細胞核・クロマチン構造のダイナミクスと遺伝子制御

• Project Area: Chromatin potential for gene regulation
• Project/Area Number: 18H05527
• Research Category: Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)
• Allocation Type: Single-year Grants
• Review Section: Biological Sciences
• Research Institution: Tokyo Institute of Technology
• Principal Investigator: 木村 宏 東京工業大学, 科学技術創成研究院, 教授 (30241392)
• Co-Investigator(Kenkyū-buntansha): 伊藤 由馬 東京工業大学, 生命理工学院, 助教 (70803245) ; 大川 恭行 九州大学, 生体防御医学研究所, 教授 (80448430)
• Project Period (FY): 2018-06-29 – 2023-03-31
• Project Status: Granted (Fiscal Year 2022)
• Budget Amount: ¥235,690,000 (Direct Cost: ¥181,300,000、Indirect Cost: ¥54,390,000); Fiscal Year 2022: ¥46,150,000 (Direct Cost: ¥35,500,000、Indirect Cost: ¥10,650,000); Fiscal Year 2021: ¥46,150,000 (Direct Cost: ¥35,500,000、Indirect Cost: ¥10,650,000); Fiscal Year 2020: ¥46,150,000 (Direct Cost: ¥35,500,000、Indirect Cost: ¥10,650,000); Fiscal Year 2019: ¥46,150,000 (Direct Cost: ¥35,500,000、Indirect Cost: ¥10,650,000); Fiscal Year 2018: ¥51,090,000 (Direct Cost: ¥39,300,000、Indirect Cost: ¥11,790,000)
• Keywords: クロマチン / 遺伝子発現 / エピジェネティクス制御 / ヒストン / 転写制御 / 細胞核 / 遺伝子発現制御 / エピジェネティクス / ヒストン修飾

Outline of Annual Research Achievements

遺伝子がクロマチンの構造変化を経て転写される基本的なメカニズムを理解するためには、細胞内で刻々と変化するクロマチン状態と転写のダイナミクスを明らかにする必要がある。本研究は、生細胞解析と少数細胞エピゲノム解析により、転写活性化のされやすさ（ポテンシャル）という観点から、ヒストン修飾を介したクロマチン構造の機能を明らかにすること目的に行っている。
（1）遺伝子活性化に働くクロマチン構造と動態の解析：ゼブラフィッシュ胚性ゲノム活性化（ZGA; zygotic genome activation）に着目し、単一胚の転写伸長型（Ser2リン酸化型）RNAポリメラーゼII（RNAP2Ser2ph）とヒストンH3K27アセチル化修飾の局在を明らかにするために、クロマチン挿入標識法（ChIL）を行い、データ解析を行っている。
（2）遺伝子発現変動に働くクロマチン構造の解析：EGFP-RNAP2をノックインした細胞を用いて、RNAP2が濃縮する凝集体の動態を解析した。RNAP2凝集体は細胞周期のS期にヒストンローカスボディやカハルボディの近傍に形成されることを明らかにした。
RNAP2Ser2ph特異的な遺伝子コード型プローブ（RNAP2Ser2ph-mintbody）を開発し、転写伸長部位と転写関連タンパク質との局在比較、及び、転写伸長部位の生細胞動態を解析した。RNAP2Ser2ph-mintbody部位には、転写の開始や伸長への移行に働くタンパク質はあまり局在化しなかったのに対して、転写伸長に働くタンパク質の局在化が見られた。また、RNAP2Ser2ph-mintbody部位は、クロマチン比べてより動く様子が観察された。
（3）遺伝子発現安定化状態でのクロマチン構造と動態の解析：終末分化状態のクロマチン構造を明らかにするため、各種ヒストン修飾抗体で分化細胞を染色した。

Current Status of Research Progress

2: Research has progressed on the whole more than it was originally planned.

Reason

（1）遺伝子活性化に働くクロマチン構造と動態の解析：単一胚のChIL解析に関して、解析手法をほぼ確立し、データ解析を進めている。
（2）遺伝子発現変動に働くクロマチン構造の解析：生細胞の転写動態に関しては、RNAP2凝集体の生細胞動態を明らかにし、さらに、RNAP2Ser2ph-mintbodyを用いた動態を明らかにするなど、研究は順調に進んでいる。
（3）遺伝子発現安定化状態でのクロマチン構造と動態の解析：終末分化細胞解析のためのノックイン動物の作製にはまだ至っておらず、引き続き進める必要がある。
全体的には、予定どおり進展している。

Strategy for Future Research Activity

（1）遺伝子活性化に働くクロマチン構造と動態の解析：ゼブラフィッシュ胚を用いた生細胞動態解析とChIL解析が順調に進んでおり、引き続き進めていく。
（2）遺伝子発現変動に働くクロマチン構造の解析：Mintbody発現細胞を用いて、転写活性化と抑制に伴うクロマチン構造の変化を明らかにする。
（3）遺伝子発現安定化状態でのクロマチン構造と動態の解析：終末分化細胞解析のためのノックイン動物の作製を引き続き進めつつ、in vitro分化系を用いた解析も進めていく。

Research Products

• [Int'l Joint Research] European Moleclar Biology Laboratory/Max Planck Institute-CBG/Karlsruhe Institute of Technology(ドイツ)
• [Int'l Joint Research] University of Copenhagen(デンマーク)
• [Int'l Joint Research] University of Cambridge/Crick Institute(英国)
• [Int'l Joint Research] Colorado State University(米国)
• [Int'l Joint Research] New York University/Colorado State University/Florida State University(米国)
• [Int'l Joint Research] Cambridge University/New Castle University(英国)
• [Int'l Joint Research] EMBL/Max Panck Institute, Dresden/Karlsruhe Institute of Technology(ドイツ)
• [Int'l Joint Research] Colorado State University/HHMI Janelia Research Campus(米国)
• [Int'l Joint Research] Cambridge University(英国)
• [Int'l Joint Research] MPI - Molecular Cell Biology & Genetics/Karlsruhe Institute of Technology/EMBL(ドイツ)
• [Int'l Joint Research] Curie Insitute(フランス)
• [Journal Article] Simple Fluorogenic Cellular Assay for Histone Deacetylase Inhibitors Based on Split-Yellow Fluorescent Protein and Intrabodies (2021)
  • Author(s): Ohmuro-Matsuyama Yuki、Kitaguchi Tetsuya、Kimura Hiroshi、Ueda Hiroshi
  • Journal Title: ACS Omega Volume: 6 Pages: 10039-10046
  • DOI: 10.1021/acsomega.0c06281
  • NAID: 120007034011
  • Peer Reviewed / Open Access
• [Journal Article] Structural basis of nucleosomal histone H4 lysine 20 methylation by SET8 methyltransferase (2021)
  • Author(s): Ho Cheng-Han、Takizawa Yoshimasa、Kobayashi Wataru、Arimura Yasuhiro、Kimura Hiroshi、Kurumizaka Hitoshi
  • Journal Title: Life Science Alliance Volume: 4
  • DOI: 10.26508/lsa.202000919
  • Peer Reviewed / Open Access
• [Journal Article] RNA polymerase II condensate formation and association with Cajal and histone locus bodies in living human cells (2021)
  • Author(s): Imada Takashi、Shimi Takeshi、Kaiho Ai、Saeki Yasushi、Kimura Hiroshi
  • Journal Title: Genes to Cells Volume: -
  • DOI: 10.1111/gtc.12840
  • Peer Reviewed / Open Access
• [Journal Article] H4K20me1 and H3K27me3 are concurrently loaded onto the inactive X chromosome but dispensable for inducing gene silencing (2021)
  • Author(s): Tjalsma Sjoerd J D、Hori Mayako、Sato Yuko、Bousard Aurelie、Ohi Akito、Raposo Ana Claudia、Roensch Julia、Le Saux Agnes、Nogami Jumpei、Maehara Kazumitsu、Kujirai Tomoya、Handa Tetsuya、Bages‐Arnal Sandra、Ohkawa Yasuyuki、Kurumizaka Hitoshi、da Rocha Simao Teixeira、Zylicz Jan J、Kimura Hiroshi、Heard Edith
  • Journal Title: EMBO reports Volume: 22
  • DOI: 10.15252/embr.202051989
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Dynamics of transcription-mediated conversion from euchromatin to facultative heterochromatin at the Xist promoter by Tsix (2021)
  • Author(s): Ohhata Tatsuya、Yamazawa Kazuki、Miura-Kamio Asuka、Takahashi Saori、Sakai Satoshi、Tamura Yuka、Uchida Chiharu、Kitagawa Kyoko、Niida Hiroyuki、Hiratani Ichiro、Kobayashi Hisato、Kimura Hiroshi、Wutz Anton、Kitagawa Masatoshi
  • Journal Title: Cell Reports Volume: 34 Pages: 108912-108912
  • DOI: 10.1016/j.celrep.2021.108912
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Live-cell epigenome manipulation by synthetic histone acetylation catalyst system (2021)
  • Author(s): Fujiwara Yusuke、Yamanashi Yuki、Fujimura Akiko、Sato Yuko、Kujirai Tomoya、Kurumizaka Hitoshi、Kimura Hiroshi、Yamatsugu Kenzo、Kawashima Shigehiro A.、Kanai Motomu
  • Journal Title: Proceedings of the National Academy of Sciences Volume: 118
  • DOI: 10.1073/pnas.2019554118
  • Peer Reviewed
• [Journal Article] Genome-wide analysis of chromatin structure changes upon MyoD binding in proliferative myoblasts during the cell cycle. (2021)
  • Author(s): Qianmei Wu, Takeru Fujii, Akihito Harada, Kosuke Tomimatsu, Atsuko Miyawaki-Kuwakado, Masatoshi Fujita, Kazumitsu Maehara, Yasuyuki Ohkawa.
  • Journal Title: The Journal of Biochemistry Volume: －
  • DOI: 10.1093/jb/mvab001
  • NAID: 40022687719
  • Peer Reviewed / Open Access
• [Journal Article] Transcription organizes euchromatin via microphase separation (2021)
  • Author(s): Hilbert Lennart、Sato Yuko、Kuznetsova Ksenia、Bianucci Tommaso、Kimura Hiroshi、Julicher Frank、Honigmann Alf、Zaburdaev Vasily、Vastenhouw Nadine L.
  • Journal Title: Nature Communications Volume: 12 Pages: 1360-1360
  • DOI: 10.1038/s41467-021-21589-3
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Variable immersion microscopy with a high numerical aperture (2021)
  • Author(s): Keita Ishida, Kanta Naruse, Yuta Mizouchi, Yoshihiro Ogawa, Michio Matsushita, Takeshi Shimi, Hiroshi Kimura, Satoru Fujiyoshi
  • Journal Title: Optics Letters Volume: 46 Pages: 856-856
  • DOI: 10.1364/ol.416006
  • Peer Reviewed
• [Journal Article] Visualizing transcription sites in living cells using a genetically encoded probe specific for the elongating form of RNA polymerase II (2021)
  • Author(s): Uchino Satoshi、Ito Yuma、Sato Yuko、Handa Tetsuya、Ohkawa Yasuyuki、Tokunaga Makio、Kimura Hitoshi
  • Journal Title: bioRxiv Volume: - Pages: 441582-441582
  • DOI: 10.1101/2021.04.27.441582
  • Open Access
• [Journal Article] Discriminative feature of cells characterizes cell populations of interest by a small subset of genes (2021)
  • Author(s): Fujii Takeru、Maehara Kazumitsu、Fujita Masatoshi、Ohkawa Yasuyuki
  • Journal Title: bioRxiv Volume: - Pages: 435089-435089
  • DOI: 10.1101/2021.03.12.435089
  • Open Access
• [Journal Article] Cohesin and condensin extrude DNA loops in a cell cycle-dependent manner (2020)
  • Author(s): Golfier Stefan、Quail Thomas、Kimura Hiroshi、Brugues Jan
  • Journal Title: eLife Volume: 9
  • DOI: 10.7554/elife.53885
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Transcription-dependent cohesin repositioning rewires chromatin loops in cellular senescence (2020)
  • Author(s): Olan Ioana、Parry Aled J.、Schoenfelder Stefan、Narita Masako、Ito Yoko、Chan Adelyne S. L.、Slater Guy St.C.、Bihary Dora、Bando Masashige、Shirahige Katsuhiko、Kimura Hiroshi、Samarajiwa Shamith A.、Fraser Peter、Narita Masashi
  • Journal Title: Nat Commun Volume: 11 Pages: 6049-6049
  • DOI: 10.1038/s41467-020-19878-4
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Single-molecule imaging reveals control of parental histone recycling by free histones during DNA replication (2020)
  • Author(s): Gruszka D. T.、Xie S.、Kimura H.、Yardimci H.
  • Journal Title: Science Advances Volume: 6
  • DOI: 10.1126/sciadv.abc0330
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Histone modification dynamics as revealed by multicolor immunofluorescence-based single-cell analysis (2020)
  • Author(s): Hayashi-Takanaka Yoko、Kina Yuto、Nakamura Fumiaki、Becking Leontine E.、Nakao Yoichi、Nagase Takahiro、Nozaki Naohito、Kimura Hiroshi
  • Journal Title: Journal of Cell Science Volume: 133
  • DOI: 10.1242/jcs.243444
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Genome-wide kinetic properties of transcriptional bursting in mouse embryonic stem cells (2020)
  • Author(s): Ochiai Hiroshi、Hayashi Tetsutaro、Umeda Mana、Yoshimura Mika、Harada Akihito、Shimizu Yukiko、Nakano Kenta、Saitoh Noriko、Liu Zhe、Yamamoto Takashi、Okamura Tadashi、Ohkawa Yasuyuki、Kimura Hiroshi、Nikaido Itoshi
  • Journal Title: Sci Adv Volume: 6
  • DOI: 10.1126/sciadv.aaz6699
  • Peer Reviewed / Open Access
• [Journal Article] Genomic Profiling by ALaP-Seq Reveals Transcriptional Regulation by PML Bodies through DNMT3A Exclusion (2020)
  • Author(s): Misuzu Kurihara, Kagayaki Kato, Chiaki Sanbo, Yasuyuki Ohkawa, Takeshi Fuchigami, Yusuke Miyanari
  • Journal Title: Molecular Cell Volume: 78 Pages: 493-505
  • DOI: 10.1016/j.molcel.2020.04.004
  • Peer Reviewed / Open Access
• [Journal Article] Physics of chromatin dynamics at the 57th Biophysical Society of Japan meeting. (2020)
  • Author(s): Yuma Ito、Akatsuki Kimura
  • Journal Title: Biophysical Reviews Volume: - Pages: 265-266
  • DOI: 10.1007/s12551-020-00642-3
  • Peer Reviewed / Open Access
• [Journal Article] Modeling population size independent tissue epigenomes by ChIL-seq with single-thin sections (2020)
  • Author(s): Maehara Kazumitsu、Tomimatsu Kosuke、Harada Akihito、Tanaka Kaori、Sato Shoko、Okada Seiji、Handa Tetsuya、Kurumizaka Hitoshi、Kimura Hiroshi、Ohkawa Yasuyuki
  • Journal Title: bioRxiv Volume: - Pages: 423434-423434
  • DOI: 10.1101/2020.12.18.423434
  • Open Access
• [Journal Article] Live-cell imaging reveals the spatiotemporal organization of endogenous RNA polymerase II phosphorylation at a single gene (2020)
  • Author(s): Forero-Quintero Linda S.、Raymond William、Handa Tetsuya、Saxton Matthew、Morisaki Tatsuya、Kimura Hiroshi、Bertrand Edouard、Munsky Brian、Stasevich Timothy J.
  • Journal Title: bioRxiv Volume: - Pages: 024414-024414
  • DOI: 10.1101/2020.04.03.024414
  • Open Access / Int'l Joint Research
• [Journal Article] Subnuclear gene positioning through lamina association affects copper tolerance (2020)
  • Author(s): Sakamoto Y., Sato M., Sato Y., Harada A., Suzuki T., Goto C., Tamura K., Toyooka K., Kimura H., Ohkawa Y., Hara-Nishimura I., Takagi S., Matsunaga S.
  • Journal Title: Nature Communications Volume: 11 Pages: 5914-5914
  • DOI: 10.1038/s41467-020-19621-z
  • Peer Reviewed / Open Access
• [Journal Article] Kinase inhibition profiles as a tool to identify kinases for specific phosphorylation sites (2020)
  • Author(s): Watson Nikolaus A.、Cartwright Tyrell N.、Lawless Conor、Camara-Donoso Marcos、Sen Onur、Sako Kosuke、Hirota Toru、Kimura Hiroshi、Higgins Jonathan M. G.
  • Journal Title: Nature Communications Volume: 11 Pages: 1684-1684
  • DOI: 10.1038/s41467-020-15428-0
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Coordinated demethylation of H3K9 and H3K27 is required for rapid inflammatory responses of endothelial cells (2020)
  • Author(s): Higashijima Y, Matsui Y, Shimamura T, Nakaki R, Nagai N, Tsutsumi S, Abe Y, Link VM, Osaka M, Yoshida M, Watanabe R, Tanaka T, Taguchi A, Miura M, Ruan X, Li G, Inoue T, Nangaku M, Kimura H, Furukawa T, Aburatani H, Wada Y, Ruan Y, Glass CK, Kanki Y
  • Journal Title: EMBO Journal Volume: 39 Pages: 1-1
  • DOI: 10.15252/embj.2019103949
  • NAID: 120006902140
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Histone modification dynamics as revealed by a multicolor immunofluorescence-based single-cell analysis (2020)
  • Author(s): Hayashi-Takanaka Yoko、Kina Yuto、Nakamura Fumiaki、Becking Leontine E.、Nakao Yoichi、Nagase Takahiro、Nozaki Naohito、Kimura Hiroshi
  • Journal Title: bioRxiv Volume: - Pages: 892299-892299
  • DOI: 10.1101/2020.01.01.892299
  • Open Access / Int'l Joint Research
• [Journal Article] ヒストン修飾解析の最前線 (2020)
  • Author(s): 半田哲也、木村 宏
  • Journal Title: 遺伝子医学 Volume: 10 Pages: 124-129
  • NAID: 40022142663
• [Journal Article] タンパク質1分子を翻訳過程からイメージング可能なプローブ「HA Frankenbody」 (2020)
  • Author(s): 趙 寧、森崎達也、小田春佳、佐藤優子、木村 宏、Stasevich Timothy J
  • Journal Title: 実験医学 Volume: 38 Pages: 617-613
  • Int'l Joint Research
• [Journal Article] Comprehensive epigenome characterization reveals diverse transcriptional regulation across human vascular endothelial cells (2019)
  • Author(s): Nakato R, Wada Y, Nakaki R, Nagae G, Katou Y, Tsutsumi S, Nakajima N, Fukuhara H, Iguchi A, Kohro T, Kanki Y, Saito Y, Kobayashi M, Izumi-Taguchi A, Osato N, Tatsuno K, Kamio A, Hayashi-Takanaka Y, Wada H, Ohta S, Aikawa M, Nakajima H, Nakamura M, McGee RC, Heppner KW, Kawakatsu T, Genno M, Yanase H, Kume H, et al.
  • Journal Title: Epigenetics & Chromatin Volume: 12 Pages: 77-77
  • DOI: 10.1186/s13072-019-0319-0
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] A genetically encoded probe for imaging nascent and mature HA-tagged proteins in vivo (2019)
  • Author(s): Zhao Ning、Kamijo Kouta、Fox Philip D.、Oda Haruka、Morisaki Tatsuya、Sato Yuko、Kimura Hiroshi、Stasevich Timothy J.
  • Journal Title: Nature Communications Volume: 10 Pages: 2947-2947
  • DOI: 10.1038/s41467-019-10846-1
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Intrabody-based FRET probe to visualize endogenous histone acetylation (2019)
  • Author(s): Chung Chan-I、Sato Yuko、Ohmuro-Matsuyama Yuki、Machida Shinichi、Kurumizaka Hitoshi、Kimura Hiroshi、Ueda Hiroshi
  • Journal Title: Sci Rep. Volume: 9 Pages: 10188-10188
  • DOI: 10.1038/s41598-019-46573-2
  • NAID: 120006936925
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Incorporation and influence of Leishmania histone H3 in chromatin (2019)
  • Author(s): Dacher Mariko、Tachiwana Hiroaki、Horikoshi Naoki、Kujirai Tomoya、Taguchi Hiroyuki、Kimura Hiroshi、Kurumizaka Hitoshi
  • Journal Title: Nucleic Acids Research Volume: 47 Pages: 11637-11648
  • DOI: 10.1093/nar/gkz1040
  • Peer Reviewed / Open Access
• [Journal Article] The CENP-A centromere targeting domain facilitates H4K20 monomethylation in the nucleosome by structural polymorphism. (2019)
  • Author(s): Arimura Y, Tachiwana H, Takagi H, Hori T, Kimura H, Fukagawa T, Kurumizaka H.
  • Journal Title: Nature Commun Volume: 10 Pages: 1-10
  • DOI: 10.1038/s41467-019-08314-x
  • Peer Reviewed / Open Access
• [Journal Article] Histone H3K27 acetylation precedes active transcription during zebrafish zygotic genome activation as revealed by live cell analysis. (2019)
  • Author(s): Sato Y, Hilbert L, Oda H, Wan Y, Heddleston JM, Chew T-L, Zaburdaev V, Keller P, Lionnet T, Vastenhouw N, and Kimura H
  • Journal Title: Development Volume: 146
  • DOI: 10.1242/dev.179127
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Structure-based design of an H2A.Z.1 mutant stabilizing a nucleosome in vitro and in vivo (2019)
  • Author(s): Horikoshi Naoki、Kujirai Tomoya、Sato Koichi、Kimura Hiroshi、Kurumizaka Hitoshi
  • Journal Title: Biochemical and Biophysical Research Communications Volume: 515 Pages: 719-724
  • DOI: 10.1016/j.bbrc.2019.06.012
  • Peer Reviewed / Open Access
• [Journal Article] Effect of mycalolides isolated from a marine sponge Mycale aff. nullarosette on actin in living cells (2019)
  • Author(s): Hayashi-Takanaka Yoko、Kina Yuto、Nakamura Fumiaki、Yamazaki Shota、Harata Masahiko、Soest Rob W. M. van、Kimura Hiroshi、Nakao Yoichi
  • Journal Title: Sci. Rep. Volume: 9 Pages: 7540-7540
  • DOI: 10.1038/s41598-019-44036-2
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Chromatin-bound CRM1 recruits SET-Nup214 and NPM1c onto HOX clusters causing aberrant HOX expression in leukemia cells. (2019)
  • Author(s): Oka M, Mura S, Otani M, Miyamoto Y, Nogami J, Maehara K, Harada A, Tachibana T, Yoneda Y, Ohkawa Y
  • Journal Title: eLife Volume: 8
  • DOI: 10.7554/elife.46667
  • Peer Reviewed / Open Access
• [Journal Article] Cell competition corrects noisy Wnt morphogen gradients to achieve robust patterning in the zebrafish embryo (2019)
  • Author(s): Akieda Yuki、Ogamino Shohei、Furuie Hironobu、Ishitani Shizuka、Akiyoshi Ryutaro、Nogami Jumpei、Masuda Takamasa、Shimizu Nobuyuki、Ohkawa Yasuyuki、Ishitani Tohru
  • Journal Title: Nat Commun. Volume: 10 Pages: 4710-4710
  • DOI: 10.1038/s41467-019-12609-4
  • Peer Reviewed / Open Access
• [Journal Article] The Eleanor ncRNAs activate the topological domain of the ESR1 locus to balance against apoptosis. (2019)
  • Author(s): †Abdalla MOA, †Yamamoto T, Maehara K, Ohkawa Y, Miura H, Hiratani I, Nakayama H, Nakao M, *Saitoh N
  • Journal Title: Nat. Commun. Volume: 10 Pages: 3778-3778
  • DOI: 10.1038/s41467-019-11378-4
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Dmrt factors determine the positional information of cerebral cortical progenitors via differential suppression of homeobox genes. (2019)
  • Author(s): Konno D, Kishida C, Maehara K, Ohkawa Y, Kiyonari H, Okada S, Matsuzaki F
  • Journal Title: Development. Volume: 146 Pages: 1-13
  • DOI: 10.1242/dev.174243
  • Peer Reviewed / Open Access
• [Journal Article] Calcineurin Broadly Regulates the Initiation of Skeletal Muscle-Specific Gene Expression by Binding Target Promoters and Facilitating the Interaction of the SWI/SNF Chromatin Remodeling Enzyme. (2019)
  • Author(s): Witwicka H, Nogami J, Syed SA, Maehara K, Padilla-Benavides T, Ohkawa Y, Imbalzano AN
  • Journal Title: Molecular and Cellular Biology Volume: 39
  • DOI: 10.1128/mcb.00063-19
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Cohesin and condensin extrude loops in a cell-cycle dependent manner (2019)
  • Author(s): Golfier Stefan、Quail Thomas、Kimura Hiroshi、Brugues Jan
  • Journal Title: bioRxiv Volume: - Pages: 821306-821306
  • DOI: 10.1101/821306
  • Open Access / Int'l Joint Research
• [Journal Article] Single-molecule imaging reveals control of parental histone recycling by free histones during DNA replication (2019)
  • Author(s): Gruszka Dominika T.、Xie Sherry、Kimura Hiroshi、Yardimci Hasan
  • Journal Title: bioRxiv Volume: - Pages: 789578-789578
  • DOI: 10.1101/789578
  • Open Access / Int'l Joint Research
• [Journal Article] Transcription-driven cohesin repositioning rewires chromatin loops in cellular senescence (2019)
  • Author(s): Olan Ioana、Parry Aled J.、Schoenfelder Stefan、Narita Masako、Ito Yoko、Chan Adelyne S.L.、Slater Guy St.C.、Bihary Dora、Bando Masashige、Shirahige Katsuhiko、Kimura Hiroshi、Samarajiwa Shamith A.、Fraser Peter、Narita Masashi
  • Journal Title: bioRxiv Volume: - Pages: 823831-823831
  • DOI: 10.1101/823831
  • Open Access / Int'l Joint Research
• [Journal Article] 遺伝子発現の理解と制御のための「ヌクレオーム」研究とエピゲノム編集 (2019)
  • Author(s): 木村 宏、佐藤優子
  • Journal Title: JATAFFジャーナル Volume: 7 Pages: 3-6
• [Journal Article] クロマチン挿入標識法（ChIL）による単一細胞エピゲノム解析 (2019)
  • Author(s): 原田 哲仁、大川 恭行
  • Journal Title: 実験医学（増刊） Volume: 37 Pages: 178-183
• [Journal Article] Signs of biological activities of 28,000-year-old mammoth nuclei in mouse oocytes visualized by live-cell imaging (2019)
  • Author(s): Kazuo Yamagata, Kouhei Nagai, Hiroshi Miyamoto, ...., Tetsuya Handa (17番目), Hiroshi Kimura, Yoshihiko Hosoi, Tasuku Mitani, Kazuya Matsumoto, Akira Iritani
  • Journal Title: Scientific Reports Volume: 9 巻 Pages: 4050-4050
  • DOI: 10.1038/s41598-019-40546-1
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] A mosaic of old and young nucleoporins (2019)
  • Author(s): Shimi Takeshi、Kimura Hiroshi
  • Journal Title: Journal of Cell Biology Volume: 218 Pages: 385-386
  • DOI: 10.1083/jcb.201811170
  • Peer Reviewed / Open Access
• [Journal Article] A chromatin integration labelling method enables epigenomic profiling with lower input (2019)
  • Author(s): Harada Akihito、Maehara Kazumitsu、Handa Tetsuya、Arimura Yasuhiro、Nogami Jumpei、Hayashi-Takanaka Yoko、Shirahige Katsuhiko、Kurumizaka Hitoshi、Kimura Hiroshi、Ohkawa Yasuyuki
  • Journal Title: Nat Cell Biol Volume: 21 Pages: 287-296
  • DOI: 10.1038/s41556-018-0248-3
  • Peer Reviewed / Open Access
• [Journal Article] Heterochromatin suppresses gross chromosomal rearrangements at centromeres by repressing Tfs1/TFIIS-dependent transcription (2019)
  • Author(s): Okita Akiko K.、Zafar Faria、Su Jie、Weerasekara Dayalini、Kajitani Takuya、Takahashi Tatsuro S.、Kimura Hiroshi、Murakami Yota、Masukata Hisao、Nakagawa Takuro
  • Journal Title: Communications Biology Volume: 2 Pages: 17-17
  • DOI: 10.1038/s42003-018-0251-z
  • Peer Reviewed / Open Access
• [Journal Article] Quantitative measurements of chromatin modification dynamics during zygotic genome activation (2019)
  • Author(s): Yuko Sato, Lennart Hilbert, Haruka Oda, Yinan Wan, John M. Heddleston, Teng-Leong Chew, Vasily Zaburdaev, Philipp Keller, Timothee Lionnet, Nadine Vastenhouw, Hiroshi Kimura
  • Journal Title: bioRxiv Volume: 601393 Pages: 601393-601393
  • DOI: 10.1101/601393
  • Open Access / Int'l Joint Research
• [Journal Article] 生細胞内の1分子動態と相互作用の定量解析 (2019)
  • Author(s): 伊藤由馬、徳永万喜洋
  • Journal Title: パリティ Volume: 36 Pages: 72-74
  • Peer Reviewed
• [Journal Article] Modeling latent flows on single-cell data using the Hodge decomposition (2019)
  • Author(s): Maehara Kazumitsu、Ohkawa Yasuyuki
  • Journal Title: bioRxiv Volume: - Pages: 592089-592089
  • DOI: 10.1101/592089
  • Open Access
• [Journal Article] Visualizing the Dynamics of Inactive X Chromosomes in Living Cells Using Antibody-Based Fluorescent Probes (2018)
  • Author(s): Sato Yuko、Stasevich Timothy J.、Kimura Hiroshi
  • Journal Title: Methods in Molecular Biology Volume: 1861 Pages: 91-102
  • DOI: 10.1007/978-1-4939-8766-5_8
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] 遺伝子不活性化マークを生細胞で観察できる蛍光プローブ (2018)
  • Author(s): 佐藤優子、木村宏
  • Journal Title: 化學工業 Volume: 69 Pages: 589-594
• [Journal Article] Nucleome Consortium (2018)
  • Author(s): TASHIRO Satoshi、KIMURA Hiroshi
  • Journal Title: Biophysics Volume: 58 Issue: 4 Pages: 221-222
  • DOI: 10.2142/biophys.58.221
  • NAID: 130007420879
  • ISSN: 0582-4052, 1347-4219
  • Open Access
• [Journal Article] A genetically encoded probe for imaging HA-tagged protein translation, localization, and dynamics in living cells and animals (2018)
  • Author(s): Zhao Ning、Kamijo Kouta、Fox Philip、Oda Haruka、Morisaki Tatsuya、Sato Yuko、Kimura Hiroshi、Stasevich Timothy J.
  • Journal Title: bioRxiv Volume: - Pages: 474668-474668
  • DOI: 10.1101/474668
  • Open Access / Int'l Joint Research
• [Journal Article] Coordinated demethylation of H3K9 and H3K27 is required for rapid inflammatory responses of endothelial cells (2018)
  • Author(s): Higashijima Y, Matsui Y, Shimamura T, Tsutsumi S, Nakaki R, Abe Y, Link VM, Osaka M, Yoshida M, Watanabe R, Tanaka T, Taguchi A, Miura M, Inoue T, Nangaku M, Kimura H, Furukawa T, Aburatani H, Wada Y, Glass CK, Kanki Y
  • Journal Title: BioRxiv Volume: - Pages: 0-0
  • DOI: 10.1101/456491
  • NAID: 120006902140
  • Open Access / Int'l Joint Research
• [Journal Article] CLIP-170 is essential for MTOC repositioning during T cell activation by regulating dynein localisation on the cell surface (2018)
  • Author(s): Lim Wei Ming、Ito Yuma、Sakata-Sogawa Kumiko、Tokunaga Makio
  • Journal Title: Scientific Reports Volume: 8 Pages: 17747-17747
  • DOI: 10.1038/s41598-018-35593-z
  • Peer Reviewed / Open Access
• [Journal Article] 全反射照明蛍光顕微鏡 ― 対物レンズ型 (2018)
  • Author(s): 徳永万喜洋、伊藤由馬
  • Journal Title: 実験医学増刊 Volume: 36 Pages: 36-37
• [Journal Article] 共焦点レーザー走査顕微鏡 iii. FRAP/FLIP (2018)
  • Author(s): 木村 宏
  • Journal Title: 実験医学増刊 Volume: 36 Pages: 50-51
• [Presentation] Tracking histone and RNA polymerase II modifications in living cells using genetically encoded probes (2021)
  • Author(s): Hiroshi Kimura
  • Organizer: RIKEN BDR Symposium
  • Int'l Joint Research / Invited
• [Presentation] Gene regulation and chromatin dynamics in living cells (2020)
  • Author(s): Hiroshi Kimura
  • Organizer: The 79th of Annual Meeting of the Japanese Cancer Association
  • Invited
• [Presentation] 転写活性化に伴うヒストンアセチル化とクロマチンのダイナミクス (2020)
  • Author(s): 木村 宏
  • Organizer: 第93回 日本生化学会大会
  • Invited
• [Presentation] Roles of histone acetylation and nuclear F-actin in zebrafish embryo development (2020)
  • Author(s): Hiroshi Kimura
  • Organizer: Chromosome Dynamics - An international symposium on chromatin and chromosome stability
  • Int'l Joint Research / Invited
• [Presentation] ゼブラフィッシュ胚性ゲノム活性化におけるヒストンアセチル化の役割と核内環境変化 (2019)
  • Author(s): 木村 宏
  • Organizer: 第42回日本分子生物学会年会
  • Invited
• [Presentation] Single-cell histone modification analysis: from live-cell imaging to epigenome profiling (2019)
  • Author(s): Hiroshi Kimura
  • Organizer: Single Cell Omics Germany Workshop "Advances in single cell epigenomics 2019"
  • Int'l Joint Research / Invited
• [Presentation] Tracking RNA polymerase II and histone modification dynamics during the zygotic genome activation (2019)
  • Author(s): Hiroshi Kimura
  • Organizer: 第92回日本生化学会大会
  • Invited
• [Presentation] Chromatin modification dynamics during the activation and inactivation of transcription (2019)
  • Author(s): Hiroshi Kimura
  • Organizer: Gordon Research Conference "Genome Architecture in Cell Fate and Disease"
  • Int'l Joint Research / Invited
• [Presentation] クロマチン挿入法による単一細胞エピゲノム解析 (2019)
  • Author(s): 大川 恭行
  • Organizer: 日本人類遺伝学会第64回大会
  • Invited
• [Presentation] Modification-specific intracellular antibodies for monitoring histone modification in vivo (2019)
  • Author(s): Hiroshi Kimura
  • Organizer: 3rd Epigenetics and Bioengineering Conference (EpiBio 2019)
  • Int'l Joint Research
• [Presentation] A single-molecule localization approach to quantify the interaction between transcriptional machinery and chromatin structure (2019)
  • Author(s): Yuma Ito, Makio Tokunaga
  • Organizer: 第57回日本生物物理学会年会
• [Presentation] Chromatin integration labelling Technology for expanding multi-omics (2019)
  • Author(s): Yasuyuki Ohkawa
  • Organizer: EMBO Symposia: Multi-Omics
  • Int'l Joint Research
• [Presentation] 遺伝子の発現されやすさはどのように決まるのか？～クロマチンが規定する遺伝子発現制御能力～ (2019)
  • Author(s): 大川 恭行
  • Organizer: 第42回日本分子生物学会年会
• [Presentation] Histone H3.3 sub-variants are required for regulating skeletal muscle differentiation (2019)
  • Author(s): Yasuyuki Ohkawa
  • Organizer: 2018 Federation of American Societies for Experimental Biology (FASEB)
  • Int'l Joint Research
• [Presentation] Chromatin Integration Labeling- an Epigenomic Profiling for Single Cell Analysis (2019)
  • Author(s): Yasuyuki Ohkawa
  • Organizer: Cell Symposium: Single Cells: Technology to Biology
  • Int'l Joint Research
• [Presentation] Chromatin modification dynamics during gene activation and inactivation in living cells (2018)
  • Author(s): Hiroshi Kimura
  • Organizer: CSHL Meeting "Nuclear Organization & Function"
  • Int'l Joint Research / Invited
• [Presentation] Chromatin Modification Dynamics in Living Cells (2018)
  • Author(s): Hiroshi Kimura
  • Organizer: Gordon Research Conference "Chromatin Structure and Function"
  • Int'l Joint Research / Invited
• [Presentation] Sensing Histone Modification and Transcription Dynamics in Living Cells (2018)
  • Author(s): Hiroshi Kimura
  • Organizer: 2nd Epigenetics and Bioengineering Conference
  • Int'l Joint Research / Invited
• [Presentation] Chromatin modification dynamics during gene activation in living cells and embryos (2018)
  • Author(s): Hiroshi Kimura
  • Organizer: Joint Annual Meeting of JSDB 51st and JSCB 70th
  • Int'l Joint Research / Invited
• [Presentation] A chromatin integration labeling method enables epigenomic profiling with lower input (2018)
  • Author(s): Tetsuya Handa, Akihito Harada, Kazumitsu Maehara, Yasuhiro Arimura, Jumpei Nogami, Yoko Hayashi-Takanaka, Katsuhiko Shirahige, Hitoshi Kurumizaka, Yasuyuki Ohkawa and Hiroshi Kimura
  • Organizer: 3R&3C Symposium
  • Int'l Joint Research
• [Presentation] クロマチン修飾ダイナミクス 生細胞イメージングとエピゲノム解析の融合に向けて (2018)
  • Author(s): 木村 宏
  • Organizer: 第91回日本生化学会大会
  • Invited
• [Presentation] ヒストン修飾と転写の生細胞動態から捉えるクロマチンポテンシャル (2018)
  • Author(s): 木村 宏
  • Organizer: 第41回日本分子生物学会年会
  • Invited
• [Presentation] Chromatin integration labeling (ChIL) technology: an immunoprecipitation-free method for low-input epigenomic profiling (2018)
  • Author(s): Hiroshi Kimura
  • Organizer: IHEC Meeting 2018
  • Int'l Joint Research
• [Presentation] 蛍光１分子イメージングにおける動態解析法の開発と核内タンパク質挙動の定量解析 (2018)
  • Author(s): 伊藤由馬
  • Organizer: 第91回大会日本生化学会大会
  • Invited
• [Presentation] 骨格筋分化・再生司るクロマチン構造制御機構の解明 (2018)
  • Author(s): 大川恭行
  • Organizer: 日本筋学会第4回学術集会
  • Invited
• [Presentation] 免疫沈降をしない１細胞エピゲノム解析技術の開発 (2018)
  • Author(s): 大川恭行
  • Organizer: 第91回日本生化学会学大会
  • Invited
• [Presentation] 空間トランスクリプトミクスで解明する骨格筋再生 (2018)
  • Author(s): 大川恭行
  • Organizer: 第41回日本分子生物学会年会
  • Invited
• [Presentation] 骨格筋再生におけるヒストン転換 (2018)
  • Author(s): 大川恭行
  • Organizer: 第７回骨格筋生物学研究会
  • Invited
• [Presentation] ChILT-an Epigenomic Profiling for Single Cell Analysis (2018)
  • Author(s): Yasuyuki Ohkawa
  • Organizer: Gordon Research Conference"Chromatin Structure and Function"
  • Int'l Joint Research
• [Book] クロマチン解析実践プロトコール (2020)
  • Author(s): 大川 恭行、宮成 悠介
  • Total Pages: 270
  • Publisher: 羊土社
  • ISBN: 9784758122481
• [Remarks] 東京工業大学・科学技術創成研究院・細胞制御工学研究センター
  • URL: http://www.rcb.iir.titech.ac.jp/index.html
• [Remarks] 東京工業大学・科学技術創成研究院・細胞制御工学研究センター・木村研究室
  • URL: http://kimura-lab.bio.titech.ac.jp/
• [Remarks] 東京工業大学リサーチディボジトリ／木村宏
  • URL: http://t2r2.star.titech.ac.jp/cgi-bin/researcherinfo.cgi?q_researcher_content_number=CTT100673940
• [Remarks] 新学術領域「クロマチン潜在能」
  • URL: http://www.nibb.ac.jp/potentia/
• [Remarks] 東工大 木村研
  • URL: http://kimura-lab.bio.titech.ac.jp/
• [Remarks] 東工大 科学技術創成研究院 細胞制御工学研究センター
  • URL: http://www.rcb.iir.titech.ac.jp/
• [Remarks] 東工大 T2R2 リサーチディポジトリ
  • URL: http://t2r2.star.titech.ac.jp/cgi-bin/researcherinfo.cgi?q_researcher_content_number=CTT100673940
• [Remarks] 東京工業大学 木村宏研究室
  • URL: http://kimura-lab.bio.titech.ac.jp/
• [Remarks] 東京工業大学 科学技術創成研究院 細胞制御工学研究センター
  • URL: http://www.rcb.iir.titech.ac.jp/
• [Remarks] 東京工業大学 研究者情報
  • URL: https://t2r2.star.titech.ac.jp/cgi-bin/researcherinfo.cgi?q_researcher_content_number=CTT100673940