the phosphorylated N-tail and a basic segment at the CD end. Furthermore, we reveal that mutation of this basic segment in HP1\u03b1 affects the size of heterochromatin foci in cultured mammalian cells, suggesting that this interaction plays an important role in heterochromatin formation in vivo.&lt;\/jats:p&gt;},<br \/>\r\nkeywords = {Nakayama G},<br \/>\r\npubstate = {published},<br \/>\r\ntppubtype = {article}<br \/>\r\n}<br \/>\r\n<\/pre><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('21','tp_bibtex')\">Close<\/a><\/p><\/div><div class=\"tp_abstract\" id=\"tp_abstract_21\" style=\"display:none;\"><div class=\"tp_abstract_entry\">&lt;jats:title&gt;Abstract&lt;\/jats:title&gt;<br \/>\r\n               &lt;jats:p&gt;The heterochromatin protein HP1\u03b1 consists of an N-terminal disordered tail (N-tail), chromodomain (CD), hinge region (HR), and C-terminal chromo shadow domain (CSD). While CD binds to the lysine9-trimethylated histone H3 (H3K9me3) tail in nucleosomes, CSD forms a dimer bridging two nucleosomes with H3K9me3. Phosphorylation of serine residues in the N-tail enhances both H3K9me3 binding and liquid\u2013liquid phase separation (LLPS) by HP1\u03b1. We have used integrative structural methods, including nuclear magnetic resonance, small-angle X-ray scattering (SAXS), and multi-angle-light scattering combined with size-exclusion chromatography, and coarse-grained molecular dynamics simulation with SAXS, to probe the HP1\u03b1 dimer and its CSD deletion monomer. We show that dynamic intra- and intermolecular interactions between the N-tails and basic segments in CD and HR depend on N-tail phosphorylation. While the phosphorylated HP1\u03b1 dimer undergoes LLPS via the formation of aggregated multimers, the N-tail phosphorylated mutant without CSD still undergoes LLPS, but its structural unit is a dynamic intermolecular dimer formed via the phosphorylated N-tail and a basic segment at the CD end. Furthermore, we reveal that mutation of this basic segment in HP1\u03b1 affects the size of heterochromatin foci in cultured mammalian cells, suggesting that this interaction plays an important role in heterochromatin formation in vivo.&lt;\/jats:p&gt;<\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('21','tp_abstract')\">Close<\/a><\/p><\/div><div class=\"tp_links\" id=\"tp_links_21\" style=\"display:none;\"><div class=\"tp_links_entry\"><ul class=\"tp_pub_list\"><li><i class=\"ai ai-doi\"><\/i><a class=\"tp_pub_list\" href=\"https:\/\/dx.doi.org\/10.1093\/nar\/gkaf154\" title=\"Follow DOI:10.1093\/nar\/gkaf154\" target=\"_blank\">doi:10.1093\/nar\/gkaf154<\/a><\/li><\/ul><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('21','tp_links')\">Close<\/a><\/p><\/div><\/div><\/div><div class=\"tp_publication tp_publication_article\"><div class=\"tp_pub_number\">21.<\/div><div class=\"tp_pub_info\"><p class=\"tp_pub_author\">Masahiro Naganuma,  Tomoya Kujirai,  Haruhiko Ehara,  Tamami Uejima,  Tomoko Ito,  Mie Goto,  Mari Aoki,  Masami Henmi,  Sayako Miyamoto-Kohno,  Mikako Shirouzu,  Hitoshi Kurumizaka,  Shun-ichi Sekine<\/p><p class=\"tp_pub_title\"><a class=\"tp_title_link\" href=\"https:\/\/dx.doi.org\/10.1126\/sciadv.adu0577\" title=\"Structural insights into promoter-proximal pausing of RNA polymerase II at +1 nucleosome\" target=\"blank\">Structural insights into promoter-proximal pausing of RNA polymerase II at +1 nucleosome<\/a> <span class=\"tp_pub_type article\">Journal Article<\/span> <\/p><p class=\"tp_pub_additional\"><span class=\"tp_pub_additional_in\">In: <\/span><span class=\"tp_pub_additional_journal\">Sci. Adv., <\/span><span class=\"tp_pub_additional_volume\">vol. 11, <\/span><span class=\"tp_pub_additional_number\">no. 10, <\/span><span class=\"tp_pub_additional_year\">2025<\/span>, <span class=\"tp_pub_additional_issn\">ISSN: 2375-2548<\/span>.<\/p><p class=\"tp_pub_menu\"><span class=\"tp_abstract_link\"><a id=\"tp_abstract_sh_20\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('20','tp_abstract')\" title=\"Show abstract\" style=\"cursor:pointer;\">Abstract<\/a><\/span> | <span class=\"tp_resource_link\"><a id=\"tp_links_sh_20\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('20','tp_links')\" title=\"Show links and resources\" style=\"cursor:pointer;\">Links<\/a><\/span> | <span class=\"tp_pub_tags_label\">\u30bf\u30b0: <\/span><a rel=\"nofollow\" href=\"https:\/\/www.bioreg.kyushu-u.ac.jp\/ext\/epicode\/publications?tgid=4#tppubs\" title=\"Show all publications which have a relationship to this tag\">Kurumizaka G<\/a><\/p><div class=\"tp_bibtex\" id=\"tp_bibtex_20\" style=\"display:none;\"><div class=\"tp_bibtex_entry\"><pre>@article{Naganuma2025,<br \/>\r\ntitle = {Structural insights into promoter-proximal pausing of RNA polymerase II at +1 nucleosome},<br \/>\r\nauthor = {Masahiro Naganuma and Tomoya Kujirai and Haruhiko Ehara and Tamami Uejima and Tomoko Ito and Mie Goto and Mari Aoki and Masami Henmi and Sayako Miyamoto-Kohno and Mikako Shirouzu and Hitoshi Kurumizaka and Shun-ichi Sekine},<br \/>\r\ndoi = {10.1126\/sciadv.adu0577},<br \/>\r\nissn = {2375-2548},<br \/>\r\nyear  = {2025},<br \/>\r\ndate = {2025-03-07},<br \/>\r\nurldate = {2025-03-07},<br \/>\r\njournal = {Sci. Adv.},<br \/>\r\nvolume = {11},<br \/>\r\nnumber = {10},<br \/>\r\npublisher = {American Association for the Advancement of Science (AAAS)},<br \/>\r\nabstract = {&lt;jats:p&gt;<br \/>\r\n            The metazoan transcription elongation complex (EC) of RNA polymerase II (RNAPII) generally stalls between the transcription start site and the first (+1) nucleosome. This promoter-proximal pausing involves negative elongation factor (NELF), 5,6-dichloro-1-\u03b2-<br \/>\r\n            &lt;jats:sc&gt;d&lt;\/jats:sc&gt;<br \/>\r\n            -ribobenzimidazole sensitivity-inducing factor (DSIF), and transcription elongation factor IIS (TFIIS) and is critical for subsequent productive transcription elongation. However, the detailed pausing mechanism and the involvement of the +1 nucleosome remain enigmatic. Here, we report cryo\u2013electron microscopy structures of ECs stalled on nucleosomal DNA. In the absence of TFIIS, the EC is backtracked\/arrested due to conflicts between NELF and the nucleosome. We identified two alternative binding modes of NELF, one of which reveals a critical contact with the downstream DNA through the conserved NELF-E basic helix. Upon binding with TFIIS, the EC progressed to the nucleosome to establish a paused EC with a partially unwrapped nucleosome. This paused EC strongly restricts EC progression further downstream. These structures illuminate the mechanism of RNAPII pausing\/stalling at the +1 nucleosome.<br \/>\r\n          &lt;\/jats:p&gt;},<br \/>\r\nkeywords = {Kurumizaka G},<br \/>\r\npubstate = {published},<br \/>\r\ntppubtype = {article}<br \/>\r\n}<br \/>\r\n<\/pre><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('20','tp_bibtex')\">Close<\/a><\/p><\/div><div class=\"tp_abstract\" id=\"tp_abstract_20\" style=\"display:none;\"><div class=\"tp_abstract_entry\">&lt;jats:p&gt;<br \/>\r\n            The metazoan transcription elongation complex (EC) of RNA polymerase II (RNAPII) generally stalls between the transcription start site and the first (+1) nucleosome. This promoter-proximal pausing involves negative elongation factor (NELF), 5,6-dichloro-1-\u03b2-<br \/>\r\n            &lt;jats:sc&gt;d&lt;\/jats:sc&gt;<br \/>\r\n            -ribobenzimidazole sensitivity-inducing factor (DSIF), and transcription elongation factor IIS (TFIIS) and is critical for subsequent productive transcription elongation. However, the detailed pausing mechanism and the involvement of the +1 nucleosome remain enigmatic. Here, we report cryo\u2013electron microscopy structures of ECs stalled on nucleosomal DNA. In the absence of TFIIS, the EC is backtracked\/arrested due to conflicts between NELF and the nucleosome. We identified two alternative binding modes of NELF, one of which reveals a critical contact with the downstream DNA through the conserved NELF-E basic helix. Upon binding with TFIIS, the EC progressed to the nucleosome to establish a paused EC with a partially unwrapped nucleosome. This paused EC strongly restricts EC progression further downstream. These structures illuminate the mechanism of RNAPII pausing\/stalling at the +1 nucleosome.<br \/>\r\n          &lt;\/jats:p&gt;<\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('20','tp_abstract')\">Close<\/a><\/p><\/div><div class=\"tp_links\" id=\"tp_links_20\" style=\"display:none;\"><div class=\"tp_links_entry\"><ul class=\"tp_pub_list\"><li><i class=\"ai ai-doi\"><\/i><a class=\"tp_pub_list\" href=\"https:\/\/dx.doi.org\/10.1126\/sciadv.adu0577\" title=\"Follow DOI:10.1126\/sciadv.adu0577\" target=\"_blank\">doi:10.1126\/sciadv.adu0577<\/a><\/li><\/ul><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('20','tp_links')\">Close<\/a><\/p><\/div><\/div><\/div><div class=\"tp_publication tp_publication_article\"><div class=\"tp_pub_number\">20.<\/div><div class=\"tp_pub_info\"><p class=\"tp_pub_author\">Chikashi Obuse,  Jun-ichi Nakayama<\/p><p class=\"tp_pub_title\"><a class=\"tp_title_link\" href=\"https:\/\/dx.doi.org\/10.1016\/j.bbagen.2025.130790\" title=\"Functional involvement of RNAs and intrinsically disordered proteins in the assembly of heterochromatin\" target=\"blank\">Functional involvement of RNAs and intrinsically disordered proteins in the assembly of heterochromatin<\/a> <span class=\"tp_pub_type article\">Journal Article<\/span> <\/p><p class=\"tp_pub_additional\"><span class=\"tp_pub_additional_in\">In: <\/span><span class=\"tp_pub_additional_journal\">Biochimica et Biophysica Acta (BBA) - General Subjects, <\/span><span class=\"tp_pub_additional_year\">2025<\/span>, <span class=\"tp_pub_additional_issn\">ISSN: 0304-4165<\/span>.<\/p><p class=\"tp_pub_menu\"><span class=\"tp_resource_link\"><a id=\"tp_links_sh_19\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('19','tp_links')\" title=\"Show links and resources\" style=\"cursor:pointer;\">Links<\/a><\/span> | <span class=\"tp_pub_tags_label\">\u30bf\u30b0: <\/span><a rel=\"nofollow\" href=\"https:\/\/www.bioreg.kyushu-u.ac.jp\/ext\/epicode\/publications?tgid=7#tppubs\" title=\"Show all publications which have a relationship to this tag\">Nakayama G<\/a><\/p><div class=\"tp_bibtex\" id=\"tp_bibtex_19\" style=\"display:none;\"><div class=\"tp_bibtex_entry\"><pre>@article{Obuse2025,<br \/>\r\ntitle = {Functional involvement of RNAs and intrinsically disordered proteins in the assembly of heterochromatin},<br \/>\r\nauthor = {Chikashi Obuse and Jun-ichi Nakayama},<br \/>\r\ndoi = {10.1016\/j.bbagen.2025.130790},<br \/>\r\nissn = {0304-4165},<br \/>\r\nyear  = {2025},<br \/>\r\ndate = {2025-03-06},<br \/>\r\njournal = {Biochimica et Biophysica Acta (BBA) - General Subjects},<br \/>\r\npublisher = {Elsevier BV},<br \/>\r\nkeywords = {Nakayama G},<br \/>\r\npubstate = {published},<br \/>\r\ntppubtype = {article}<br \/>\r\n}<br \/>\r\n<\/pre><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('19','tp_bibtex')\">Close<\/a><\/p><\/div><div class=\"tp_links\" id=\"tp_links_19\" style=\"display:none;\"><div class=\"tp_links_entry\"><ul class=\"tp_pub_list\"><li><i class=\"ai ai-doi\"><\/i><a class=\"tp_pub_list\" href=\"https:\/\/dx.doi.org\/10.1016\/j.bbagen.2025.130790\" title=\"Follow DOI:10.1016\/j.bbagen.2025.130790\" target=\"_blank\">doi:10.1016\/j.bbagen.2025.130790<\/a><\/li><\/ul><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('19','tp_links')\">Close<\/a><\/p><\/div><\/div><\/div><div class=\"tp_publication tp_publication_article\"><div class=\"tp_pub_number\">19.<\/div><div class=\"tp_pub_info\"><p class=\"tp_pub_author\">Tomoya Kujirai,  Kenta Echigoya,  Yusuke Kishi,  Mai Saeki,  Tomoko Ito,  Junko Kato,  Lumi Negishi,  Hiroshi Kimura,  Hiroshi Masumoto,  Yoshimasa Takizawa,  Yukiko Gotoh,  Hitoshi Kurumizaka<\/p><p class=\"tp_pub_title\"><a class=\"tp_title_link\" href=\"https:\/\/dx.doi.org\/10.1038\/s41594-025-01493-w\" title=\"Structural insights into how DEK nucleosome binding facilitates H3K27 trimethylation in chromatin\" target=\"blank\">Structural insights into how DEK nucleosome binding facilitates H3K27 trimethylation in chromatin<\/a> <span class=\"tp_pub_type article\">Journal Article<\/span> <\/p><p class=\"tp_pub_additional\"><span class=\"tp_pub_additional_in\">In: <\/span><span class=\"tp_pub_additional_journal\">Nature Structural &amp; Molecular Biology, <\/span><span class=\"tp_pub_additional_year\">2025<\/span>, <span class=\"tp_pub_additional_issn\">ISSN: 1545-9993<\/span>.<\/p><p class=\"tp_pub_menu\"><span class=\"tp_abstract_link\"><a id=\"tp_abstract_sh_18\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('18','tp_abstract')\" title=\"Show abstract\" style=\"cursor:pointer;\">Abstract<\/a><\/span> | <span class=\"tp_resource_link\"><a id=\"tp_links_sh_18\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('18','tp_links')\" title=\"Show links and resources\" style=\"cursor:pointer;\">Links<\/a><\/span> | <span class=\"tp_pub_tags_label\">\u30bf\u30b0: <\/span><a rel=\"nofollow\" href=\"https:\/\/www.bioreg.kyushu-u.ac.jp\/ext\/epicode\/publications?tgid=11#tppubs\" title=\"Show all publications which have a relationship to this tag\">Gotoh G<\/a>, <a rel=\"nofollow\" href=\"https:\/\/www.bioreg.kyushu-u.ac.jp\/ext\/epicode\/publications?tgid=2#tppubs\" title=\"Show all publications which have a relationship to this tag\">Kimura G<\/a>, <a rel=\"nofollow\" href=\"https:\/\/www.bioreg.kyushu-u.ac.jp\/ext\/epicode\/publications?tgid=4#tppubs\" title=\"Show all publications which have a relationship to this tag\">Kurumizaka G<\/a><\/p><div class=\"tp_bibtex\" id=\"tp_bibtex_18\" style=\"display:none;\"><div class=\"tp_bibtex_entry\"><pre>@article{10.1038\/s41594-025-01493-w,<br \/>\r\ntitle = {Structural insights into how DEK nucleosome binding facilitates H3K27 trimethylation in chromatin},<br \/>\r\nauthor = {Tomoya Kujirai and Kenta Echigoya and Yusuke Kishi and Mai Saeki and Tomoko Ito and Junko Kato and Lumi Negishi and Hiroshi Kimura and Hiroshi Masumoto and Yoshimasa Takizawa and Yukiko Gotoh and Hitoshi Kurumizaka},<br \/>\r\ndoi = {10.1038\/s41594-025-01493-w},<br \/>\r\nissn = {1545-9993},<br \/>\r\nyear  = {2025},<br \/>\r\ndate = {2025-02-21},<br \/>\r\nurldate = {2025-02-21},<br \/>\r\njournal = {Nature Structural & Molecular Biology},<br \/>\r\nabstract = {Structural diversity of the nucleosome affects chromatin conformations and regulates eukaryotic genome functions. Here we identify DEK, whose function is unknown, as a nucleosome-binding protein. In embryonic neural progenitor cells, DEK colocalizes with H3 K27 trimethylation (H3K27me3), the facultative heterochromatin mark. DEK stimulates the methyltransferase activity of Polycomb repressive complex 2 (PRC2), which is responsible for H3K27me3 deposition in vitro. Cryo-electron microscopy structures of the DEK\u2013nucleosome complexes reveal that DEK binds the nucleosome by its tripartite DNA-binding mode on the dyad and linker DNAs and interacts with the nucleosomal acidic patch by its newly identified histone-binding region. The DEK\u2013nucleosome interaction mediates linker DNA reorientation and induces chromatin compaction, which may facilitate PRC2 activation. These findings provide mechanistic insights into chromatin structure-mediated gene regulation by DEK.},<br \/>\r\nkeywords = {Gotoh G, Kimura G, Kurumizaka G},<br \/>\r\npubstate = {published},<br \/>\r\ntppubtype = {article}<br \/>\r\n}<br \/>\r\n<\/pre><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('18','tp_bibtex')\">Close<\/a><\/p><\/div><div class=\"tp_abstract\" id=\"tp_abstract_18\" style=\"display:none;\"><div class=\"tp_abstract_entry\">Structural diversity of the nucleosome affects chromatin conformations and regulates eukaryotic genome functions. Here we identify DEK, whose function is unknown, as a nucleosome-binding protein. In embryonic neural progenitor cells, DEK colocalizes with H3 K27 trimethylation (H3K27me3), the facultative heterochromatin mark. DEK stimulates the methyltransferase activity of Polycomb repressive complex 2 (PRC2), which is responsible for H3K27me3 deposition in vitro. Cryo-electron microscopy structures of the DEK\u2013nucleosome complexes reveal that DEK binds the nucleosome by its tripartite DNA-binding mode on the dyad and linker DNAs and interacts with the nucleosomal acidic patch by its newly identified histone-binding region. The DEK\u2013nucleosome interaction mediates linker DNA reorientation and induces chromatin compaction, which may facilitate PRC2 activation. These findings provide mechanistic insights into chromatin structure-mediated gene regulation by DEK.<\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('18','tp_abstract')\">Close<\/a><\/p><\/div><div class=\"tp_links\" id=\"tp_links_18\" style=\"display:none;\"><div class=\"tp_links_entry\"><ul class=\"tp_pub_list\"><li><i class=\"ai ai-doi\"><\/i><a class=\"tp_pub_list\" href=\"https:\/\/dx.doi.org\/10.1038\/s41594-025-01493-w\" title=\"Follow DOI:10.1038\/s41594-025-01493-w\" target=\"_blank\">doi:10.1038\/s41594-025-01493-w<\/a><\/li><\/ul><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('18','tp_links')\">Close<\/a><\/p><\/div><\/div><\/div><div class=\"tp_publication tp_publication_article\"><div class=\"tp_pub_number\">18.<\/div><div class=\"tp_pub_info\"><p class=\"tp_pub_author\">Tomoyuki Oya,  Mayo Tanaka,  Aki Hayashi,  Yuriko Yoshimura,  Rinko Nakamura,  Kyohei Arita,  Yota Murakami,  Jun\u2010ichi Nakayama<\/p><p class=\"tp_pub_title\"><a class=\"tp_title_link\" href=\"https:\/\/dx.doi.org\/10.1096\/fj.202402264RR\" title=\"Characterization of the Swi6\/HP1 binding motif in its partner protein reveals the basis for the functional divergence of the HP1 family proteins in fission yeast\" target=\"blank\">Characterization of the Swi6\/HP1 binding motif in its partner protein reveals the basis for the functional divergence of the HP1 family proteins in fission yeast<\/a> <span class=\"tp_pub_type article\">Journal Article<\/span> <\/p><p class=\"tp_pub_additional\"><span class=\"tp_pub_additional_in\">In: <\/span><span class=\"tp_pub_additional_journal\">The FASEB Journal, <\/span><span class=\"tp_pub_additional_volume\">vol. 39, <\/span><span class=\"tp_pub_additional_number\">no. 4, <\/span><span class=\"tp_pub_additional_year\">2025<\/span>, <span class=\"tp_pub_additional_issn\">ISSN: 0892-6638<\/span>.<\/p><p class=\"tp_pub_menu\"><span class=\"tp_abstract_link\"><a id=\"tp_abstract_sh_14\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('14','tp_abstract')\" title=\"Show abstract\" style=\"cursor:pointer;\">Abstract<\/a><\/span> | <span class=\"tp_resource_link\"><a id=\"tp_links_sh_14\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('14','tp_links')\" title=\"Show links and resources\" style=\"cursor:pointer;\">Links<\/a><\/span> | <span class=\"tp_pub_tags_label\">\u30bf\u30b0: <\/span><a rel=\"nofollow\" href=\"https:\/\/www.bioreg.kyushu-u.ac.jp\/ext\/epicode\/publications?tgid=7#tppubs\" title=\"Show all publications which have a relationship to this tag\">Nakayama G<\/a><\/p><div class=\"tp_bibtex\" id=\"tp_bibtex_14\" style=\"display:none;\"><div class=\"tp_bibtex_entry\"><pre>@article{10.1096\/fj.202402264RR,<br \/>\r\ntitle = {Characterization of the Swi6\/HP1 binding motif in its partner protein reveals the basis for the functional divergence of the HP1 family proteins in fission yeast},<br \/>\r\nauthor = {Tomoyuki Oya and Mayo Tanaka and Aki Hayashi and Yuriko Yoshimura and Rinko Nakamura and Kyohei Arita and Yota Murakami and Jun\u2010ichi Nakayama},<br \/>\r\ndoi = {10.1096\/fj.202402264RR},<br \/>\r\nissn = {0892-6638},<br \/>\r\nyear  = {2025},<br \/>\r\ndate = {2025-02-13},<br \/>\r\nurldate = {2025-01-01},<br \/>\r\njournal = {The FASEB Journal},<br \/>\r\nvolume = {39},<br \/>\r\nnumber = {4},<br \/>\r\nabstract = {The heterochromatin protein 1 (HP1) family recognizes lysine 9\u2010methylated histone H3 (H3K9me) and recruits other transacting factors to establish higher order chromatin structures. In the fission yeast Schizosaccharomyces pombe (S. pombe), two HP1 family proteins, Swi6 and Chp2, play distinct roles in recruiting transacting factors: Swi6 primarily recruits Epe1, a Jumonji C domain\u2010containing protein involved in histone H3K9 demethylation, whereas Chp2 recruits Mit1, a component of the Snf2\/Hdac Repressive Complex. However, detailed mechanisms of how multiple HP1 family proteins and their respective interactors work cooperatively or exclusively to form higher order chromatin structures remain elusive. In this study, we investigated the interactions between Swi6 and Epe1. We found that Swi6 interacts with Epe1 through its chromoshadow domain, and identified a unique motif, named the FVI motif, in Epe1 involved in this interaction through detailed mapping of the region. Enhanced green fluorescent protein (EGFP) tethering assays showed that the FVI motif is sufficient to recruit ectopically expressed EGFP to heterochromatic regions, and mutational analyses revealed that conserved hydrophobic residues in this motif are essential for proper targeting. Structural simulations further supported the importance of these residues in Swi6 binding. Interestingly, Mit1 containing the Epe1 FVI motif was recruited to the heterochromatic regions by Swi6 but not by Chp2. Cells expressing mutant Mit1 maintained heterochromatic silencing even in chp2\u2206 cells, suggesting that Chp2 is not required for heterochromatin formation when Mit1 is recruited by Swi6. These findings highlight distinct HP1\u2010binding motifs in interactors, contributing to functional divergence among HP1 family proteins. In fission yeast, two HP1 proteins, Swi6 and Chp2, play nonoverlapping roles by recruiting distinct binding partners. We have investigated the interactions between Swi6 and Epe1 and identified a unique motif, the FVI motif, in Epe1 that is involved in this interaction. Interestingly, cells expressing mutant Mit1 containing the Epe1 FVI motif maintained proper heterochromatic silencing even in chp2\u2206 cells. These results provide mechanistic insights into the division of labor among the HP1 family proteins.},<br \/>\r\nkeywords = {Nakayama G},<br \/>\r\npubstate = {published},<br \/>\r\ntppubtype = {article}<br \/>\r\n}<br \/>\r\n<\/pre><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('14','tp_bibtex')\">Close<\/a><\/p><\/div><div class=\"tp_abstract\" id=\"tp_abstract_14\" style=\"display:none;\"><div class=\"tp_abstract_entry\">The heterochromatin protein 1 (HP1) family recognizes lysine 9\u2010methylated histone H3 (H3K9me) and recruits other transacting factors to establish higher order chromatin structures. In the fission yeast Schizosaccharomyces pombe (S. pombe), two HP1 family proteins, Swi6 and Chp2, play distinct roles in recruiting transacting factors: Swi6 primarily recruits Epe1, a Jumonji C domain\u2010containing protein involved in histone H3K9 demethylation, whereas Chp2 recruits Mit1, a component of the Snf2\/Hdac Repressive Complex. However, detailed mechanisms of how multiple HP1 family proteins and their respective interactors work cooperatively or exclusively to form higher order chromatin structures remain elusive. In this study, we investigated the interactions between Swi6 and Epe1. We found that Swi6 interacts with Epe1 through its chromoshadow domain, and identified a unique motif, named the FVI motif, in Epe1 involved in this interaction through detailed mapping of the region. Enhanced green fluorescent protein (EGFP) tethering assays showed that the FVI motif is sufficient to recruit ectopically expressed EGFP to heterochromatic regions, and mutational analyses revealed that conserved hydrophobic residues in this motif are essential for proper targeting. Structural simulations further supported the importance of these residues in Swi6 binding. Interestingly, Mit1 containing the Epe1 FVI motif was recruited to the heterochromatic regions by Swi6 but not by Chp2. Cells expressing mutant Mit1 maintained heterochromatic silencing even in chp2\u2206 cells, suggesting that Chp2 is not required for heterochromatin formation when Mit1 is recruited by Swi6. These findings highlight distinct HP1\u2010binding motifs in interactors, contributing to functional divergence among HP1 family proteins. In fission yeast, two HP1 proteins, Swi6 and Chp2, play nonoverlapping roles by recruiting distinct binding partners. We have investigated the interactions between Swi6 and Epe1 and identified a unique motif, the FVI motif, in Epe1 that is involved in this interaction. Interestingly, cells expressing mutant Mit1 containing the Epe1 FVI motif maintained proper heterochromatic silencing even in chp2\u2206 cells. These results provide mechanistic insights into the division of labor among the HP1 family proteins.<\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('14','tp_abstract')\">Close<\/a><\/p><\/div><div class=\"tp_links\" id=\"tp_links_14\" style=\"display:none;\"><div class=\"tp_links_entry\"><ul class=\"tp_pub_list\"><li><i class=\"ai ai-doi\"><\/i><a class=\"tp_pub_list\" href=\"https:\/\/dx.doi.org\/10.1096\/fj.202402264RR\" title=\"Follow DOI:10.1096\/fj.202402264RR\" target=\"_blank\">doi:10.1096\/fj.202402264RR<\/a><\/li><\/ul><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('14','tp_links')\">Close<\/a><\/p><\/div><\/div><\/div><div class=\"tp_publication tp_publication_article\"><div class=\"tp_pub_number\">17.<\/div><div class=\"tp_pub_info\"><p class=\"tp_pub_author\">Naoki Horikoshi,  Ryosuke Miyake,  Chizuru Sogawa-Fujiwara,  Mitsuo Ogasawara,  Yoshimasa Takizawa,  Hitoshi Kurumizaka<\/p><p class=\"tp_pub_title\"><a class=\"tp_title_link\" href=\"https:\/\/dx.doi.org\/10.1038\/s41467-025-56823-9\" title=\"Cryo-EM structures of the BAF-Lamin A\/C complex bound to nucleosomes\" target=\"blank\">Cryo-EM structures of the BAF-Lamin A\/C complex bound to nucleosomes<\/a> <span class=\"tp_pub_type article\">Journal Article<\/span> <\/p><p class=\"tp_pub_additional\"><span class=\"tp_pub_additional_in\">In: <\/span><span class=\"tp_pub_additional_journal\">Nat Commun, <\/span><span class=\"tp_pub_additional_volume\">vol. 16, <\/span><span class=\"tp_pub_additional_number\">no. 1, <\/span><span class=\"tp_pub_additional_year\">2025<\/span>, <span class=\"tp_pub_additional_issn\">ISSN: 2041-1723<\/span>.<\/p><p class=\"tp_pub_menu\"><span class=\"tp_abstract_link\"><a id=\"tp_abstract_sh_13\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('13','tp_abstract')\" title=\"Show abstract\" style=\"cursor:pointer;\">Abstract<\/a><\/span> | <span class=\"tp_resource_link\"><a id=\"tp_links_sh_13\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('13','tp_links')\" title=\"Show links and resources\" style=\"cursor:pointer;\">Links<\/a><\/span> | <span class=\"tp_pub_tags_label\">\u30bf\u30b0: <\/span><a rel=\"nofollow\" href=\"https:\/\/www.bioreg.kyushu-u.ac.jp\/ext\/epicode\/publications?tgid=8#tppubs\" title=\"Show all publications which have a relationship to this tag\">Horikoshi G<\/a>, <a rel=\"nofollow\" href=\"https:\/\/www.bioreg.kyushu-u.ac.jp\/ext\/epicode\/publications?tgid=4#tppubs\" title=\"Show all publications which have a relationship to this tag\">Kurumizaka G<\/a><\/p><div class=\"tp_bibtex\" id=\"tp_bibtex_13\" style=\"display:none;\"><div class=\"tp_bibtex_entry\"><pre>@article{Horikoshi2025,<br \/>\r\ntitle = {Cryo-EM structures of the BAF-Lamin A\/C complex bound to nucleosomes},<br \/>\r\nauthor = {Naoki Horikoshi and Ryosuke Miyake and Chizuru Sogawa-Fujiwara and Mitsuo Ogasawara and Yoshimasa Takizawa and Hitoshi Kurumizaka},<br \/>\r\ndoi = {10.1038\/s41467-025-56823-9},<br \/>\r\nissn = {2041-1723},<br \/>\r\nyear  = {2025},<br \/>\r\ndate = {2025-02-10},<br \/>\r\njournal = {Nat Commun},<br \/>\r\nvolume = {16},<br \/>\r\nnumber = {1},<br \/>\r\npublisher = {Springer Science and Business Media LLC},<br \/>\r\nabstract = {&lt;jats:title&gt;Abstract&lt;\/jats:title&gt;<br \/>\r\n          &lt;jats:p&gt;Barrier-to-autointegration factor (BAF) associates with mitotic chromosomes and promotes nuclear envelope assembly by recruiting proteins, such as Lamins, required for the reconstruction of the nuclear envelope and lamina. BAF also mediates chromatin anchoring to the nuclear lamina via Lamin A\/C. However, the mechanism by which BAF and Lamin A\/C bind chromatin and affect the chromatin organization remains elusive. Here we report the cryo-electron microscopy structures of BAF-Lamin A\/C-nucleosome complexes. We find that the BAF dimer complexed with the Lamin A\/C IgF domain occupies the nucleosomal dyad position, forming a tripartite nucleosomal DNA binding structure. We also show that the Lamin A\/C Lys486 and His506 residues, which are reportedly mutated in lipodystrophy patients, directly contact the DNA at the nucleosomal dyad. Excess BAF-Lamin A\/C complexes symmetrically bind other nucleosomal DNA sites and connect two BAF-Lamin A\/C-nucleosome complexes. Although the linker histone H1 competes with BAF-Lamin A\/C binding at the nucleosomal dyad region, the two BAF-Lamin A\/C molecules still bridge two nucleosomes. These findings provide insights into the mechanism by which BAF, Lamin A\/C, and\/or histone H1 bind nucleosomes and influence chromatin organization within the nucleus.&lt;\/jats:p&gt;},<br \/>\r\nkeywords = {Horikoshi G, Kurumizaka G},<br \/>\r\npubstate = {published},<br \/>\r\ntppubtype = {article}<br \/>\r\n}<br \/>\r\n<\/pre><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('13','tp_bibtex')\">Close<\/a><\/p><\/div><div class=\"tp_abstract\" id=\"tp_abstract_13\" style=\"display:none;\"><div class=\"tp_abstract_entry\">&lt;jats:title&gt;Abstract&lt;\/jats:title&gt;<br \/>\r\n          &lt;jats:p&gt;Barrier-to-autointegration factor (BAF) associates with mitotic chromosomes and promotes nuclear envelope assembly by recruiting proteins, such as Lamins, required for the reconstruction of the nuclear envelope and lamina. BAF also mediates chromatin anchoring to the nuclear lamina via Lamin A\/C. However, the mechanism by which BAF and Lamin A\/C bind chromatin and affect the chromatin organization remains elusive. Here we report the cryo-electron microscopy structures of BAF-Lamin A\/C-nucleosome complexes. We find that the BAF dimer complexed with the Lamin A\/C IgF domain occupies the nucleosomal dyad position, forming a tripartite nucleosomal DNA binding structure. We also show that the Lamin A\/C Lys486 and His506 residues, which are reportedly mutated in lipodystrophy patients, directly contact the DNA at the nucleosomal dyad. Excess BAF-Lamin A\/C complexes symmetrically bind other nucleosomal DNA sites and connect two BAF-Lamin A\/C-nucleosome complexes. Although the linker histone H1 competes with BAF-Lamin A\/C binding at the nucleosomal dyad region, the two BAF-Lamin A\/C molecules still bridge two nucleosomes. These findings provide insights into the mechanism by which BAF, Lamin A\/C, and\/or histone H1 bind nucleosomes and influence chromatin organization within the nucleus.&lt;\/jats:p&gt;<\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('13','tp_abstract')\">Close<\/a><\/p><\/div><div class=\"tp_links\" id=\"tp_links_13\" style=\"display:none;\"><div class=\"tp_links_entry\"><ul class=\"tp_pub_list\"><li><i class=\"ai ai-doi\"><\/i><a class=\"tp_pub_list\" href=\"https:\/\/dx.doi.org\/10.1038\/s41467-025-56823-9\" title=\"Follow DOI:10.1038\/s41467-025-56823-9\" target=\"_blank\">doi:10.1038\/s41467-025-56823-9<\/a><\/li><\/ul><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('13','tp_links')\">Close<\/a><\/p><\/div><\/div><\/div><div class=\"tp_publication tp_publication_unpublished\"><div class=\"tp_pub_number\">16.<\/div><div class=\"tp_pub_info\"><p class=\"tp_pub_author\">Gabriel Galindo,  Daiki Maejima,  Jacob DeRoo,  Scott R. Burlingham,  Gretchen Fixen,  Tatsuya Morisaki,  Hallie P. Febvre,  Ryan Hasbrook,  Ning Zhao,  Soham Ghosh,  E. Handly Mayton,  Christopher D. Snow,  Brian J. Geiss,  Yasuyuki Ohkawa,  Yuko Sato,  Hiroshi Kimura,  Timothy J. Stasevich<\/p><p class=\"tp_pub_title\"><a class=\"tp_title_link\" href=\"https:\/\/dx.doi.org\/10.1101\/2025.02.06.636921\" title=\"AI-assisted protein design to rapidly convert antibody sequences to intrabodies targeting diverse peptides and histone modifications\" target=\"blank\">AI-assisted protein design to rapidly convert antibody sequences to intrabodies targeting diverse peptides and histone modifications<\/a> <span class=\"tp_pub_type unpublished\">Unpublished<\/span> <\/p><p class=\"tp_pub_additional\"><span class=\"tp_pub_additional_howpublished\">bioRxiv, <\/span><span class=\"tp_pub_additional_year\">2025<\/span>.<\/p><p class=\"tp_pub_menu\"><span class=\"tp_abstract_link\"><a id=\"tp_abstract_sh_17\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('17','tp_abstract')\" title=\"Show abstract\" style=\"cursor:pointer;\">Abstract<\/a><\/span> | <span class=\"tp_resource_link\"><a id=\"tp_links_sh_17\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('17','tp_links')\" title=\"Show links and resources\" style=\"cursor:pointer;\">Links<\/a><\/span> | <span class=\"tp_pub_tags_label\">\u30bf\u30b0: <\/span><a rel=\"nofollow\" href=\"https:\/\/www.bioreg.kyushu-u.ac.jp\/ext\/epicode\/publications?tgid=2#tppubs\" title=\"Show all publications which have a relationship to this tag\">Kimura G<\/a>, <a rel=\"nofollow\" href=\"https:\/\/www.bioreg.kyushu-u.ac.jp\/ext\/epicode\/publications?tgid=1#tppubs\" title=\"Show all publications which have a relationship to this tag\">Ohkawa G<\/a><\/p><div class=\"tp_bibtex\" id=\"tp_bibtex_17\" style=\"display:none;\"><div class=\"tp_bibtex_entry\"><pre>@unpublished{Galindo2025,<br \/>\r\ntitle = {AI-assisted protein design to rapidly convert antibody sequences to intrabodies targeting diverse peptides and histone modifications},<br \/>\r\nauthor = {Gabriel Galindo and Daiki Maejima and Jacob DeRoo and Scott R. Burlingham and Gretchen Fixen and Tatsuya Morisaki and Hallie P. Febvre and Ryan Hasbrook and Ning Zhao and Soham Ghosh and E. Handly Mayton and Christopher D. Snow and Brian J. Geiss and Yasuyuki Ohkawa and Yuko Sato and Hiroshi Kimura and Timothy J. Stasevich},<br \/>\r\nurl = {http:\/\/biorxiv.org\/lookup\/doi\/10.1101\/2025.02.06.636921},<br \/>\r\ndoi = {10.1101\/2025.02.06.636921},<br \/>\r\nyear  = {2025},<br \/>\r\ndate = {2025-02-08},<br \/>\r\nurldate = {2025-02-08},<br \/>\r\npublisher = {Cold Spring Harbor Laboratory},<br \/>\r\nabstract = {&lt;jats:title&gt;ABSTRACT&lt;\/jats:title&gt;&lt;jats:p&gt;Intrabodies are engineered antibodies that function inside living cells, enabling therapeutic, diagnostic, and imaging applications. While powerful, their development has been hindered by challenges associated with their folding, solubility, and stability in the reduced intracellular environment. Here, we present an AI-driven pipeline integrating AlphaFold2, ProteinMPNN, and live-cell screening to optimize antibody framework regions while preserving epitope-binding complementarity-determining regions. Using this approach, we successfully converted 19 out of 26 antibody sequences into functional single-chain variable fragment (scFv) intrabodies, including a panel targeting diverse histone modifications for real-time imaging of chromatin dynamics and gene regulation. Notably, 18 of these 19 sequences had failed to convert using the standard approach, demonstrating the unique effectiveness of our method. As antibody sequence databases expand, our method will accelerate intrabody design, making their development easier, more cost-effective, and broadly accessible for biological research.&lt;\/jats:p&gt;},<br \/>\r\nhowpublished = {bioRxiv},<br \/>\r\nkeywords = {Kimura G, Ohkawa G},<br \/>\r\npubstate = {published},<br \/>\r\ntppubtype = {unpublished}<br \/>\r\n}<br \/>\r\n<\/pre><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('17','tp_bibtex')\">Close<\/a><\/p><\/div><div class=\"tp_abstract\" id=\"tp_abstract_17\" style=\"display:none;\"><div class=\"tp_abstract_entry\">&lt;jats:title&gt;ABSTRACT&lt;\/jats:title&gt;&lt;jats:p&gt;Intrabodies are engineered antibodies that function inside living cells, enabling therapeutic, diagnostic, and imaging applications. While powerful, their development has been hindered by challenges associated with their folding, solubility, and stability in the reduced intracellular environment. Here, we present an AI-driven pipeline integrating AlphaFold2, ProteinMPNN, and live-cell screening to optimize antibody framework regions while preserving epitope-binding complementarity-determining regions. Using this approach, we successfully converted 19 out of 26 antibody sequences into functional single-chain variable fragment (scFv) intrabodies, including a panel targeting diverse histone modifications for real-time imaging of chromatin dynamics and gene regulation. Notably, 18 of these 19 sequences had failed to convert using the standard approach, demonstrating the unique effectiveness of our method. As antibody sequence databases expand, our method will accelerate intrabody design, making their development easier, more cost-effective, and broadly accessible for biological research.&lt;\/jats:p&gt;<\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('17','tp_abstract')\">Close<\/a><\/p><\/div><div class=\"tp_links\" id=\"tp_links_17\" style=\"display:none;\"><div class=\"tp_links_entry\"><ul class=\"tp_pub_list\"><li><i class=\"fas fa-globe\"><\/i><a class=\"tp_pub_list\" href=\"http:\/\/biorxiv.org\/lookup\/doi\/10.1101\/2025.02.06.636921\" title=\"http:\/\/biorxiv.org\/lookup\/doi\/10.1101\/2025.02.06.636921\" target=\"_blank\">http:\/\/biorxiv.org\/lookup\/doi\/10.1101\/2025.02.06.636921<\/a><\/li><li><i class=\"ai ai-doi\"><\/i><a class=\"tp_pub_list\" href=\"https:\/\/dx.doi.org\/10.1101\/2025.02.06.636921\" title=\"Follow DOI:10.1101\/2025.02.06.636921\" target=\"_blank\">doi:10.1101\/2025.02.06.636921<\/a><\/li><\/ul><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('17','tp_links')\">Close<\/a><\/p><\/div><\/div><\/div><div class=\"tp_publication tp_publication_article\"><div class=\"tp_pub_number\">15.<\/div><div class=\"tp_pub_info\"><p class=\"tp_pub_author\">Karin Shigenobu-Ueno,  Reihi Sakamoto,  Eiichiro Kanatsu,  Yoshitaka Kawasoe,  Tatsuro S Takahashi<\/p><p class=\"tp_pub_title\"><a class=\"tp_title_link\" href=\"https:\/\/dx.doi.org\/10.1093\/jb\/mvaf007\" title=\"Replication across <i>O<\/i>6-methylguanine activates futile cycling of DNA mismatch repair attempts assisted by the chromatin remodeling enzyme Smarcad1\" target=\"blank\">Replication across <i>O<\/i>6-methylguanine activates futile cycling of DNA mismatch repair attempts assisted by the chromatin remodeling enzyme Smarcad1<\/a> <span class=\"tp_pub_type article\">Journal Article<\/span> <\/p><p class=\"tp_pub_additional\"><span class=\"tp_pub_additional_in\">In: <\/span><span class=\"tp_pub_additional_journal\">The Journal of Biochemistry, <\/span><span class=\"tp_pub_additional_year\">2025<\/span>, <span class=\"tp_pub_additional_issn\">ISSN: 1756-2651<\/span>.<\/p><p class=\"tp_pub_menu\"><span class=\"tp_abstract_link\"><a id=\"tp_abstract_sh_16\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('16','tp_abstract')\" title=\"Show abstract\" style=\"cursor:pointer;\">Abstract<\/a><\/span> | <span class=\"tp_resource_link\"><a id=\"tp_links_sh_16\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('16','tp_links')\" title=\"Show links and resources\" style=\"cursor:pointer;\">Links<\/a><\/span> | <span class=\"tp_pub_tags_label\">\u30bf\u30b0: <\/span><a rel=\"nofollow\" href=\"https:\/\/www.bioreg.kyushu-u.ac.jp\/ext\/epicode\/publications?tgid=10#tppubs\" title=\"Show all publications which have a relationship to this tag\">Takahashi G<\/a><\/p><div class=\"tp_bibtex\" id=\"tp_bibtex_16\" style=\"display:none;\"><div class=\"tp_bibtex_entry\"><pre>@article{Shigenobu-Ueno2025,<br \/>\r\ntitle = {Replication across \\textit{O}6-methylguanine activates futile cycling of DNA mismatch repair attempts assisted by the chromatin remodeling enzyme Smarcad1},<br \/>\r\nauthor = {Karin Shigenobu-Ueno and Reihi Sakamoto and Eiichiro Kanatsu and Yoshitaka Kawasoe and Tatsuro S Takahashi},<br \/>\r\ndoi = {10.1093\/jb\/mvaf007},<br \/>\r\nissn = {1756-2651},<br \/>\r\nyear  = {2025},<br \/>\r\ndate = {2025-01-30},<br \/>\r\nurldate = {2025-01-30},<br \/>\r\njournal = {The Journal of Biochemistry},<br \/>\r\npublisher = {Oxford University Press (OUP)},<br \/>\r\nabstract = {&lt;jats:title&gt;Abstract&lt;\/jats:title&gt;<br \/>\r\n               &lt;jats:p&gt;SN1-type alkylating reagents generate O6-methylguanine (meG) lesions that activate the mismatch repair (MMR) response. Since post-replicative MMR specifically targets the nascent strand, meG on the template strand is refractory to rectification by MMR and, therefore, can induce non-productive MMR reactions. The cycling of futile MMR attempts is proposed to cause DNA double-strand breaks in the subsequent S phase, leading to ATR-checkpoint-mediated G2 arrest and apoptosis. However, the mechanistic details of futile MMR cycling, especially how this reaction is maintained in chromatin, remain unclear. Using replication-competent Xenopus egg extracts, we herein establish an in vitro system that recapitulates futile MMR cycling in the chromatin context. The meG\u2013T mispair, but not the meG\u2013C pair, is efficiently targeted by MMR in our system. MMR attempts on the meG-strand result in the meG-to-A correction, while those on the T-strand induce iterative cycles of strand excision and resynthesis. Likewise, replication across meG generates persistent single-strand breaks on the daughter DNA containing meG. Moreover, the depletion of Smarcad1, a chromatin remodeler previously reported to facilitate MMR, impairs the retention of single-strand breaks. Our study thus provides experimental evidence that chromatin replication across meG induces futile MMR cycling that is assisted by Smarcad1.&lt;\/jats:p&gt;},<br \/>\r\nkeywords = {Takahashi G},<br \/>\r\npubstate = {published},<br \/>\r\ntppubtype = {article}<br \/>\r\n}<br \/>\r\n<\/pre><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('16','tp_bibtex')\">Close<\/a><\/p><\/div><div class=\"tp_abstract\" id=\"tp_abstract_16\" style=\"display:none;\"><div class=\"tp_abstract_entry\">&lt;jats:title&gt;Abstract&lt;\/jats:title&gt;<br \/>\r\n               &lt;jats:p&gt;SN1-type alkylating reagents generate O6-methylguanine (meG) lesions that activate the mismatch repair (MMR) response. Since post-replicative MMR specifically targets the nascent strand, meG on the template strand is refractory to rectification by MMR and, therefore, can induce non-productive MMR reactions. The cycling of futile MMR attempts is proposed to cause DNA double-strand breaks in the subsequent S phase, leading to ATR-checkpoint-mediated G2 arrest and apoptosis. However, the mechanistic details of futile MMR cycling, especially how this reaction is maintained in chromatin, remain unclear. Using replication-competent Xenopus egg extracts, we herein establish an in vitro system that recapitulates futile MMR cycling in the chromatin context. The meG\u2013T mispair, but not the meG\u2013C pair, is efficiently targeted by MMR in our system. MMR attempts on the meG-strand result in the meG-to-A correction, while those on the T-strand induce iterative cycles of strand excision and resynthesis. Likewise, replication across meG generates persistent single-strand breaks on the daughter DNA containing meG. Moreover, the depletion of Smarcad1, a chromatin remodeler previously reported to facilitate MMR, impairs the retention of single-strand breaks. Our study thus provides experimental evidence that chromatin replication across meG induces futile MMR cycling that is assisted by Smarcad1.&lt;\/jats:p&gt;<\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('16','tp_abstract')\">Close<\/a><\/p><\/div><div class=\"tp_links\" id=\"tp_links_16\" style=\"display:none;\"><div class=\"tp_links_entry\"><ul class=\"tp_pub_list\"><li><i class=\"ai ai-doi\"><\/i><a class=\"tp_pub_list\" href=\"https:\/\/dx.doi.org\/10.1093\/jb\/mvaf007\" title=\"Follow DOI:10.1093\/jb\/mvaf007\" target=\"_blank\">doi:10.1093\/jb\/mvaf007<\/a><\/li><\/ul><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('16','tp_links')\">Close<\/a><\/p><\/div><\/div><\/div><div class=\"tp_publication tp_publication_article\"><div class=\"tp_pub_number\">14.<\/div><div class=\"tp_pub_info\"><p class=\"tp_pub_author\">Yuki Yamanashi,  Shinpei Takamaru,  Atsushi Okabe,  Satoshi Kaito,  Yuto Azumaya,  Yugo R. Kamimura,  Kenzo Yamatsugu,  Tomoya Kujirai,  Hitoshi Kurumizaka,  Atsushi Iwama,  Atsushi Kaneda,  Shigehiro A. Kawashima,  Motomu Kanai<\/p><p class=\"tp_pub_title\"><a class=\"tp_title_link\" href=\"https:\/\/dx.doi.org\/10.1038\/s41467-025-56204-2\" title=\"Chemical catalyst manipulating cancer epigenome and transcription\" target=\"blank\">Chemical catalyst manipulating cancer epigenome and transcription<\/a> <span class=\"tp_pub_type article\">Journal Article<\/span> <\/p><p class=\"tp_pub_additional\"><span class=\"tp_pub_additional_in\">In: <\/span><span class=\"tp_pub_additional_journal\">Nat Commun, <\/span><span class=\"tp_pub_additional_volume\">vol. 16, <\/span><span class=\"tp_pub_additional_number\">no. 1, <\/span><span class=\"tp_pub_additional_year\">2025<\/span>, <span class=\"tp_pub_additional_issn\">ISSN: 2041-1723<\/span>.<\/p><p class=\"tp_pub_menu\"><span class=\"tp_abstract_link\"><a id=\"tp_abstract_sh_23\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('23','tp_abstract')\" title=\"Show abstract\" style=\"cursor:pointer;\">Abstract<\/a><\/span> | <span class=\"tp_resource_link\"><a id=\"tp_links_sh_23\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('23','tp_links')\" title=\"Show links and resources\" style=\"cursor:pointer;\">Links<\/a><\/span> | <span class=\"tp_pub_tags_label\">\u30bf\u30b0: <\/span><a rel=\"nofollow\" href=\"https:\/\/www.bioreg.kyushu-u.ac.jp\/ext\/epicode\/publications?tgid=4#tppubs\" title=\"Show all publications which have a relationship to this tag\">Kurumizaka G<\/a><\/p><div class=\"tp_bibtex\" id=\"tp_bibtex_23\" style=\"display:none;\"><div class=\"tp_bibtex_entry\"><pre>@article{Yamanashi2025,<br \/>\r\ntitle = {Chemical catalyst manipulating cancer epigenome and transcription},<br \/>\r\nauthor = {Yuki Yamanashi and Shinpei Takamaru and Atsushi Okabe and Satoshi Kaito and Yuto Azumaya and Yugo R. Kamimura and Kenzo Yamatsugu and Tomoya Kujirai and Hitoshi Kurumizaka and Atsushi Iwama and Atsushi Kaneda and Shigehiro A. Kawashima and Motomu Kanai},<br \/>\r\ndoi = {10.1038\/s41467-025-56204-2},<br \/>\r\nissn = {2041-1723},<br \/>\r\nyear  = {2025},<br \/>\r\ndate = {2025-01-24},<br \/>\r\njournal = {Nat Commun},<br \/>\r\nvolume = {16},<br \/>\r\nnumber = {1},<br \/>\r\npublisher = {Springer Science and Business Media LLC},<br \/>\r\nabstract = {The number and variety of identified histone post-translational modifications (PTMs) are continually increasing. However, the specific consequences of each histone PTM remain largely unclear, primarily due to the lack of methods for selectively and rapidly introducing a desired histone PTM in living cells without genetic engineering. Here, we report the development of a cell-permeable histone acetylation catalyst, BAHA-LANA-PEG-CPP44, which selectively enters leukemia cells, binds to chromatin, and acetylates H2BK120 of endogenous histones in a short reaction time. Time-course analyses of this in-cell catalytic reaction revealed that H2BK120 acetylation attenuates the chromatin binding of negative elongation factor E (NELFE), an onco-transcription factor. This H2BK120 acetylation-mediated removal of NELFE from chromatin reshapes transcription, slows leukemia cell viability, and reduces their tumorigenic potential in mice. Therefore, this histone acetylation catalyst provides a unique tool for elucidating the time-resolved consequences of histone PTMs and may offer a modality for cancer chemotherapy.},<br \/>\r\nkeywords = {Kurumizaka G},<br \/>\r\npubstate = {published},<br \/>\r\ntppubtype = {article}<br \/>\r\n}<br \/>\r\n<\/pre><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('23','tp_bibtex')\">Close<\/a><\/p><\/div><div class=\"tp_abstract\" id=\"tp_abstract_23\" style=\"display:none;\"><div class=\"tp_abstract_entry\">The number and variety of identified histone post-translational modifications (PTMs) are continually increasing. However, the specific consequences of each histone PTM remain largely unclear, primarily due to the lack of methods for selectively and rapidly introducing a desired histone PTM in living cells without genetic engineering. Here, we report the development of a cell-permeable histone acetylation catalyst, BAHA-LANA-PEG-CPP44, which selectively enters leukemia cells, binds to chromatin, and acetylates H2BK120 of endogenous histones in a short reaction time. Time-course analyses of this in-cell catalytic reaction revealed that H2BK120 acetylation attenuates the chromatin binding of negative elongation factor E (NELFE), an onco-transcription factor. This H2BK120 acetylation-mediated removal of NELFE from chromatin reshapes transcription, slows leukemia cell viability, and reduces their tumorigenic potential in mice. Therefore, this histone acetylation catalyst provides a unique tool for elucidating the time-resolved consequences of histone PTMs and may offer a modality for cancer chemotherapy.<\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('23','tp_abstract')\">Close<\/a><\/p><\/div><div class=\"tp_links\" id=\"tp_links_23\" style=\"display:none;\"><div class=\"tp_links_entry\"><ul class=\"tp_pub_list\"><li><i class=\"ai ai-doi\"><\/i><a class=\"tp_pub_list\" href=\"https:\/\/dx.doi.org\/10.1038\/s41467-025-56204-2\" title=\"Follow DOI:10.1038\/s41467-025-56204-2\" target=\"_blank\">doi:10.1038\/s41467-025-56204-2<\/a><\/li><\/ul><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('23','tp_links')\">Close<\/a><\/p><\/div><\/div><\/div><h3 class=\"tp_h3\" id=\"tp_h3_2024\">2024<\/h3><div class=\"tp_publication tp_publication_article\"><div class=\"tp_pub_number\">13.<\/div><div class=\"tp_pub_info\"><p class=\"tp_pub_author\">Reina Nagamura,  Tomoya Kujirai,  Junko Kato,  Yutaro Shuto,  Tsukasa Kusakizako,  Hisato Hirano,  Masaki Endo,  Seiichi Toki,  Hiroaki Saika,  Hitoshi Kurumizaka,  Osamu Nureki<\/p><p class=\"tp_pub_title\"><a class=\"tp_title_link\" href=\"https:\/\/dx.doi.org\/10.1038\/s41467-024-54768-z\" title=\"Structural insights into how Cas9 targets nucleosomes\" target=\"blank\">Structural insights into how Cas9 targets nucleosomes<\/a> <span class=\"tp_pub_type article\">Journal Article<\/span> <\/p><p class=\"tp_pub_additional\"><span class=\"tp_pub_additional_in\">In: <\/span><span class=\"tp_pub_additional_journal\">Nat Commun, <\/span><span class=\"tp_pub_additional_volume\">vol. 15, <\/span><span class=\"tp_pub_additional_number\">no. 10744, <\/span><span class=\"tp_pub_additional_year\">2024<\/span>, <span class=\"tp_pub_additional_issn\">ISSN: 2041-1723<\/span>.<\/p><p class=\"tp_pub_menu\"><span class=\"tp_resource_link\"><a id=\"tp_links_sh_12\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('12','tp_links')\" title=\"Show links and resources\" style=\"cursor:pointer;\">Links<\/a><\/span> | <span class=\"tp_pub_tags_label\">\u30bf\u30b0: <\/span><a rel=\"nofollow\" href=\"https:\/\/www.bioreg.kyushu-u.ac.jp\/ext\/epicode\/publications?tgid=4#tppubs\" title=\"Show all publications which have a relationship to this tag\">Kurumizaka G<\/a><\/p><div class=\"tp_bibtex\" id=\"tp_bibtex_12\" style=\"display:none;\"><div class=\"tp_bibtex_entry\"><pre>@article{Nagamura2024,<br \/>\r\ntitle = {Structural insights into how Cas9 targets nucleosomes},<br \/>\r\nauthor = {Reina Nagamura and Tomoya Kujirai and Junko Kato and Yutaro Shuto and Tsukasa Kusakizako and Hisato Hirano and Masaki Endo and Seiichi Toki and Hiroaki Saika and Hitoshi Kurumizaka and Osamu Nureki},<br \/>\r\ndoi = {10.1038\/s41467-024-54768-z},<br \/>\r\nissn = {2041-1723},<br \/>\r\nyear  = {2024},<br \/>\r\ndate = {2024-12-30},<br \/>\r\njournal = {Nat Commun},<br \/>\r\nvolume = {15},<br \/>\r\nnumber = {10744},<br \/>\r\npublisher = {Springer Science and Business Media LLC},<br \/>\r\nkeywords = {Kurumizaka G},<br \/>\r\npubstate = {published},<br \/>\r\ntppubtype = {article}<br \/>\r\n}<br \/>\r\n<\/pre><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('12','tp_bibtex')\">Close<\/a><\/p><\/div><div class=\"tp_links\" id=\"tp_links_12\" style=\"display:none;\"><div class=\"tp_links_entry\"><ul class=\"tp_pub_list\"><li><i class=\"ai ai-doi\"><\/i><a class=\"tp_pub_list\" href=\"https:\/\/dx.doi.org\/10.1038\/s41467-024-54768-z\" title=\"Follow DOI:10.1038\/s41467-024-54768-z\" target=\"_blank\">doi:10.1038\/s41467-024-54768-z<\/a><\/li><\/ul><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('12','tp_links')\">Close<\/a><\/p><\/div><\/div><\/div><div class=\"tp_publication tp_publication_article\"><div class=\"tp_pub_number\">12.<\/div><div class=\"tp_pub_info\"><p class=\"tp_pub_author\">Yukako Hattori<\/p><p class=\"tp_pub_title\"><a class=\"tp_title_link\" href=\"https:\/\/dx.doi.org\/10.2108\/zs240057\" title=\"Nutritional Adaptation and Microbes: Insights From Drosophila\" target=\"blank\">Nutritional Adaptation and Microbes: Insights From Drosophila<\/a> <span class=\"tp_pub_type article\">Journal Article<\/span> <\/p><p class=\"tp_pub_additional\"><span class=\"tp_pub_additional_in\">In: <\/span><span class=\"tp_pub_additional_journal\">Zoological Science, <\/span><span class=\"tp_pub_additional_volume\">vol. 42, <\/span><span class=\"tp_pub_additional_number\">no. 1, <\/span><span class=\"tp_pub_additional_year\">2024<\/span>, <span class=\"tp_pub_additional_issn\">ISSN: 0289-0003<\/span>.<\/p><p class=\"tp_pub_menu\"><span class=\"tp_resource_link\"><a id=\"tp_links_sh_15\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('15','tp_links')\" title=\"Show links and resources\" style=\"cursor:pointer;\">Links<\/a><\/span> | <span class=\"tp_pub_tags_label\">\u30bf\u30b0: <\/span><a rel=\"nofollow\" href=\"https:\/\/www.bioreg.kyushu-u.ac.jp\/ext\/epicode\/publications?tgid=9#tppubs\" title=\"Show all publications which have a relationship to this tag\">Hattori G<\/a><\/p><div class=\"tp_bibtex\" id=\"tp_bibtex_15\" style=\"display:none;\"><div class=\"tp_bibtex_entry\"><pre>@article{Hattori2024,<br \/>\r\ntitle = {Nutritional Adaptation and Microbes: Insights From Drosophila},<br \/>\r\nauthor = {Yukako Hattori},<br \/>\r\ndoi = {10.2108\/zs240057},<br \/>\r\nissn = {0289-0003},<br \/>\r\nyear  = {2024},<br \/>\r\ndate = {2024-12-23},<br \/>\r\nurldate = {2024-12-23},<br \/>\r\njournal = {Zoological Science},<br \/>\r\nvolume = {42},<br \/>\r\nnumber = {1},<br \/>\r\npublisher = {Zoological Society of Japan},<br \/>\r\nkeywords = {Hattori G},<br \/>\r\npubstate = {published},<br \/>\r\ntppubtype = {article}<br \/>\r\n}<br \/>\r\n<\/pre><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('15','tp_bibtex')\">Close<\/a><\/p><\/div><div class=\"tp_links\" id=\"tp_links_15\" style=\"display:none;\"><div class=\"tp_links_entry\"><ul class=\"tp_pub_list\"><li><i class=\"ai ai-doi\"><\/i><a class=\"tp_pub_list\" href=\"https:\/\/dx.doi.org\/10.2108\/zs240057\" title=\"Follow DOI:10.2108\/zs240057\" target=\"_blank\">doi:10.2108\/zs240057<\/a><\/li><\/ul><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('15','tp_links')\">Close<\/a><\/p><\/div><\/div><\/div><\/div><div class=\"tablenav\"><div class=\"tablenav-pages\"><span class=\"displaying-num\">61 entries<\/span> <a class=\"page-numbers button disabled\">&laquo;<\/a> <a class=\"page-numbers button disabled\">&lsaquo;<\/a> 1 of 2 <a href=\"https:\/\/www.bioreg.kyushu-u.ac.jp\/ext\/epicode\/publications?limit=2&amp;tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=&amp;tsr=#tppubs\" title=\"next page\" 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<\/div><\/div><\/div>\n","protected":false},"excerpt":{"rendered":"<p>\u7814\u7a76\u5b9f\u7e3e<\/p>\n","protected":false},"author":2,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-16","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/www.bioreg.kyushu-u.ac.jp\/ext\/epicode\/wp-json\/wp\/v2\/pages\/16","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.bioreg.kyushu-u.ac.jp\/ext\/epicode\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/www.bioreg.kyushu-u.ac.jp\/ext\/epicode\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/www.bioreg.kyushu-u.ac.jp\/ext\/epicode\/wp-json\/wp\/v2\/users\/2"}],"replies":[{"embeddable":true,"href":"https:\/\/www.bioreg.kyushu-u.ac.jp\/ext\/epicode\/wp-json\/wp\/v2\/comments?post=16"}],"version-history":[{"count":8,"href":"https:\/\/www.bioreg.kyushu-u.ac.jp\/ext\/epicode\/wp-json\/wp\/v2\/pages\/16\/revisions"}],"predecessor-version":[{"id":247,"href":"https:\/\/www.bioreg.kyushu-u.ac.jp\/ext\/epicode\/wp-json\/wp\/v2\/pages\/16\/revisions\/247"}],"wp:attachment":[{"href":"https:\/\/www.bioreg.kyushu-u.ac.jp\/ext\/epicode\/wp-json\/wp\/v2\/media?parent=16"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}