@article{Chudzik2026,

title = {Antibody-trapping presents a widespread pitfall for microscopy and genomics in the nucleus},

author = {Konrad Chudzik and Yuko Sato and Xingchi Yan and Simon Ullrich and Watanya Trakarnphornsombat and Lothar Schermelleh and Geoffrey Fudenberg and Hiroshi Kimura and Michael I Robson and Irina Solovei},

doi = {10.1093/nar/gkag615},

issn = {1362-4962},

year  = {2026},

date = {2026-06-27},

urldate = {2026-06-22},

journal = {Nucleic Acids Research},

volume = {54},

number = {12},

pages = {gkag615},

publisher = {Oxford University Press (OUP)},

abstract = {Chromatin has a complex 3D structure and diverse binding proteins that coordinate the genome's most essential functions. Many microscopy and genomics technologies that map chromatin proteins and modifications rely on the diffusion of antibodies (Abs) to target epitopes within whole nuclei. Here, we reveal a critical flaw in such methods that arises when Abs become trapped at the edge of nuclear structures and fail to reach internally positioned epitopes. This "Ab-trapping" results in artifactual peripheral signal that fundamentally distorts the apparent positions of chromatin features across the genome and nucleus. Using computational modeling and experimental validation, we demonstrate that Ab-trapping is caused by a combination of three compounding factors: high epitope abundance, high Ab affinity, and low Ab diffusion rates. Ab-trapping can thus systematically misrepresent the localization of many prevalent chromatin features like histone modifications, transcription factors, nucleolar proteins, and protein tags. We also show that this artifact manifests in multiple technologies, including immunofluorescence microscopy, more recent CUT&Tag-seq, and likely any method relying on Ab diffusion. Finally, we outline readily implementable strategies to identify and mitigate Ab-trapping. Combined, our work presents a previously unrecognized yet prevalent artifact in Ab-based chromatin mapping methods and the means to resolve it.},

keywords = {Kimura G},

pubstate = {published},

tppubtype = {article}

}

@article{Kato2026,

title = {Locations of consecutive G•C base pairs direct genomic nucleosome positioning},

author = {Hiroaki Kato and Tomohiro Fuse and Shoko Sato and Yohei Kurihara and Wataru Kagawa and Takeshi Urano and Yasuyuki Ohkawa and Hitoshi Kurumizaka and Mitsuhiro Shimizu},

url = {https://genome.cshlp.org/content/36/7/1417},

doi = {10.1101/gr.281372.125},

issn = {1549-5469},

year  = {2026},

date = {2026-06-25},

urldate = {2026-06-25},

journal = {Genome Research},

volume = {36},

issue = {7},

pages = {1417-1428},

publisher = {Cold Spring Harbor Laboratory},

abstract = {The nucleosome is a structural and functional subunit of chromatin, and its positioning in eukaryotic genomes serves as a key platform for gene regulation. Here, we determine the positions of fully wrapped nucleosomes across the yeast genome by chemical mapping through the histone H2A-A122C residue, which cleaves near the DNA entry/exit sites. This approach reveals the most refined sequence-dependent profile of nucleosomes reported to date. Comparisons of the H2A-A122C approach with the H3-Q85C and H4-S47C methods clearly show a sequence preference for the chemical cleavage site. Notably, depletion of CC and GG dinucleotides at nucleotide positions −11 to −9 and +9 to +11 bp, respectively, from the nucleosome dyad position (zero) is consistently accompanied by enrichment of AA/AT/TA/TT dinucleotides in both yeast and mouse genomes. Introducing consecutive C•G base pairs to the corresponding sites in the Widom 601 sequence makes reconstituted nucleosomes more likely to shift into alternative positions without affecting the thermal stability of the nucleosome particle, implying a structural constraint imposed by the DNA sequence. Thus, CC and GG dinucleotides in the major groove blocks, in which the minor groove faces out from the histone octamer, at superhelix locations (SHL) −1.0 and +1.0, respectively, destabilize histone–DNA interactions, serving as intrinsic determinants of nucleosome positioning in eukaryotic genomes.},

keywords = {Kurumizaka G, Ohkawa G},

pubstate = {published},

tppubtype = {article}

}

@article{Chen2026b,

title = {Structural basis of asymmetric transcription through a composite nucleosome formed by a hexasome and an octasome},

author = {Zhihui Chen and Cheng-Han Ho and Hiroki Tanaka and Tomoya Kujirai and Mitsuo Ogasawara and Haruhiko Ehara and Shun-ichi Sekine and Yoshimasa Takizawa and Hitoshi Kurumizaka},

doi = {10.1038/s41594-026-01837-0},

issn = {1545-9985},

year  = {2026},

date = {2026-06-25},

urldate = {2026-06-25},

journal = {Nature Structural & Molecular Biology},

pages = {1-8},

publisher = {Springer Science and Business Media LLC},

abstract = {The overlapping dinucleosome (OLDN), a composite chromatin particle consisting of a hexasome and a canonical octasome, forms immediately downstream of transcription start sites, probably through chromatin remodeling activity, and has been proposed to act as a transient regulatory intermediate during transcription. Nevertheless, how RNA polymerase II (RNAPII) engages with and transcribes through this unusual structure has remained unclear. Here we reconstituted OLDNs in vitro and performed transcription assays with RNAPII. We found that transcription efficiency was markedly higher when RNAPII initiated from the hexasome side than from the octasome side. Cryo-electron microscopy further revealed that transcription from the hexasome side induced pronounced conformational rearrangements, in which RNAPII progression dramatically opened the hexasome-octasome interface. These results identify a mechanism by which RNAPII senses the intrinsic transcriptional polarity of OLDNs and suggest that OLDNs function as dynamic, directionally sensitive regulators of transcription elongation.},

keywords = {Kurumizaka G},

pubstate = {published},

tppubtype = {article}

}

@article{Fukushima2026,

title = {Structural basis of nucleosome remodeling by Cockayne syndrome B homologue Komagataella phaffii Rad26},

author = {Yutaro Fukushima and Chiaki Kinoshita and Lumi Negishi and Tomoya Kujirai and Yuki Kobayashi and Mitsuo Ogasawara and Haruhiko Ehara and Shun-ichi Sekine and Wataru Kagawa and Hitoshi Kurumizaka and Yoshimasa Takizawa},

doi = {10.1038/s41467-026-73500-7},

issn = {2041-1723},

year  = {2026},

date = {2026-06-24},

urldate = {2026-06-24},

journal = {Nat Commun},

volume = {17},

number = {1},

publisher = {Springer Science and Business Media LLC},

abstract = {Rad26, a yeast homologue of mammalian Cockayne syndrome protein B (CSB), plays an essential role in transcription-coupled nucleotide excision repair (TC-NER). Rad26/CSB binds RNA polymerase II stalled at DNA lesions and recruits DNA repair factors, functioning as a molecular scaffold. In addition, Rad26/CSB possesses nucleosome-remodeling activity that may help restore transcription after DNA repair. Here we determine the cryo-electron microscopy structure of the Rad26/CSB-nucleosome complex. Rad26/CSB binds near the nucleosomal entry/exit region (superhelical location ±6) through a unique mechanism in which its ATPase domains, Lobe 1 and Lobe 2, engage nucleosomal DNA in a reverse orientation compared with other remodelers such as Snf2 and Ino80. Mutational, biochemical, and crosslinking mass-spectrometric analyses demonstrate the requirement of the KR loop for nucleosome binding and remodeling. Furthermore, we show that N-terminal auto-inhibition involves long-range contacts between the disordered N-terminus and the Lobe 2 region, and is relieved by mutations of Leu8 and Leu11. These findings reveal the structural basis of Rad26/CSB-mediated nucleosome remodeling in TC-NER.},

keywords = {Kurumizaka G},

pubstate = {published},

tppubtype = {article}

}

@article{Maeda2026,

title = {Dynamic regulation of H3K9 dimethylation drives mouse minor zygotic genome activation},

author = {Ryo Maeda and Shunsuke Kuroki and Hiromi Shimojo and Masahiro Nagano and Masahiro Matsuwaka and Hiroshi Sasaki and Azusa Inoue and Makoto Tachibana},

url = {https://www.nature.com/articles/s41594-026-01811-w},

doi = {10.1038/s41594-026-01811-w},

issn = {1545-9985},

year  = {2026},

date = {2026-05-26},

urldate = {2026-05-26},

journal = {Nat Struct Mol Biol},

publisher = {Springer Science and Business Media LLC},

keywords = {Tachibana G},

pubstate = {published},

tppubtype = {article}

}

@article{YAMAMOTO2026.04.29.721797,

title = {Polymeric mechanism of enhancer-promoter cooperativity in transcriptional bursting},

author = {Tetsuya Yamamoto and Koji Kawasaki and Takashi Fukaya},

url = {https://www.biorxiv.org/content/early/2026/05/02/2026.04.29.721797},

doi = {10.64898/2026.04.29.721797},

year  = {2026},

date = {2026-05-02},

urldate = {2026-05-02},

journal = {bioRxiv},

publisher = {Cold Spring Harbor Laboratory},

abstract = {Emerging evidence suggest that gene expression is controlled though the modulation of transcriptional bursting across species. However, the underlying regulatory mechanisms remain largely uncertain. Recent live-imaging studies have reported that transcription factors (TFs) form a cluster at enhancers just prior to gene activation, thereby locally concentrating the active transcription machinery. This process is thought to be mediated by multivalent interaction between Mediator recruited by TFs. Conversely, transcription itself is also suggested that to influence the assembly of the TF clustering, implicating the presence of a feedback mechanism. To understand the theoretical framework underlying the interplay between TF clustering and transcription, we here develop a polymer micelle model of transcriptional bursting. With this model, multiple RNA polymerase II (Pol II) molecules loaded to the promoter, together with enhancer-bound Mediator, assemble a micelle-like structure due to their connectivity via DNA when the chromatin fiber connecting enhancer and promoter adopts closed conformation, analogous to polysoap micelle. This assembly further recruits freely diffusing Pol II and Mediator in the nucleoplasm even at low concentration up to the optimal size. Our theoretical framework enables quantitative prediction of how dynamic transitions of enhancer-promoter conformation and the stability of the micelle impact the kinetics of transcriptional bursting.Competing Interest StatementThe authors have declared no competing interest.Japan Society for the Promotion of Science, https://ror.org/00hhkn466, 24K06969, 24K18090, 25H02301, 25H00967, 24H02327, 25H02441Japan Science and Technology Agency, https://ror.org/00097mb19, JPMJFR214W, JPMJCR25T2, JPMJAX2327},

keywords = {Fukaya G},

pubstate = {published},

tppubtype = {article}

}

@article{Kawaguchi2026,

title = {ATAC-seq of low-input and cryopreserved primordial germ cells reveals functional enhancers},

author = {Akane Kawaguchi and Mao Igari and Yasuto Murayama and Hiroko Iikawa and Mika Sakamoto and Yasukazu Nakamura and Shigehiro Kuraku and Keisuke Ishihara and Daisuke Saito},

doi = {10.1242/dev.205214},

issn = {1477-9129},

year  = {2026},

date = {2026-05-01},

urldate = {2026-05-01},

journal = {Development},

volume = {153},

number = {9},

publisher = {The Company of Biologists},

abstract = {Dynamic changes in chromatin accessibility at cis-regulatory elements underlie cell fate transitions during development. Primordial germ cells (PGCs) represent a rare population whose chromatin dynamics remain poorly understood compared to known epigenetic landscapes. Here, we utilized the chicken PGC model to bridge this gap, leveraging its capacity for in vitro expansion and in vivo colonization. We adapted the ATAC-seq workflow to obtain reproducible accessible chromatin region (ACR) profiles from as few as 200 cells, even after cryopreservation. Integrative analysis identified over 10,000 PGC-specific ACRs, many absent from somatic tissues, and revealed inherent Tn5 transposase sequence biases in the chicken genome. To validate these ACRs, we established an in vitro PGC differentiation system and utilized in vivo embryonic transplantation. Reporter assays confirmed enhancer activities in cultured PGCs, while transcriptome integration associated these ACRs with genes expressed at embryonic day 2.5. In vivo transplantation demonstrated that these enhancers exhibited early stage-specific activity, becoming silenced upon gonadal settlement. Our results provide a practical strategy for identifying functional regulatory elements from minimal starting material, facilitating the study of chromatin dynamics in rare cell populations.},

keywords = {Kawaguchi G},

pubstate = {published},

tppubtype = {article}

}

@article{Furukawa2026,

title = {Linker histone H1 represses H3 tail acetylation induced by H4 tail acetylation and alters its dynamics},

author = {Ayako Furukawa and Kenta Echigoya and Samuel Blazquez and Masatoshi Wakamori and Hideaki Ohtomo and Yasuo Tsunaka and Takashi Umehara and Tsuyoshi Terakawa and Yoshimasa Takizawa and Hitoshi Kurumizaka and Yoshifumi Nishimura},

doi = {10.1038/s42003-026-09926-y},

issn = {2399-3642},

year  = {2026},

date = {2026-04-09},

journal = {Commun Biol},

volume = {9},

number = {1},

publisher = {Springer Science and Business Media LLC},

abstract = {The nucleosome is the fundamental chromatin unit, containing two copies of histones H2A, H2B, H3, and H4 wrapped by ~ 146 bp of core DNA plus linker DNA; addition of linker histone H1 forms a chromatosome. Tetra-acetylation of the H4 N-terminal tail (H4-4Kac) enhances H3 N-tail acetylation by altering their mutual dynamics, but how H1 influences these dynamics remains unclear. Using cryo-electron microscopy and coarse-grained molecular dynamics simulations, we show that H4-4Kac and unmodified chromatosomes share essentially identical core histone–DNA structures and similar H3 N-tail dynamics. However, nuclear magnetic resonance spectroscopy reveals that in the H4-4Kac chromatosome, the H3 N-tail adopts a dynamically robust DNA-contact state distinct from that in the unmodified chromatosome, resulting in markedly reduced H3 N-tail acetylation. These findings suggest that linker histone H1 suppresses the progression of euchromatin formation.},

keywords = {Kurumizaka G},

pubstate = {published},

tppubtype = {article}

}

@article{Chen2026,

title = {Eye pigmentation–based in-ovo chicken sexing via precision breeding},

author = {Yi-Chen Chen and Shuo-Wen Hsu and Eisuke Shimokita and Tatsuya Takemoto},

doi = {10.3389/fbioe.2026.1785893},

issn = {2296-4185},

year  = {2026},

date = {2026-04-01},

urldate = {2026-04-01},

journal = {Front. Bioeng. Biotechnol.},

volume = {14},

publisher = {Frontiers Media SA},

abstract = {The systematic culling of male layer chicks raises ethical concerns, leading to bans in Germany and other European countries and spurring the search for reliable in-ovo sexing methods. Most existing strategies rely on integration of exogenous DNA or are limited to specific chicken strains, and none meet commercial requirements. Here, we present a broadly applicable in-ovo sexing method that avoids exogenous DNA integration. We developed precision-bred chickens with targeted disruption of the Z-linked SLC45A2 gene, which encodes a transporter essential for pigmentation. Hemizygous knockout females (ZW; SLC45A2KO/W) exhibited eye depigmentation at embryonic day 7 (E7), whereas heterozygous knockout males (ZZ; SLC45A2KO/+) retained normal pigmentation. This clear visual dimorphism enables accurate sexing by routine egg candling. Fertility and reproductive performance of knockouts were comparable to wild-type chickens, and genotyping confirmed 100% prediction accuracy. Unlike many current technologies, our approach requires no complex instrumentation and allows early detection during incubation. This work provides a practical and ethical solution to chick sexing, with significant advantages for commercial hatcheries. More broadly, this study illustrates the potential of precision breeding to address pressing animal welfare concerns in the modern poultry industry.},

keywords = {Takemoto G},

pubstate = {published},

tppubtype = {article}

}

@article{Ho2026b,

title = {Structural basis of RNA polymerase II transcription on the histone H3–H4 octasome},

author = {Cheng-Han Ho and Kayo Nozawa and Masahiro Nishimura and Mayuko Oi and Tomoya Kujirai and Mitsuo Ogasawara and Haruhiko Ehara and Shun-ichi Sekine and Yoshimasa Takizawa and Hitoshi Kurumizaka},

doi = {10.1016/j.jbc.2026.111340},

issn = {0021-9258},

year  = {2026},

date = {2026-03-03},

journal = {Journal of Biological Chemistry},

volume = {302},

number = {4},

publisher = {Elsevier BV},

keywords = {Kurumizaka G},

pubstate = {published},

tppubtype = {article}

}

@article{Nagai2026,

title = {Epithelial cell plasticity in metazoans: Evolutionary insights into roles and mechanisms},

author = {Hiroki Nagai and Yu-ichiro Nakajima},

doi = {10.1016/j.semcdb.2026.103670},

issn = {1084-9521},

year  = {2026},

date = {2026-03-03},

journal = {Seminars in Cell & Developmental Biology},

volume = {179-180},

publisher = {Elsevier BV},

abstract = {Epithelial tissues function as multicellular communities that preserve tissue integrity while adapting to diverse environmental stresses by altering cell behaviors. A striking manifestation of such adaptability is cell plasticity, the ability of differentiated cells to revert to stem-like states or adopt alternative fates. Once considered rare and confined to highly regenerative species, cell plasticity is now recognized across the metazoan tree. In early-branching animals such as sponges and cnidarians, transdifferentiation and dedifferentiation are integral to life-cycle transitions and regeneration, whereas in more complex organisms, these processes typically emerge under stress, including stem cell loss or environmental perturbations. Here, we examine epithelial cell plasticity through evolutionary, cellular, and molecular perspectives. Focusing on the intestinal epithelium, we explore findings from mammalian and Drosophila models showing that progenitors and even terminally differentiated cells can dedifferentiate in response to external stimuli that disrupt homeostasis, such as pathogen infection and nutrient fluctuations. We further discuss conserved mechanisms involving intercellular signaling (e.g., Notch, EGFR, and JAK-STAT) and chromatin states primed for reprogramming, modulated by metabolic cues. Together, these insights position cell plasticity as an ancient environmental adaptation strategy, shaped by conserved molecular toolkits and refined by species- and cell lineage-specific innovations.},

keywords = {Nakajima G},

pubstate = {published},

tppubtype = {article}

}

@article{Saito2026,

title = {Decoding the molecular logic of rapidly evolving ZAD zinc finger proteins in                    \textit{Drosophila}},

author = {Raku Saito and Yusuke Umemura and Shiho Makino and Takashi Fukaya},

doi = {10.1126/sciadv.ady7568},

issn = {2375-2548},

year  = {2026},

date = {2026-02-27},

urldate = {2026-02-27},

journal = {Sci. Adv.},

volume = {12},

number = {9},

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

abstract = {The zinc finger–associated domain (ZAD)–containing C2H2 zinc finger proteins (ZAD-ZnFs) represent the most abundant class of transcription factors that emerged during insect evolution, yet their molecular diversity and biological functions remain largely unclear. Here, we established a systematic CRISPR-based protein-tagging approach that enables direct, unambiguous comparison of nuclear localization and genome-wide binding profiles of endogenous ZAD-ZnFs in developing Drosophila embryos. Evidence is provided that a subset of ZAD-ZnFs forms nuclear condensates through the stacking of the N-terminal ZAD dimerization surface. Disruption of condensation activity leads to misregulation of genome-wide binding profiles and lethality, underscoring its functional and physiological significance in development. Integrative chromatin immunoprecipitation sequencing and Micro-C analyses reveal that many ZAD-ZnFs colocalize with core insulator proteins such as CCCTC-binding factor and Centrosomal protein 190 kD to control the formation of topological boundaries. We suggest that the diverse molecular functions of ZAD-ZnFs have evolutionarily arisen from their ancestral role as insulator-binding proteins.},

keywords = {Fukaya G},

pubstate = {published},

tppubtype = {article}

}

@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{Gao2026.02.08.704500,

title = {Minute-scale coupling of chromatin marks and transcriptional bursts},

author = {Xiaohui Gao and Chaebeen Ko and Yuanchao Dong and Takeru Fujii and Satoshi Uchino and Yoshiaki Kobayashi and Akihito Harada and Hiroaki Ohishi and Yasuyuki Ohkawa and Hiroshi Kimura and Hiroshi Ochiai},

url = {https://www.biorxiv.org/content/early/2026/02/10/2026.02.08.704500},

doi = {10.64898/2026.02.08.704500},

year  = {2026},

date = {2026-02-10},

urldate = {2026-01-01},

journal = {bioRxiv},

publisher = {Cold Spring Harbor Laboratory},

abstract = {Histone modifications are often described as stable epigenetic marks that contribute to maintaining gene-expression programs during development and environmental responses. However, transcription of many genes is intermittent, switching between transcriptionally active and inactive episodes within minutes. Whether chromatin marks around individual genes change on these rapid timescales remains unclear. Here we show that local chromatin modification signals around endogenous genes in mouse embryonic stem cells fluctuate reversibly with transcriptional state, using live imaging of individual genes together with fluorescent probes that report histone modifications. Activation-associated acetylation and methylation marks increased in association with transcriptional activation and decreased with inactivation, whereas a Polycomb-associated repressive mark behaved oppositely. Transcriptional coactivators and both histone acetyltransferase and deacetylase complexes were enriched during transcriptionally active state, consistent with opposing enzymatic activities shaping local acetylation levels. Inhibiting histone deacetylases altered the durations of active and inactive events, supporting a role for deacetylation in regulating transcriptional state transitions. Thus, histone modifications undergo reversible, minute-scale changes coupled to transcriptional activity. This framework helps explain how stochastic transcriptional bursts can occur with stable gene regulation over longer timescales.},

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

pubstate = {published},

tppubtype = {article}

}

@article{Umemura2026.02.03.703437,

title = {The Drosophila ZAD zinc finger protein Mulberry shapes the organization of the regulatory genome in the early embryo},

author = {Yusuke Umemura and Takashi Fukaya},

url = {https://www.biorxiv.org/content/early/2026/02/05/2026.02.03.703437},

doi = {10.64898/2026.02.03.703437},

year  = {2026},

date = {2026-02-05},

urldate = {2026-01-01},

journal = {bioRxiv},

publisher = {Cold Spring Harbor Laboratory},

abstract = {Long-range regulatory interactions play a fundamentally important role in the control of gene activity during animal development, yet the underlying mechanisms remain largely unclear. Here, we identified a zinc finger-associated domain (ZAD)-C2H2 zinc finger protein, CG31365/Mulberry, as a looping factor that mediates long-range tethering activity in the early Drosophila embryo. Evidence is provided that Mulberry is specifically recruited to a subset of loop anchors and topological boundaries at key developmental loci to shape genome organization and gene activity. Super-resolution imaging analysis revealed that Mulberry forms nuclear condensates that associate with its target loci through the structured N-terminal ZAD domain. Micro-C analysis further demonstrated that the formation of loops and boundaries is lost in the condensation-deficient Mulberry mutant in a locus-specific manner. We propose that Mulberry acts as a condensation-dependent structural regulator of genome topology, organizing "multi-way regulatory hubs" that mediate long-range gene activation during early embryogenesis.},

keywords = {Fukaya G},

pubstate = {published},

tppubtype = {article}

}

@article{Tanaka2025,

title = {Structure and evolution of the sequence-specific anti-silencing factor VANC21 and its target DNA},

author = {Yusaku Tanaka and Akihisa Osakabe and Wataru Shihoya and Hisato Hirano and Yuzuru Itoh and Tetsuji Kakutani and Osamu Nureki},

doi = {10.1266/ggs.25-00096},

issn = {1880-5779},

year  = {2026},

date = {2026-02-03},

journal = {Genes Genet. Syst.},

publisher = {Genetics Society of Japan},

abstract = {VANDAL family DNA transposons are prevalent in Arabidopsis and related plants. A notable feature of VANDALs is that they can overcome epigenetic silencing from the host, using a VANC protein encoded in each VANDAL member: VANC21 protein encoded in VANDAL21 specifically accumulates on its target DNA motifs that are concentrated in the non-coding regions of this TE and induces loss of DNA methylation, transcriptional derepression, and mobilization of the element. In this study, to elucidate the mechanism of how VANC subtypes have diverged to bind specifically to their own target motifs in their cognate VANDAL subfamilies, we determined the crystal structure of VANC21 in complex with its target DNA at 2.0 Å resolution. The VANC structure adopts a globular novel fold with a Zn ion coordinated at the DNA-binding site. Interestingly, most DNA-interacting VANC residues are located in the loops but not in the conserved regions among VANC subtypes. This observation suggests that the high variability of DNA-interacting regions of VANC proteins brought about the co-evolution of VANCs and their target sequences. This rapid differentiation by co-evolution enabled VANDAL family TEs to proliferate while avoiding deleterious effects on host fitness. Therefore, our findings help to understand the adaptive evolutionary strategy for the survival of parasitic sequences.},

keywords = {Osakabe 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{Galindo2026,

title = {AI-assisted protein design to rapidly convert antibody sequences to intrabodies targeting diverse peptides and histone modifications},

author = {Gabriel Galindo and Daiki Maejima and Jacob DeRoo and Scott R. Burlingham and Gretchen Fixen and Tatsuya Morisaki and Hallie P. Febvre and Ryan Hasbrook and Ning Zhao and Soham Ghosh and E. Handly Mayton and Christopher D. Snow and Brian J. Geiss and Yasuyuki Ohkawa and Yuko Sato and Hiroshi Kimura and Timothy J. Stasevich},

doi = {10.1126/sciadv.adx8352},

issn = {2375-2548},

year  = {2026},

date = {2026-01-02},

urldate = {2026-01-02},

journal = {Sci. Adv.},

volume = {12},

number = {1},

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

abstract = {Intrabodies are engineered antibodies that function inside living cells, enabling therapeutic, diagnostic, and imaging applications. While powerful, their development has been hindered by challenges associated with their folding, solubility, and stability in the reduced intracellular environment. Here, we present an artificial intelligence-driven pipeline integrating AlphaFold2, ProteinMPNN, and live-cell screening to optimize antibody framework regions while preserving epitope-binding complementarity-determining regions. Using this approach, we successfully converted 19 of 26 antibody sequences into functional single-chain variable fragment intrabodies, including a panel targeting diverse histone modifications for real-time imaging of chromatin dynamics and gene regulation. Notably, 18 of these 19 sequences had failed to convert using the standard approach, demonstrating the unique effectiveness of our method. As antibody sequence databases expand, our method will accelerate intrabody design, making their development easier, more cost effective, and broadly accessible for biological research.},

keywords = {Kimura G, Ohkawa G},

pubstate = {published},

tppubtype = {article}

}

@article{Maehara2025,

title = {Geometry-preserving vector field reconstruction of high-dimensional cell-state dynamics using ddHodge},

author = {Kazumitsu Maehara and Yasuyuki Ohkawa},

doi = {10.1038/s41467-025-67782-6},

issn = {2041-1723},

year  = {2025},

date = {2025-12-29},

journal = {Nat Commun},

volume = {16},

number = {1},

publisher = {Springer Science and Business Media LLC},

abstract = {The differentiation potency of cells is governed by dynamic changes in gene expression, which can be inferred from single-cell RNA sequencing (scRNA-seq) data. While velocity-based approaches have been used to analyze cell state changes as vector fields, extracting acceleration (change of change) information remains challenging because of the sparsity and high-dimensionality of the data. Here, we develop ddHodge, a framework based on Hodge decomposition for precise vector-field reconstruction. ddHodge accurately recovers all basic components of the vector field, namely, the gradient, curl, and divergence, including the acceleration of the cell state, as second-order derivatives, even from biased and sparse samples. Furthermore, we extend the method to approximate high-dimensional gene expression dynamics on lower-dimensional data manifolds. By applying ddHodge to scRNA-seq data from mouse embryogenesis, we reveal that the gene expression dynamics during development follow a gradient system shaped by potential landscapes, which has not previously been validated with real data. Furthermore, we quantify differentiation potency as cell state stability on the basis of the divergence and identify key genes that drive potency. Our general computational framework for analyzing complex biological systems can elucidate cell fate decisions in developmental processes.},

keywords = {Ohkawa 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{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}

}