@article{Matsumoto2025,

title = {Structural basis of cyclobutane pyrimidine dimer recognition by UV-DDB in the nucleosome},

author = {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},

doi = {10.1038/s41467-025-65486-5},

issn = {2041-1723},

year  = {2025},

date = {2025-11-11},

journal = {Nature Communications},

volume = {16},

number = {1},

publisher = {Springer Science and Business Media LLC},

abstract = {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.},

keywords = {Kurumizaka G},

pubstate = {published},

tppubtype = {article}

}

@article{Yoshimura2025,

title = {Mitotic Phosphorylation of Swi6/HP1 Regulates Its Chromatin Binding and Chromosome Segregation},

author = {Yuriko Yoshimura and Aki Hayashi and Mayo Tanaka and Mieko Suzuki‐Matsubara and Reiko Nakagawa and Gohei Nishibuchi and Hideaki Tagami and Masaya Oki and Jun‐ichi Nakayama},

doi = {10.1096/fj.202500384r},

issn = {1530-6860},

year  = {2025},

date = {2025-11-02},

urldate = {2025-11-15},

journal = {The FASEB Journal},

volume = {39},

number = {21},

publisher = {Wiley},

abstract = {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 HP1α 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.},

keywords = {Nakayama G},

pubstate = {published},

tppubtype = {article}

}

@article{Hatazawa_Takizawa_Kurumizaka_2025,

title = {Preparation of Chromatin Fragments From Human Cells for Cryo‐EM Analysis},

author = {Suguru Hatazawa, Yoshimasa Takizawa, Hitoshi Kurumizaka},

url = {https://bio-protocol.org/en/bpdetail?id=5472&type=0},

doi = {10.21769/BioProtoc.5472},

year  = {2025},

date = {2025-09-17},

urldate = {2025-01-01},

journal = {Bio-protocol},

volume = {15},

number = {20},

pages = {e5472},

abstract = {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–nucleosome interactions, facilitating structural analyses of chromatin organization under near-physiological conditions.},

note = {Available online: Sep 17, 2025},

keywords = {Kurumizaka G},

pubstate = {published},

tppubtype = {article}

}

@article{SHIOI2025103891,

title = {Mechanistic insights into RAD51-mediated nucleosome binding and remodeling in homologous recombination},

author = {Takuro Shioi and Suguru Hatazawa and Yoshimasa Takizawa and Hitoshi Kurumizaka},

url = {https://www.sciencedirect.com/science/article/pii/S1568786425000874},

doi = {https://doi.org/10.1016/j.dnarep.2025.103891},

issn = {1568-7864},

year  = {2025},

date = {2025-09-13},

urldate = {2025-01-01},

journal = {DNA Repair},

pages = {103891},

abstract = {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.},

keywords = {Chromatin, Chromatin remodeler, Cryo-electron microscopy, Homologous recombination, Kurumizaka G, Nucleosome, RAD51},

pubstate = {published},

tppubtype = {article}

}

@article{10.1093/nar/gkaf878,

title = {Intrinsically disordered region of Clr4/Suv39 regulates its enzymatic activity and ensures heterochromatin spreading},

author = {Rinko Nakamura and Aki Hayashi and Reiko Nakagawa and Yuriko Yoshimura and Naoki Horikoshi and Hitoshi Kurumizaka and Jun-ichi Nakayama},

url = {https://doi.org/10.1093/nar/gkaf878},

doi = {10.1093/nar/gkaf878},

issn = {1362-4962},

year  = {2025},

date = {2025-09-09},

urldate = {2025-01-01},

journal = {Nucleic Acids Research},

volume = {53},

number = {17},

pages = {gkaf878},

abstract = {Methylation of histone H3 at lysine 9 (H3K9me), a hallmark of heterochromatin, is catalyzed by Clr4/Suv39. Clr4/Suv39 contains two conserved domains—an N-terminal chromodomain and a C-terminal catalytic domain—connected 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.},

keywords = {Kurumizaka G, Nakayama G},

pubstate = {published},

tppubtype = {article}

}

@article{Matsuda2025,

title = {Organization and Dynamics of Transcription Elongation Foci in Mouse Tissues},

author = {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},

doi = {10.1016/j.jmb.2025.169395},

issn = {0022-2836},

year  = {2025},

date = {2025-08-13},

journal = {Journal of Molecular Biology},

publisher = {Elsevier BV},

abstract = {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.},

keywords = {Kimura G, Ohkawa G},

pubstate = {published},

tppubtype = {article}

}

@article{Mizutani2025,

title = {Growth phase diets diminish histone acetyltransferase Gcn5 function and shorten lifespan of Drosophila males},

author = {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},

doi = {10.1038/s44319-025-00503-8},

issn = {1469-3178},

year  = {2025},

date = {2025-07-10},

journal = {EMBO Rep},

publisher = {Springer Science and Business Media LLC},

abstract = {Abstract

          The nutritional environment in early life, referred to as the nutrition history, exerts far-reaching health effects beyond the developmental stage. Here, with Drosophila melanogaster 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 nat3 KO shortened the lifespan of male adults; and remarkably, this diet diminished the function of histone acetyltransferase Gcn5 in larvae. Concordantly, perturbation of Gcn5-mediated gene regulation in the larval whole body or neurons significantly contributed to the earlier death of adults. The nat3 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 nat3 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.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Fukaya2025,

title = {Multilayered mechanisms for long-range regulatory interactions in eukaryotic transcription},

author = {Takashi Fukaya},

doi = {10.1016/j.jmb.2025.169311},

issn = {0022-2836},

year  = {2025},

date = {2025-06-26},

journal = {Journal of Molecular Biology},

publisher = {Elsevier BV},

abstract = {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 ”Facilitators” and “Range Extenders” dynamically modulate clustering of transcription machineries at specific genomic loci to flexibly control the temporal and spatial dynamics of gene expression during development.},

keywords = {Fukaya G},

pubstate = {published},

tppubtype = {article}

}

@article{10.1038/s41586-025-09063-2,

title = {Maternal iron deficiency causes male-to-female sex reversal in mouse embryos},

author = {Naoki Okashita and Ryo Maeda and Shunsuke Kuroki and Kyona Sasaki and Yoko Uno and Peter Koopman and Makoto Tachibana},

doi = {10.1038/s41586-025-09063-2},

issn = {0028-0836},

year  = {2025},

date = {2025-06-04},

urldate = {2025-01-01},

journal = {Nature},

abstract = {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—which is required for iron incorporation—in 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.},

keywords = {Tachibana G},

pubstate = {published},

tppubtype = {article}

}

@article{https://doi.org/10.1038/s44318-025-00473-6,

title = {Structural basis of RNAPII transcription on the nucleosome containing histone variant H2A.B},

author = {Munetaka Akatsu and Rina Hirano and Tomoya Kujirai and Mitsuo Ogasawara and Haruhiko Ehara and Shun-ichi Sekine and Yoshimasa Takizawa and Hitoshi Kurumizaka},

url = {https://www.embopress.org/doi/abs/10.1038/s44318-025-00473-6},

doi = {https://doi.org/10.1038/s44318-025-00473-6},

year  = {2025},

date = {2025-05-30},

journal = {The EMBO Journal},

abstract = {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.},

keywords = {Chromatin, H2A.B, Histone Variant, Kurumizaka G, Nucleosome, Transcription},

pubstate = {published},

tppubtype = {article}

}

@article{pmid40449591,

title = {Characterization of H3K4me3 in mouse oocytes at the metaphase II stage},

author = {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},

doi = {10.1016/j.jbc.2025.110308},

issn = {1083-351X},

year  = {2025},

date = {2025-05-29},

urldate = {2025-05-01},

journal = {J Biol Chem},

pages = {110308},

abstract = {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.},

keywords = {Miyamoto G, Yamagata G},

pubstate = {published},

tppubtype = {article}

}

@article{10.1038/s41467-025-59580-x,

title = {Multiple structures of RNA polymerase II isolated from human nuclei by ChIP-CryoEM analysis},

author = {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},

doi = {10.1038/s41467-025-59580-x},

year  = {2025},

date = {2025-05-28},

urldate = {2025-01-01},

journal = {Nature Communications},

volume = {16},

number = {1},

pages = {4724},

abstract = {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) −5 in the nucleosome, suggesting that SHL(−5) 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.},

keywords = {Kurumizaka G},

pubstate = {published},

tppubtype = {article}

}

@article{Cheng2025,

title = {Identification and characterization of the de novo methyltransferases for eukaryotic            \textit{N}            ^{6}            -methyladenine (6mA)},

author = {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},

doi = {10.1126/sciadv.adq4623},

issn = {2375-2548},

year  = {2025},

date = {2025-05-16},

urldate = {2025-05-16},

journal = {Sci. Adv.},

volume = {11},

number = {20},

publisher = {American Association for the Advancement of Science (AAAS)},

abstract = {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.},

keywords = {Nakayama G},

pubstate = {published},

tppubtype = {article}

}

@article{HATAZAWA2025103054,

title = {Structural diversity of noncanonical nucleosomes: Functions in chromatin},

author = {Suguru Hatazawa and Naoki Horikoshi and Hitoshi Kurumizaka},

url = {https://www.sciencedirect.com/science/article/pii/S0959440X25000727},

doi = {https://doi.org/10.1016/j.sbi.2025.103054},

issn = {0959-440X},

year  = {2025},

date = {2025-04-30},

urldate = {2025-01-01},

journal = {Current Opinion in Structural Biology},

volume = {92},

pages = {103054},

abstract = {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–H4 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.},

keywords = {Horikoshi G, Kurumizaka G},

pubstate = {published},

tppubtype = {article}

}

@article{Hatazawa2025,

title = {Cryo‐EM Structures of Native Chromatin Units From Human Cells},

author = {Suguru Hatazawa and Yoshiyuki Fukuda and Yuki Kobayashi and Lumi Negishi and Masahide Kikkawa and Yoshimasa Takizawa and Hitoshi Kurumizaka},

url = {https://onlinelibrary.wiley.com/doi/10.1111/gtc.70019},

doi = {10.1111/gtc.70019},

issn = {1365-2443},

year  = {2025},

date = {2025-04-14},

urldate = {2025-04-14},

journal = {Genes to Cells},

volume = {30},

number = {3},

publisher = {Wiley},

abstract = {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‐ and poly‐nucleosomes 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‐ and poly‐nucleosomes were then fractionated by sucrose gradient ultracentrifugation, and their structures were analyzed by cryo‐electron microscopy. Cryo‐electron microscopy single particle analysis and cryo‐electron 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 vitro and in situ analyses of chromatin structure.},

keywords = {Kurumizaka G},

pubstate = {published},

tppubtype = {article}

}

@article{Nozaki2025,

title = {Designer Catalyst-Enabled Regiodivergent Histone Acetylation},

author = {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},

url = {https://pubs.acs.org/doi/full/10.1021/jacs.5c01699},

doi = {10.1021/jacs.5c01699},

issn = {1520-5126},

year  = {2025},

date = {2025-04-13},

urldate = {2025-04-13},

journal = {J. Am. Chem. Soc.},

publisher = {American Chemical Society (ACS)},

abstract = {The “histone code,” 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.},

keywords = {Kawashima G, Kimura G, Kurumizaka G},

pubstate = {published},

tppubtype = {article}

}

@article{Yao2025,

title = {Zinc eluted from glassware is a risk factor for embryo development in human and animal assisted reproduction},

author = {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},

doi = {10.1093/biolre/ioaf050},

issn = {1529-7268},

year  = {2025},

date = {2025-04-02},

urldate = {2025-04-02},

journal = {Biology of Reproduction},

publisher = {Oxford University Press (OUP)},

abstract = {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.},

keywords = {Yamagata G},

pubstate = {published},

tppubtype = {article}

}

@article{Hayashi2025,

title = {Wnt3a is an early regulator of the Wolffian duct directionality via the regulation of apicobasal cell polarity},

author = {Shinichi Hayashi and Hitomi Suzuki and Shinji Takada and Tatsuya Takemoto},

url = {https://www.sciencedirect.com/science/article/pii/S0012160625000776},

doi = {10.1016/j.ydbio.2025.03.015},

issn = {0012-1606},

year  = {2025},

date = {2025-03-27},

journal = {Developmental Biology},

volume = {511},

pages = {136-142},

publisher = {Elsevier BV},

abstract = {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.},

keywords = {Takemoto G},

pubstate = {published},

tppubtype = {article}

}

@article{pmid40129080,

title = {Cryo-EM Analysis of a Unique Subnucleosome Containing Centromere-Specific Histone Variant CENP-A},

author = {Osamu Kawasaki and Yoshimasa Takizawa and Iori Kiyokawa and Hitoshi Kurumizaka and Kayo Nozawa},

doi = {10.1111/gtc.70016},

issn = {1365-2443},

year  = {2025},

date = {2025-03-24},

urldate = {2025-03-01},

journal = {Genes Cells},

volume = {30},

number = {2},

pages = {e70016},

abstract = {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 vitro. We determined the structure of the CENP-A-H4 octasome at 3.66 Å 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.},

keywords = {Kurumizaka G},

pubstate = {published},

tppubtype = {article}

}

@article{Furukawa2025,

title = {A dynamic structural unit of phase-separated heterochromatin protein 1α as revealed by integrative structural analyses},

author = {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},

doi = {10.1093/nar/gkaf154},

issn = {1362-4962},

year  = {2025},

date = {2025-03-20},

urldate = {2025-03-20},

volume = {53},

number = {6},

publisher = {Oxford University Press (OUP)},

abstract = {<jats:title>Abstract</jats:title>

               <jats:p>The heterochromatin protein HP1α 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–liquid phase separation (LLPS) by HP1α. 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 HP1α 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 HP1α 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 HP1α affects the size of heterochromatin foci in cultured mammalian cells, suggesting that this interaction plays an important role in heterochromatin formation in vivo.</jats:p>},

keywords = {Nakayama G},

pubstate = {published},

tppubtype = {article}

}

@article{Naganuma2025,

title = {Structural insights into promoter-proximal pausing of RNA polymerase II at +1 nucleosome},

author = {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},

doi = {10.1126/sciadv.adu0577},

issn = {2375-2548},

year  = {2025},

date = {2025-03-07},

urldate = {2025-03-07},

journal = {Sci. Adv.},

volume = {11},

number = {10},

publisher = {American Association for the Advancement of Science (AAAS)},

abstract = {<jats:p>

            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-β-

            <jats:sc>d</jats:sc>

            -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–electron 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.

          </jats:p>},

keywords = {Kurumizaka G},

pubstate = {published},

tppubtype = {article}

}

@article{Obuse2025,

title = {Functional involvement of RNAs and intrinsically disordered proteins in the assembly of heterochromatin},

author = {Chikashi Obuse and Jun-ichi Nakayama},

doi = {10.1016/j.bbagen.2025.130790},

issn = {0304-4165},

year  = {2025},

date = {2025-03-06},

journal = {Biochimica et Biophysica Acta (BBA) - General Subjects},

publisher = {Elsevier BV},

keywords = {Nakayama G},

pubstate = {published},

tppubtype = {article}

}

@article{10.1038/s41594-025-01493-w,

title = {Structural insights into how DEK nucleosome binding facilitates H3K27 trimethylation in chromatin},

author = {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},

doi = {10.1038/s41594-025-01493-w},

issn = {1545-9993},

year  = {2025},

date = {2025-02-21},

urldate = {2025-02-21},

journal = {Nature Structural & Molecular Biology},

abstract = {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–nucleosome 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–nucleosome 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.},

keywords = {Gotoh G, Kimura G, Kurumizaka G},

pubstate = {published},

tppubtype = {article}

}

@article{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},

author = {Tomoyuki Oya and Mayo Tanaka and Aki Hayashi and Yuriko Yoshimura and Rinko Nakamura and Kyohei Arita and Yota Murakami and Jun‐ichi Nakayama},

doi = {10.1096/fj.202402264RR},

issn = {0892-6638},

year  = {2025},

date = {2025-02-13},

urldate = {2025-01-01},

journal = {The FASEB Journal},

volume = {39},

number = {4},

abstract = {The heterochromatin protein 1 (HP1) family recognizes lysine 9‐methylated 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‐containing 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∆ cells, suggesting that Chp2 is not required for heterochromatin formation when Mit1 is recruited by Swi6. These findings highlight distinct HP1‐binding 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∆ cells. These results provide mechanistic insights into the division of labor among the HP1 family proteins.},

keywords = {Nakayama G},

pubstate = {published},

tppubtype = {article}

}

@article{Horikoshi2025,

title = {Cryo-EM structures of the BAF-Lamin A/C complex bound to nucleosomes},

author = {Naoki Horikoshi and Ryosuke Miyake and Chizuru Sogawa-Fujiwara and Mitsuo Ogasawara and Yoshimasa Takizawa and Hitoshi Kurumizaka},

doi = {10.1038/s41467-025-56823-9},

issn = {2041-1723},

year  = {2025},

date = {2025-02-10},

journal = {Nat Commun},

volume = {16},

number = {1},

publisher = {Springer Science and Business Media LLC},

abstract = {<jats:title>Abstract</jats:title>

          <jats:p>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.</jats:p>},

keywords = {Horikoshi G, Kurumizaka G},

pubstate = {published},

tppubtype = {article}

}

@article{Shigenobu-Ueno2025,

title = {Replication across \textit{O}6-methylguanine activates futile cycling of DNA mismatch repair attempts assisted by the chromatin remodeling enzyme Smarcad1},

author = {Karin Shigenobu-Ueno and Reihi Sakamoto and Eiichiro Kanatsu and Yoshitaka Kawasoe and Tatsuro S Takahashi},

doi = {10.1093/jb/mvaf007},

issn = {1756-2651},

year  = {2025},

date = {2025-01-30},

urldate = {2025-01-30},

journal = {The Journal of Biochemistry},

publisher = {Oxford University Press (OUP)},

abstract = {<jats:title>Abstract</jats:title>

               <jats:p>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–T mispair, but not the meG–C 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.</jats:p>},

keywords = {Takahashi G},

pubstate = {published},

tppubtype = {article}

}

@article{Yamanashi2025,

title = {Chemical catalyst manipulating cancer epigenome and transcription},

author = {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},

doi = {10.1038/s41467-025-56204-2},

issn = {2041-1723},

year  = {2025},

date = {2025-01-24},

journal = {Nat Commun},

volume = {16},

number = {1},

publisher = {Springer Science and Business Media LLC},

abstract = {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.},

keywords = {Kurumizaka G},

pubstate = {published},

tppubtype = {article}

}

@article{Nagamura2024,

title = {Structural insights into how Cas9 targets nucleosomes},

author = {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},

doi = {10.1038/s41467-024-54768-z},

issn = {2041-1723},

year  = {2024},

date = {2024-12-30},

journal = {Nat Commun},

volume = {15},

number = {10744},

publisher = {Springer Science and Business Media LLC},

keywords = {Kurumizaka G},

pubstate = {published},

tppubtype = {article}

}

@article{Hattori2024,

title = {Nutritional Adaptation and Microbes: Insights From Drosophila},

author = {Yukako Hattori},

doi = {10.2108/zs240057},

issn = {0289-0003},

year  = {2024},

date = {2024-12-23},

urldate = {2024-12-23},

journal = {Zoological Science},

volume = {42},

number = {1},

publisher = {Zoological Society of Japan},

keywords = {Hattori G},

pubstate = {published},

tppubtype = {article}

}

@article{Ohishi2024,

title = {Transcription-coupled changes in genomic region proximities during transcriptional bursting},

author = {Hiroaki Ohishi and Soya Shinkai and Hitoshi Owada and Takeru Fujii and Kazufumi Hosoda and Shuichi Onami and Takashi Yamamoto and Yasuyuki Ohkawa and Hiroshi Ochiai},

doi = {10.1126/sciadv.adn0020},

issn = {2375-2548},

year  = {2024},

date = {2024-12-06},

urldate = {2024-12-06},

journal = {Sci. Adv.},

volume = {10},

number = {49},

publisher = {American Association for the Advancement of Science (AAAS)},

abstract = {<jats:p>The orchestration of our genes heavily relies on coordinated communication between enhancers and promoters, yet the mechanisms behind this dynamic interplay during active transcription remain unclear. Here, we investigated enhancer-promoter (E-P) interactions in relation to transcriptional bursting in mouse embryonic stem cells using sequential DNA/RNA/immunofluorescence–fluorescence in situ hybridization analyses. Our data reveal that the active state of specific genes is characterized by specific proximities between different genomic regions and the accumulation of transcriptional regulatory factors. Mathematical simulations suggest that an increase in local viscosity could potentially contribute to stabilizing the duration of these E-P proximities. Our study provides insights into the association among E-P proximity, protein accumulation, and transcriptional dynamics, paving the way for a more nuanced understanding of gene-specific regulatory mechanisms.</jats:p>},

keywords = {Ochiai G, Ohkawa G},

pubstate = {published},

tppubtype = {article}

}

@article{Ding2024,

title = {Proteins and noncoding <scp>RNAs</scp> that promote homologous chromosome recognition and pairing in fission yeast meiosis undergo condensate formation in vitro},

author = {Da‐Qiao Ding and Kasumi Okamasa and Yuriko Yoshimura and Atsushi Matsuda and Takaharu G. Yamamoto and Yasushi Hiraoka and Jun‐ichi Nakayama},

doi = {10.1096/fj.202302563rr},

issn = {1530-6860},

year  = {2024},

date = {2024-11-15},

urldate = {2024-11-15},

journal = {The FASEB Journal},

volume = {38},

number = {21},

publisher = {Wiley},

abstract = {<jats:title>Abstract</jats:title><jats:p>Pairing of homologous chromosomes during meiosis is crucial for successful sexual reproduction. Previous studies have shown that the fission yeast <jats:italic>sme2</jats:italic> RNA, a meiosis‐specific long noncoding RNA (lncRNA), accumulates at the <jats:italic>sme2</jats:italic> locus and plays a key role in mediating robust pairing during meiosis. Several RNA‐binding proteins accumulate at the <jats:italic>sme2</jats:italic> and other lncRNA gene loci in conjunction with the lncRNAs transcribed from these loci. These lncRNA‐protein complexes form condensates that exhibit phase separation properties on chromosomes and are necessary for robust pairing of homologous chromosomes. To further understand the mechanisms by which phase separation affects homologous chromosome pairing, we conducted an in vitro phase separation assay with the <jats:italic>sme2</jats:italic> RNA‐associated proteins (Smps) and RNAs. Our findings reveal that one of the Smps, Seb1, forms condensates resembling phase separation; the observed number and size of these condensates increase upon the addition of another Smp, Rhn1, and purified RNAs. Additionally, we have found that RNAs protect Smp condensates from treatment with 1,6‐hexanediol. The Smp condensates containing different types of RNA display distinct FRAP profiles, and the Smp condensates containing the same type of RNA tend to fuse together more readily than those containing different types of RNAs. Collectively, these results indicate that the specific RNA species within condensates modulate their physical properties, potentially enabling the formation of regional RNA‐Smp condensates with distinct characteristics that facilitate homologous chromosome pairing.</jats:p>},

keywords = {Nakayama G},

pubstate = {published},

tppubtype = {article}

}

@article{Shimizu2024,

title = {Asymmetric fluctuation of overlapping dinucleosome studied by cryo-electron microscopy and small-angle X-ray scattering},

author = {Masahiro Shimizu and Hiroki Tanaka and Masahiro Nishimura and Nobuhiro Sato and Kayo Nozawa and Haruhiko Ehara and Shun-ichi Sekine and Ken Morishima and Rintaro Inoue and Yoshimasa Takizawa and Hitoshi Kurumizaka and Masaaki Sugiyama},

url = {https://academic.oup.com/pnasnexus/advance-article/doi/10.1093/pnasnexus/pgae484/7845919},

doi = {10.1093/pnasnexus/pgae484},

issn = {2752-6542},

year  = {2024},

date = {2024-10-27},

urldate = {2024-10-27},

journal = {PNAS Nexus},

pages = {484},

publisher = {Oxford University Press (OUP)},

abstract = {<jats:title>Abstract</jats:title>

               <jats:p>Nucleosome remodelers modify the local structure of chromatin to release the region from nucleosome-mediated transcriptional suppression. Overlapping dinucleosomes (OLDNs) are nucleoprotein complexes formed around transcription start sites as a result of remodeling, and they consist of two nucleosome moieties: a histone octamer wrapped by DNA (octasome) and a histone hexamer wrapped by DNA (hexasome). While OLDN formation alters chromatin accessibility to proteins, the structural mechanism behind this process is poorly understood. Thus, this study investigated the characteristics of structural fluctuations in OLDNs. First, multiple structures of the OLDN were visualized through cryo-electron microscopy (cryo-EM), providing an overview of the tilting motion of the hexasome relative to the octasome at the near-atomistic resolution. Second, small-angle X-ray scattering (SAXS) revealed the presence of OLDN conformations with a larger radius of gyration than cryo-EM structures. A more complete description of OLDN fluctuation was proposed by SAXS-based ensemble modeling, which included possible transient structures. The ensemble model supported the tilting motion of the OLDN outlined by the cryo-EM models, further suggesting the presence of more diverse conformations. The amplitude of the relative tilting motion of the hexasome was larger, and the nanoscale fluctuation in distance between the octasome and hexasome was also proposed. The cryo-EM models were found to be mapped in the energetically stable region of the conformational distribution of the ensemble. Exhaustive complex modeling using all conformations that appeared in the structural ensemble suggested that conformational and motional asymmetries of the OLDN result in asymmetries in the accessibility of OLDN-binding proteins.</jats:p>},

keywords = {Kurumizaka G},

pubstate = {published},

tppubtype = {article}

}

@article{10.1038/s41598-024-72362-7,

title = {Comprehensive posttranslational modifications in the testis-specific histone variant H3t protein validated in tagged knock-in mice},

author = {Takayuki Kawaguchi and Michihiro Hashimoto and Reiko Nakagawa and Ryunosuke Minami and Masahito Ikawa and Jun-ichi Nakayama and Jun Ueda},

doi = {10.1038/s41598-024-72362-7},

year  = {2024},

date = {2024-09-12},

urldate = {2024-01-01},

journal = {Scientific Reports},

volume = {14},

number = {1},

pages = {21305},

abstract = {During the development of multicellular organisms and cell differentiation, the chromatin structure in the cell nucleus undergoes extensive changes, and the nucleosome structure is formed by a combination of various histone variants. Histone variants with diverse posttranslational modifications are known to play crucial roles in different regulatory functions. We have previously reported that H3t, a testis-specific histone variant, is essential for spermatogenesis. To elucidate the function of this chromatin molecule in vivo, we generated knock-in mice with a FLAG tag attached to the carboxyl terminus of H3t. In the present study, we evaluated the utility of the generated knock-in mice and comprehensively analyzed posttranslational modifications of canonical H3 and H3t using mass spectrometry. Herein, we found that H3t-FLAG was incorporated into spermatogonia and meiotic cells in the testes, as evidenced by immunostaining of testicular tissue. According to the mass spectrometry analysis, the overall pattern of H3t-FLAG posttranslational modification was comparable to that of the control H3, while the relative abundances of certain specific modifications differed between H3t-FLAG and the control bulk H3. The generated knock-in mice could be valuable for analyzing the function of histone variants in vivo.},

keywords = {Nakayama G},

pubstate = {published},

tppubtype = {article}

}

@article{pmid39140385,

title = {Reconstruction of artificial nuclei with nuclear import activity in living mouse oocytes},

author = {Nao Yonezawa and Tomoko Shindo and Haruka Oda and Hiroshi Kimura and Yasushi Hiraoka and Tokuko Haraguchi and Kazuo Yamagata},

doi = {10.1111/gtc.13149},

issn = {1365-2443},

year  = {2024},

date = {2024-08-01},

urldate = {2024-08-01},

journal = {Genes Cells},

abstract = {In eukaryotes, DNA is housed within the cell nucleus. Molecules required for the formation of a nucleus have been identified using in vitro systems with frog egg extracts and in vivo imaging of somatic cells. However, little is known about the physicochemical factors and conditions required for nuclear formation in mouse oocytes. In this study, using a reconstitution approach with purified DNA, we aimed to determine factors, such as the amount and timing of DNA introduction, required for the formation of nuclei with nuclear transport activity in mouse oocytes. T4 phage DNA (~166 kbp) was microinjected into strontium-activated oocytes to evaluate the conditions appropriate for nuclear formation. Microinjection of 100-500 ng/μL of T4 DNA, but not 20 ng/μL, was sufficient for the formation of nucleus-like structures. Furthermore, microinjection of DNA during metaphase II to telophase II, but not during interphase, was sufficient. Electron and fluorescence microscopy showed that T4 DNA-induced nucleus-like structures had nuclear lamina and nuclear pore complex structures similar to those of natural nuclei, as well as nuclear import activity. These results suggest that exogenous DNA can form artificial nuclei with nuclear transport functions in mouse oocytes, regardless of the sequence or source of the DNA.},

keywords = {Kimura G, Yamagata G},

pubstate = {published},

tppubtype = {article}

}

@article{pmid38709169,

title = {ISWI chromatin remodeling complexes recruit NSD2 and H3K36me2 in pericentromeric heterochromatin},

author = {Naoki Goto and Kazuma Suke and Nao Yonezawa and Hidenori Nishihara and Tetsuya Handa and Yuko Sato and Tomoya Kujirai and Hitoshi Kurumizaka and Kazuo Yamagata and Hiroshi Kimura},

doi = {10.1083/jcb.202310084},

issn = {1540-8140},

year  = {2024},

date = {2024-08-01},

urldate = {2024-08-01},

journal = {J Cell Biol},

volume = {223},

number = {8},

abstract = {Histone H3 lysine36 dimethylation (H3K36me2) is generally distributed in the gene body and euchromatic intergenic regions. However, we found that H3K36me2 is enriched in pericentromeric heterochromatin in some mouse cell lines. We here revealed the mechanism of heterochromatin targeting of H3K36me2. Among several H3K36 methyltransferases, NSD2 was responsible for inducing heterochromatic H3K36me2. Depletion and overexpression analyses of NSD2-associating proteins revealed that NSD2 recruitment to heterochromatin was mediated through the imitation switch (ISWI) chromatin remodeling complexes, such as BAZ1B-SMARCA5 (WICH), which directly binds to AT-rich DNA via a BAZ1B domain-containing AT-hook-like motifs. The abundance and stoichiometry of NSD2, SMARCA5, and BAZ1B could determine the localization of H3K36me2 in different cell types. In mouse embryos, H3K36me2 heterochromatin localization was observed at the two- to four-cell stages, suggesting its physiological relevance.},

keywords = {Kimura G, Kurumizaka G, Yamagata G},

pubstate = {published},

tppubtype = {article}

}

@article{pmid38972377,

title = {Cryo-EM structure and biochemical analyses of the nucleosome containing the cancer-associated histone H3 mutation E97K},

author = {Tomoaki Kimura and Seiya Hirai and Tomoya Kujirai and Risa Fujita and Mitsuo Ogasawara and Haruhiko Ehara and Shun-Ichi Sekine and Yoshimasa Takizawa and Hitoshi Kurumizaka},

doi = {10.1111/gtc.13143},

issn = {1365-2443},

year  = {2024},

date = {2024-07-01},

urldate = {2024-07-01},

journal = {Genes Cells},

abstract = {The Lys mutation of the canonical histone H3.1 Glu97 residue (H3E97K) is found in cancer cells. Previous biochemical analyses revealed that the nucleosome containing the H3E97K mutation is extremely unstable as compared to the wild-type nucleosome. However, the mechanism by which the H3E97K mutation causes nucleosome instability has not been clarified yet. In the present study, the cryo-electron microscopy structure of the nucleosome containing the H3E97K mutation revealed that the entry/exit DNA regions of the H3E97K nucleosome are disordered, probably by detachment of the nucleosomal DNA from the H3 N-terminal regions. This may change the intra-molecular amino acid interactions with the replaced H3 Lys97 residue, inducing structural distortion around the mutated position in the nucleosome. Consistent with the nucleosomal DNA end flexibility and the nucleosome instability, the H3E97K mutation exhibited reduced binding of linker histone H1 to the nucleosome, defective activation of PRC2 (the essential methyltransferase for facultative heterochromatin formation) with a poly-nucleosome, and enhanced nucleosome transcription by RNA polymerase II.},

keywords = {Kurumizaka G},

pubstate = {published},

tppubtype = {article}

}

@article{pmid38922969,

title = {Dynamic modulation of enhancer-promoter and promoter-promoter connectivity in gene regulation},

author = {Shiho Makino and Takashi Fukaya},

doi = {10.1002/bies.202400101},

issn = {1521-1878},

year  = {2024},

date = {2024-06-01},

urldate = {2024-06-01},

journal = {Bioessays},

pages = {e2400101},

abstract = {Enhancers are short segments of regulatory DNA that control when and in which cell-type genes should be turned on in response to a variety of extrinsic and intrinsic signals. At the molecular level, enhancers serve as a genomic scaffold that recruits sequence-specific transcription factors and co-activators to facilitate transcription from linked promoters. However, it remains largely unclear how enhancers communicate with appropriate target promoters in the context of higher-order genome topology. In this review, we discuss recent progress in our understanding of the functional interplay between enhancers, genome topology, and the molecular properties of transcription machineries in gene regulation. We suggest that the activities of transcription hubs are highly regulated through the dynamic rearrangement of enhancer-promoter and promoter-promoter connectivity during animal development.},

keywords = {Fukaya G},

pubstate = {published},

tppubtype = {article}

}

@article{pmid38902223,

title = {Plasma cell differentiation is regulated by the expression of histone variant H3.3},

author = {Yuichi Saito and Akihito Harada and Miho Ushijima and Kaori Tanaka and Ryota Higuchi and Akemi Baba and Daisuke Murakami and Stephen L Nutt and Takashi Nakagawa and Yasuyuki Ohkawa and Yoshihiro Baba},

doi = {10.1038/s41467-024-49375-x},

issn = {2041-1723},

year  = {2024},

date = {2024-06-01},

urldate = {2024-06-01},

journal = {Nat Commun},

volume = {15},

number = {1},

pages = {5004},

abstract = {The differentiation of B cells into plasma cells is associated with substantial transcriptional and epigenetic remodeling. H3.3 histone variant marks active chromatin via replication-independent nucleosome assembly. However, its role in plasma cell development remains elusive. Herein, we show that during plasma cell differentiation, H3.3 is downregulated, and the deposition of H3.3 and chromatin accessibility are dynamically changed. Blockade of H3.3 downregulation by enforced H3.3 expression impairs plasma cell differentiation in an H3.3-specific sequence-dependent manner. Mechanistically, enforced H3.3 expression inhibits the upregulation of plasma cell-associated genes such as Irf4, Prdm1, and Xbp1 and maintains the expression of B cell-associated genes, Pax5, Bach2, and Bcl6. Concomitantly, sustained H3.3 expression prevents the structure of chromatin accessibility characteristic for plasma cells. Our findings suggest that appropriate H3.3 expression and deposition control plasma cell differentiation.},

keywords = {Ohkawa G},

pubstate = {published},

tppubtype = {article}

}

@article{10.1038/s41467-024-47989-9,

title = {Precise immunofluorescence canceling for highly multiplexed imaging to capture specific cell states},

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

doi = {10.1038/s41467-024-47989-9},

year  = {2024},

date = {2024-05-08},

urldate = {2024-05-08},

journal = {Nat Commun},

volume = {15},

number = {1},

pages = {3657},

abstract = {Cell states are regulated by the response of signaling pathways to receptor ligand-binding and intercellular interactions. High-resolution imaging has been attempted to explore the dynamics of these processes and, recently, multiplexed imaging has profiled cell states by achieving a comprehensive acquisition of spatial protein information from cells. However, the specificity of antibodies is still compromised when visualizing activated signals. Here, we develop Precise Emission Canceling Antibodies (PECAbs) that have cleavable fluorescent labeling. PECAbs enable high-specificity sequential imaging using hundreds of antibodies, allowing for reconstruction of the spatiotemporal dynamics of signaling pathways. Additionally, combining this approach with seq-smFISH can effectively classify cells and identify their signal activation states in human tissue. Overall, the PECAb system can serve as a comprehensive platform for analyzing complex cell processes. Multiplexed imaging to study cellular pathways can be hampered by lack of antibody specificity, especially when assessing signal activation. Here, the authors present Precise Emission Canceling Antibodies (PECAbs), which enable high-specificity sequential imaging and the study of signaling pathways.},

keywords = {Kimura G, Ochiai G, Ohkawa G},

pubstate = {published},

tppubtype = {article}

}

@article{pmid38762823,

title = {Visualizing histone H4K20me1 in knock-in mice expressing the mCherry-tagged modification-specific intracellular antibody},

author = {Yuko Sato and Maoko Takenoshita and Miku Ueoka and Jun Ueda and Kazuo Yamagata and Hiroshi Kimura},

doi = {10.1007/s00418-024-02296-8},

issn = {1432-119X},

year  = {2024},

date = {2024-05-01},

urldate = {2024-05-01},

journal = {Histochem Cell Biol},

abstract = {During development and differentiation, histone modifications dynamically change locally and globally, associated with transcriptional regulation, DNA replication and repair, and chromosome condensation. The level of histone H4 Lys20 monomethylation (H4K20me1) increases during the G2 to M phases of the cell cycle and is enriched in facultative heterochromatin, such as inactive X chromosomes in cycling cells. To track the dynamic changes of H4K20me1 in living cells, we have developed a genetically encoded modification-specific intracellular antibody (mintbody) probe that specifically binds to the modification. Here, we report the generation of knock-in mice in which the coding sequence of the mCherry-tagged version of the H4K20me1-mintbody is inserted into the Rosa26 locus. The knock-in mice, which ubiquitously expressed the H4K20me1-mintbody, developed normally and were fertile, indicating that the expression of the probe does not disturb the cell growth, development, or differentiation. Various tissues isolated from the knock-in mice exhibited nuclear fluorescence without the need for fixation. The H4K20me1-mintbody was enriched in inactive X chromosomes in developing embryos and in XY bodies during spermatogenesis. The knock-in mice will be useful for the histochemical analysis of H4K20me1 in any cell types.},

keywords = {Kimura G, Yamagata G},

pubstate = {published},

tppubtype = {article}

}