業績リスト

2025

46.

Hiroaki Ohishi, Hiroshi Ochiai

Image Analysis Protocol for DNA/RNA/Immunofluorescence (IF)-seqFISH Data Journal Article

In: Methods Mol. Biol., vol. Methods Mol. Biol. (Clifton, NJ), pp. 419–432, 2025, ISBN: 978-1-0716-4136-1.

Abstract | Links

2024

45.

Soundhararajan Gopi, Giovanni B Brandani, Cheng Tan, Jaewoon Jung, Chenyang Gu, Azuki Mizutani, Hiroshi Ochiai, Yuji Sugita, Shoji Takada

In silico nanoscope to study the interplay of genome organization and transcription regulation Unpublished

bioRxiv, 2024.

Abstract | Links

44.

Bitong Li, Yew Yan Wong, Neftali Flores-Rodriguez, Tara Davidson, Matthew S Graus, Valeriia Smialkovska, Hiroaki Ohishi, Angelika Feldmann, Hiroshi Ochiai, Mathias Francois

Anti-phase clustering of regulatory factors shapes gene bursting Journal Article

In: bioRxiv, 2024.

Abstract | Links

43.

Yosuke Yoneyama, Ran-Ran Zhang, Masaki Kimura, Yuqi Cai, Mike Adam, Sreeja Parameswaran, Hideki Masaki, Naoaki Mizuno, Joydeep Bhadury, So Maezawa, Hiroshi Ochiai, Hiromitsu Nakauchi, S. Steven Potter, Matthew T. Weirauch, Takanori Takebe

Inter-cellular mRNA Transfer Alters Human Pluripotent Stem Cell State Journal Article

In: bioRxiv, 2024.

Abstract | Links

42.

Ximena Garate, Pablo Aurelio Gómez-García, Manuel Fernández Merino, Marta Cadevall Angles, Chenggan Zhu, Alvaro Castells-García, Ilyas Ed-Daoui, Laura Martin, Hiroshi Ochiai, Maria Victoria Neguembor, Maria Pia Cosma

The relationship between nanoscale genome organization and gene expression in mouse embryonic stem cells during pluripotency transition Journal Article

In: Nucleic Acids Res, 2024, ISSN: 1362-4962.

Abstract | Links

41.

Kosuke Tomimatsu, Takeru Fujii, Ryoma Bise, Kazufumi Hosoda, Yosuke Taniguchi, Hiroshi Ochiai, Hiroaki Ohishi, Kanta Ando, Ryoma Minami, Kaori Tanaka, Taro Tachibana, Seiichi Mori, Akihito Harada, Kazumitsu Maehara, Masao Nagasaki, Seiichi Uchida, Hiroshi Kimura, Masashi Narita, Yasuyuki Ohkawa

Precise immunofluorescence canceling for highly multiplexed imaging to capture specific cell states Journal Article

In: Nature Communications, vol. 15, no. 1, pp. 3657, 2024.

Abstract | Links

2023

40.

Hiroaki Ohishi, Soya Shinkai, Hitoshi Owada, Takeru Fujii, Kazufumi Hosoda, Shuichi Onami, Takashi Yamamoto, Yasuyuki Ohkawa, Hiroshi Ochiai

Transcription-coupled changes in higher-order genomic structure and transcription hub viscosity prolong enhancer-promoter connectivity Journal Article

In: bioRxiv, pp. 2023.11.27.568629, 2023.

Abstract | Links

39.

Kosuke Tomimatsu, Takeru Fujii, Ryoma Bise, Kazufumi Hosoda, Yosuke Taniguchi, Hiroshi Ochiai, Hiroaki Ohishi, Kanta Ando, Ryoma Minami, Kaori Tanaka, Taro Tachibana, Seiichi Mori, Akihito Harada, Kazumitsu Maehara, Masao Nagasaki, Seiichi Uchida, Hiroshi Kimura, Masashi Narita, Yasuyuki Ohkawa

Precise immunofluorescence canceling for highly multiplexed imaging capturing specific cell state Journal Article

In: bioRxiv, pp. 2023.10.17.561810, 2023.

Abstract | Links

2022

38.

Hiroaki Ohishi, Seiru Shimada, Satoshi Uchino, Jieru Li, Yuko Sato, Manabu Shintani, Hitoshi Owada, Yasuyuki Ohkawa, Alexandros Pertsinidis, Takashi Yamamoto, Hiroshi Kimura, Hiroshi Ochiai

STREAMING-tag system reveals spatiotemporal relationships between transcriptional regulatory factors and transcriptional activity Journal Article

In: Nat Commun, vol. 13, no. 1, pp. 7672, 2022, ISSN: 2041-1723.

Abstract | Links

37.

Hiroshi Ochiai

Facilitating genome function understanding using genome editing dependent bioimaging techniques Journal Article

In: Gene and Genome Editing, vol. 5, pp. 100022, 2022, ISSN: 2666-3880.

Abstract | Links

36.

Hiroaki Ohishi, Hiroshi Ochiai

Epigenomics, Methods and Protocols Book Chapter

In: vol. 2577, pp. 103–122, 2022, ISSN: 1064-3745.

Abstract | Links

35.

Haruka Matsumori, Kenji Watanabe, Hiroaki Tachiwana, Tomoko Fujita, Yuma Ito, Makio Tokunaga, Kumiko Sakata-Sogawa, Hiroko Osakada, Tokuko Haraguchi, Akinori Awazu, Hiroshi Ochiai, Yuka Sakata, Koji Ochiai, Tsutomu Toki, Etsuro Ito, Ilya G Goldberg, Kazuaki Tokunaga, Mitsuyoshi Nakao, Noriko Saitoh

Ribosomal protein L5 facilitates rDNA-bundled condensate and nucleolar assembly Journal Article

In: Life Science Alliance, vol. 5, no. 7, 2022, ISSN: 2575-1077.

Abstract | Links

34.

Silvia Natsuko Akutsu, Tatsuo Miyamoto, Daiju Oba, Keita Tomioka, Hiroshi Ochiai, Hirofumi Ohashi, Shinya Matsuura

iPSC reprogramming-mediated aneuploidy correction in autosomal trisomy syndromes Journal Article

In: PLoS ONE, vol. 17, no. 3, pp. e0264965, 2022.

Abstract | Links

2021

33.

Yasunori Horikoshi, Hiroki Shima, Jiying Sun, Wataru Kobayashi, Volker J. Schmid, Hiroshi Ochiai, Lin Shi, Atsuhiko Fukuto, Yasuha Kinugasa, Hitoshi Kurumizaka, Tsuyoshi Ikura, Yolanda Markaki, Shin-ichi Tate, Kazuhiko Igarashi, Thomas Cremer, Satoshi Tashiro

Distinctive nuclear zone for RAD51-mediated homologous recombinational DNA repair Journal Article

In: bioRxiv, pp. 2021.11.29.470307, 2021.

Abstract | Links

2020

32.

Hiroshi Ochiai, Tetsutaro Hayashi, Mana Umeda, Mika Yoshimura, Akihito Harada, Yukiko Shimizu, Kenta Nakano, Noriko Saitoh, Zhe Liu, Takashi Yamamoto, Tadashi Okamura, Yasuyuki Ohkawa, Hiroshi Kimura, Itoshi Nikaido

Genome-wide kinetic properties of transcriptional bursting in mouse embryonic stem cells Journal Article

In: Science Advances, vol. 6, no. 25, pp. eaaz6699, 2020.

Abstract | Links

31.

Tatsuo Miyamoto, Kosuke Hosoba, Takeshi Itabashi, Atsuko H Iwane, Silvia Natsuko Akutsu, Hiroshi Ochiai, Yumiko Saito, Takashi Yamamoto, Shinya Matsuura

Insufficiency of ciliary cholesterol in hereditary Zellweger syndrome Journal Article

In: The EMBO Journal, vol. 39, no. 12, pp. e103499, 2020, ISSN: 0261-4189.

Abstract | Links

30.

Soya Shinkai, Masaki Nakagawa, Takeshi Sugawara, Yuichi Togashi, Hiroshi Ochiai, Ryuichiro Nakato, Yuichi Taniguchi, Shuichi Onami

PHi-C: deciphering Hi-C data into polymer dynamics Journal Article

In: NAR Genomics and Bioinformatics, vol. 2, no. 2, pp. lqaa020, 2020.

Abstract | Links

29.

Jieru Li, Angela Hsu, Yujing Hua, Guanshi Wang, Lingling Cheng, Hiroshi Ochiai, Takashi Yamamoto, Alexandros Pertsinidis

Single-gene imaging links genome topology, promoter-enhancer communication and transcription control Journal Article

In: Nature structural & molecular biology, vol. 27, no. 11, pp. 1032–1040, 2020, ISSN: 1545-9993.

Abstract | Links

2019

28.

Sungrim Seirin-Lee, Fumitaka Osakada, Junichi Takeda, Satoshi Tashiro, Ryo Kobayashi, Takashi Yamamoto, Hiroshi Ochiai

Role of dynamic nuclear deformation on genomic architecture reorganization Journal Article

In: PLoS Computational Biology, vol. 15, no. 9, pp. e1007289, 2019, ISSN: 1553-734X.

Abstract | Links

27.

Jieru Li, Ankun Dong, Kamola Saydaminova, Hill Chang, Guanshi Wang, Hiroshi Ochiai, Takashi Yamamoto, Alexandros Pertsinidis

Single-Molecule Nanoscopy Elucidates RNA Polymerase II Transcription at Single Genes in Live Cells Journal Article

In: Cell, vol. 178, no. 2, pp. 491–506.e28, 2019, ISSN: 0092-8674.

Abstract | Links

26.

Hiroshi Ochiai

Real-Time Observation of Localization and Expression (ROLEX) System for Live Imaging of the Transcriptional Activity and Nuclear Position of a Specific Endogenous Gene. Book Chapter

In: vol. 2038, pp. 35–45, Humana, New York, NY, 2019.

Abstract | Links

2017

25.

Masaya Matsushita, Hiroshi Ochiai, Ken-ichi T. Suzuki, Sayaka Hayashi, Takashi Yamamoto, Akinori Awazu, Naoaki Sakamoto

Dynamic changes in the interchromosomal interaction of early histone gene loci during development of sea urchin Journal Article

In: Journal of Cell Science, vol. 130, no. 24, pp. 4097–4107, 2017, ISSN: 0021-9533.

Abstract | Links

24.

Satoru Ishihara, Naoe Kotomura, Naoki Yamamoto, Hiroshi Ochiai

Ligation-mediated PCR with a back-to-back adapter reduces amplification bias resulting from variations in GC content Journal Article

In: Analytical Biochemistry, vol. 531, pp. 37–44, 2017, ISSN: 0003-2697.

Abstract | Links

23.

Hiroshi Ochiai, Takashi Yamamoto

Construction and Evaluation of Zinc Finger Nucleases. Book Chapter

In: vol. 1630, pp. 1–24, 2017.

Abstract | Links

2016

22.

Shinya Matsuura, Ekaterina Royba, Silvia N Akutsu, Hiromi Yanagihara, Hiroshi Ochiai, Yoshiki Kudo, Satoshi Tashiro, Tatsuo Miyamoto

Analysis of individual differences in radiosensitivity using genome editing. Journal Article

In: Ann ICRP, vol. 45, no. 1 Suppl, pp. 290–296, 2016.

Abstract | Links

2015

21.

Hiroshi Ochiai

Single-Base Pair Genome Editing in Human Cells by Using Site-Specific Endonucleases Journal Article

In: Int J Mol Sci, vol. 16, no. 9, pp. 21128–21137, 2015.

Abstract | Links

20.

Hiroshi Ochiai, Takeshi Sugawara, Takashi Yamamoto

Simultaneous live imaging of the transcription and nuclear position of specific genes Journal Article

In: Nucleic Acids Research, vol. 43, no. 19, pp. e127–e127, 2015, ISSN: 0305-1048.

Abstract | Links

19.

Tatsuo Miyamoto, Kosuke Hosoba, Hiroshi Ochiai, Ekaterina Royba, Hideki Izumi, Tetsushi Sakuma, Takashi Yamamoto, Brian David Dynlacht, Shinya Matsuura

The Microtubule-Depolymerizing Activity of a Mitotic Kinesin Protein KIF2A Drives Primary Cilia Disassembly Coupled with Cell Proliferation Journal Article

In: Cell Reports, vol. 10, no. 5, pp. 664–673, 2015, ISSN: 2211-1247.

Abstract | Links

18.

Hiroshi Ochiai, Takashi Yamamoto

Genome Editing Using Zinc-Finger Nucleases (ZFNs) and Transcription Activator-Like Effector Nucleases (TALENs) Book Section

In: Targeted Genome Editing Using Site-Specific Nucleases, pp. 3–24, Springer, Tokyo, 2015.

Abstract | Links

2014

17.

Hiroshi Ochiai, Tatsuo Miyamoto, Akinori Kanai, Kosuke Hosoba, Tetsushi Sakuma, Yoshiki Kudo, Keiko Asami, Atsushi Ogawa, Akihiro Watanabe, Tadashi Kajii, Takashi Yamamoto, Shinya Matsuura

TALEN-mediated single-base-pair editing identification of an intergenic mutation upstream of BUB1B as causative of PCS (MVA) syndrome Journal Article

In: Proceedings of the National Academy of Sciences, vol. 111, no. 4, pp. 1461–1466, 2014, ISSN: 0027-8424.

Abstract | Links

16.

Hiroshi Ochiai, Takeshi Sugawara, Tetsushi Sakuma, Takashi Yamamoto

Stochastic promoter activation affects Nanog expression variability in mouse embryonic stem cells Journal Article

In: Scientific Reports, vol. 4, no. 1, pp. 7125, 2014.

Abstract | Links

2013

15.

Tetsushi Sakuma, Hiroshi Ochiai, Takehito Kaneko, Tomoji Mashimo, Daisuke Tokumasu, Yuto Sakane, Ken-ichi Suzuki, Tatsuo Miyamoto, Naoaki Sakamoto, Shinya Matsuura, Takashi Yamamoto

Repeating pattern of non-RVD variations in DNA-binding modules enhances TALEN activity Journal Article

In: Scientific Reports, vol. 3, no. 1, pp. 3379, 2013.

Abstract | Links

14.

Tetsushi Sakuma, Sayaka Hosoi, Knut Woltjen, Ken‐ichi Suzuki, Keiko Kashiwagi, Housei Wada, Hiroshi Ochiai, Tatsuo Miyamoto, Narudo Kawai, Yasunori Sasakura, Shinya Matsuura, Yasushi Okada, Atsuo Kawahara, Shigeo Hayashi, Takashi Yamamoto

Efficient TALEN construction and evaluation methods for human cell and animal applications Journal Article

In: Genes to Cells, vol. 18, no. 4, pp. 315–326, 2013, ISSN: 1365-2443.

Abstract | Links

13.

Ken-ichi T. Suzuki, Yukiko Isoyama, Keiko Kashiwagi, Tetsushi Sakuma, Hiroshi Ochiai, Naoaki Sakamoto, Nobuaki Furuno, Akihiko Kashiwagi, Takashi Yamamoto

High efficiency TALENs enable F0 functional analysis by targeted gene disruption in Xenopus laevis embryos Journal Article

In: Biology Open, vol. 2, no. 5, pp. 448–452, 2013, ISSN: 2046-6390.

Abstract | Links

2012

12.

Hiroshi Ochiai, Naoaki Sakamoto, Kazumasa Fujita, Masatoshi Nishikawa, Ken-ichi Suzuki, Shinya Matsuura, Tatsuo Miyamoto, Tetsushi Sakuma, Tatsuo Shibata, Takashi Yamamoto

Zinc-finger nuclease-mediated targeted insertion of reporter genes for quantitative imaging of gene expression in sea urchin embryos Journal Article

In: Proceedings of the National Academy of Sciences, vol. 109, no. 27, pp. 10915–10920, 2012, ISSN: 0027-8424.

Abstract | Links

11.

Satoshi Ansai, Hiroshi Ochiai, Yuta Kanie, Yasuhiro Kamei, Yuki Gou, Takeshi Kitano, Takashi Yamamoto, Masato Kinoshita

Targeted disruption of exogenous EGFP gene in medaka using zinc‐finger nucleases Journal Article

In: Development, Growth & Differentiation, vol. 54, no. 5, pp. 546–556, 2012, ISSN: 1440-169X.

Abstract | Links

10.

Takahito Watanabe, Hiroshi Ochiai, Tetsushi Sakuma, Hadley W. Horch, Naoya Hamaguchi, Taro Nakamura, Tetsuya Bando, Hideyo Ohuchi, Takashi Yamamoto, Sumihare Noji, Taro Mito

Non-transgenic genome modifications in a hemimetabolous insect using zinc-finger and TAL effector nucleases Journal Article

In: Nature Communications, vol. 3, no. 1, pp. 1017, 2012.

Abstract | Links

9.

Xiaohong Song, Yuya Sato, Athary Felemban, Ayako Ito, Mahmud Hossain, Hiroshi Ochiai, Takashi Yamamoto, Kiyotoshi Sekiguchi, Hideaki Tanaka, Kunimasa Ohta

Equarin is involved as an FGF signaling modulator in chick lens differentiation Journal Article

In: Developmental Biology, vol. 368, no. 1, pp. 109–117, 2012, ISSN: 0012-1606.

Abstract | Links

8.

Narudo Kawai, Hiroshi Ochiai, Tetsushi Sakuma, Lixy Yamada, Hitoshi Sawada, Takashi Yamamoto, Yasunori Sasakura

Efficient targeted mutagenesis of the chordate Ciona intestinalis genome with zinc‐finger nucleases Journal Article

In: Development, Growth & Differentiation, vol. 54, no. 5, pp. 535–545, 2012, ISSN: 1440-169X.

Abstract | Links

2011

7.

Tetsushi Sakuma, Kazuya Ohnishi, Kazumasa Fujita, Hiroshi Ochiai, Naoaki Sakamoto, Takashi Yamamoto

HpSumf1 is involved in the activation of sulfatases responsible for regulation of skeletogenesis during sea urchin development Journal Article

In: Development Genes and Evolution, vol. 221, no. 3, pp. 157–166, 2011, ISSN: 0949-944X.

Abstract | Links

2010

6.

Hiroshi Ochiai, Kazumasa Fujita, Ken‐ichi Suzuki, Masatoshi Nishikawa, Tatsuo Shibata, Naoaki Sakamoto, Takashi Yamamoto

Targeted mutagenesis in the sea urchin embryo using zinc‐finger nucleases Journal Article

In: Genes to Cells, vol. 15, no. 8, pp. 875–885, 2010, ISSN: 1365-2443.

Abstract | Links

5.

Yuka Okamitsu, Takashi Yamamoto, Takayoshi Fujii, Hiroshi Ochiai, Naoaki Sakamoto

Dicer is Required for the Normal Development of Sea Urchin, Hemicentrotus pulcherrimus Journal Article

In: Zoological Science, vol. 27, no. 6, pp. 477–486, 2010, ISSN: 0289-0003.

Abstract | Links

2009

4.

Koji Karasawa, Naoaki Sakamoto, Kazumasa Fujita, Hiroshi Ochiai, Takayoshi Fujii, Koji Akasaka, Takashi Yamamoto

Suppressor of Hairless (Su(H)) is Required for Foregut Development in the Sea Urchin Embryo Journal Article

In: Zoological Science, vol. 26, no. 10, pp. 686–690, 2009, ISSN: 0289-0003.

Abstract | Links

3.

Takayoshi Fujii, Naoaki Sakamoto, Hiroshi Ochiai, Kazumasa Fujita, Yuka Okamitsu, Noriko Sumiyoshi, Takuya Minokawa, Takashi Yamamoto

Role of the nanos homolog during sea urchin development Journal Article

In: Developmental Dynamics, vol. 238, no. 10, pp. 2511–2521, 2009, ISSN: 1097-0177.

Abstract | Links

2008

2.

Hiroshi Ochiai, Naoaki Sakamoto, Kenichi Suzuki, Koji Akasaka, Takashi Yamamoto

The Ars insulator facilitates I‐SceI meganuclease‐mediated transgenesis in the sea urchin embryo Journal Article

In: Developmental Dynamics, vol. 237, no. 9, pp. 2475–2482, 2008, ISSN: 1097-0177.

Abstract | Links

1.

Hiroshi Ochiai, Naoaki Sakamoto, Asuka Momiyama, Koji Akasaka, Takashi Yamamoto

Analysis of cis-regulatory elements controlling spatio-temporal expression of T-brain gene in sea urchin, Hemicentrotus pulcherrimus Journal Article

In: Mechanisms of Development, vol. 125, no. 1-2, pp. 2–17, 2008, ISSN: 0925-4773.

Abstract | Links