@article{Hamano2026,

title = {ImmuBubbles: Antibody-Shelled Gas-Core Nanobubbles as Ultrasound Contrast Agents},

author = {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},

doi = {10.1021/acsanm.5c05403},

issn = {2574-0970},

year  = {2026},

date = {2026-02-11},

urldate = {2026-02-11},

journal = {ACS Appl. Nano Mater.},

publisher = {American Chemical Society (ACS)},

abstract = {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–liquid interface, forming shells without lipid incorporation. Herceptin-shelled IBs (Her-IBs) were uniform (∼95 nm) and positively charged (ζ ≈ + 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–guided interventions in solid tumors and tissues protected by restrictive biological barriers, including the central nervous system.},

keywords = {Kurumizaka G},

pubstate = {published},

tppubtype = {article}

}

@article{<LineBreak>doi:10.1126/sciadv.aed1952,

title = {Structural basis of transcription-coupled H3K36 trimethylation by Set2 in coordination with FACT},

author = {Tomoya Kujirai and Haruhiko Ehara and Tomoko Ito and Masami Henmi and Eriko Oya and Takehiko Kobayashi and Shun-ichi Sekine and Hitoshi Kurumizaka},

url = {https://www.science.org/doi/abs/10.1126/sciadv.aed1952},

doi = {10.1126/sciadv.aed1952},

year  = {2026},

date = {2026-01-28},

urldate = {2026-01-01},

journal = {Science Advances},

volume = {12},

number = {5},

pages = {eaed1952},

abstract = {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–electron 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.},

keywords = {Kurumizaka G},

pubstate = {published},

tppubtype = {article}

}

@article{Horikoshi2026,

title = {Nucleosome Bundling by Barrier‐to‐Autointegration Factor: Implications for Its Diverse Functions},

author = {Naoki Horikoshi and Hitoshi Kurumizaka},

doi = {10.1002/bies.70104},

issn = {1521-1878},

year  = {2026},

date = {2026-01-22},

journal = {BioEssays},

volume = {48},

number = {1},

publisher = {Wiley},

abstract = {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.},

keywords = {Horikoshi G, Kurumizaka G},

pubstate = {published},

tppubtype = {article}

}

@article{Fujii2025,

title = {Reconstructing epigenomic dynamics through a single-cell multi-epigenome data integration framework},

author = {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},

doi = {10.1038/s41467-025-67016-9},

issn = {2041-1723},

year  = {2025},

date = {2025-12-17},

journal = {Nat Commun},

volume = {16},

number = {1},

publisher = {Springer Science and Business Media LLC},

abstract = {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.},

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

pubstate = {published},

tppubtype = {article}

}

@article{Ho2026,

title = {A method for cryo-EM analysis of eukaryotic nucleosomes reconstituted in bacterial cells},

author = {Cheng-Han Ho and Yuki Kobayashi and Mitsuo Ogasawara and Yoshimasa Takizawa and Hitoshi Kurumizaka},

doi = {10.1016/j.isci.2025.114453},

issn = {2589-0042},

year  = {2025},

date = {2025-12-15},

journal = {iScience},

volume = {29},

number = {1},

publisher = {Elsevier BV},

abstract = {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 Å 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.},

keywords = {Kurumizaka G},

pubstate = {published},

tppubtype = {article}

}

@article{Fukai2025,

title = {Gene-scale in vitro reconstitution reveals histone acetylation directly controls chromatin architecture},

author = {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},

doi = {10.1126/sciadv.adx9282},

issn = {2375-2548},

year  = {2025},

date = {2025-11-21},

urldate = {2025-11-21},

journal = {Sci. Adv.},

volume = {11},

number = {47},

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

abstract = {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.},

keywords = {Kurumizaka G},

pubstate = {published},

tppubtype = {article}

}

@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{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{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{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{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{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{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{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{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{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{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{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}

}