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細胞核・クロマチン構造のダイナミクスと遺伝子制御

Planned

Project AreaChromatin 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 TypeSingle-year Grants
Review Section Biological Sciences
Research InstitutionTokyo 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 *help
¥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
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。

Report

(3 results)
  • 2020 Annual Research Report
  • 2019 Annual Research Report
  • 2018 Annual Research Report

Research Products

(110 results)

All 2021 2020 2019 2018 Other

All Int'l Joint Research (11 results) Journal Article (59 results) (of which Int'l Joint Research: 27 results,  Peer Reviewed: 39 results,  Open Access: 47 results) Presentation (29 results) (of which Int'l Joint Research: 15 results,  Invited: 20 results) Book (1 results) Remarks (10 results)

  • [Int'l Joint Research] European Moleclar Biology Laboratory/Max Planck Institute-CBG/Karlsruhe Institute of Technology(ドイツ)

    • Related Report
      2020 Annual Research Report
  • [Int'l Joint Research] University of Copenhagen(デンマーク)

    • Related Report
      2020 Annual Research Report
  • [Int'l Joint Research] University of Cambridge/Crick Institute(英国)

    • Related Report
      2020 Annual Research Report
  • [Int'l Joint Research] Colorado State University(米国)

    • Related Report
      2020 Annual Research Report
  • [Int'l Joint Research] New York University/Colorado State University/Florida State University(米国)

    • Related Report
      2019 Annual Research Report
  • [Int'l Joint Research] Cambridge University/New Castle University(英国)

    • Related Report
      2019 Annual Research Report
  • [Int'l Joint Research] EMBL/Max Panck Institute, Dresden/Karlsruhe Institute of Technology(ドイツ)

    • Related Report
      2019 Annual Research Report
  • [Int'l Joint Research] Colorado State University/HHMI Janelia Research Campus(米国)

    • Related Report
      2018 Annual Research Report
  • [Int'l Joint Research] Cambridge University(英国)

    • Related Report
      2018 Annual Research Report
  • [Int'l Joint Research] MPI - Molecular Cell Biology & Genetics/Karlsruhe Institute of Technology/EMBL(ドイツ)

    • Related Report
      2018 Annual Research Report
  • [Int'l Joint Research] Curie Insitute(フランス)

    • Related Report
      2018 Annual Research Report
  • [Journal Article] Simple Fluorogenic Cellular Assay for Histone Deacetylase Inhibitors Based on Split-Yellow Fluorescent Protein and Intrabodies2021

    • 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

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Structural basis of nucleosomal histone H4 lysine 20 methylation by SET8 methyltransferase2021

    • 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

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] RNA polymerase II condensate formation and association with Cajal and histone locus bodies in living human cells2021

    • Author(s)
      Imada Takashi、Shimi Takeshi、Kaiho Ai、Saeki Yasushi、Kimura Hiroshi
    • Journal Title

      Genes to Cells

      Volume: -

    • DOI

      10.1111/gtc.12840

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] H4K20me1 and H3K27me3 are concurrently loaded onto the inactive X chromosome but dispensable for inducing gene silencing2021

    • 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

    • Related Report
      2020 Annual Research Report
    • 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 Tsix2021

    • 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

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Live-cell epigenome manipulation by synthetic histone acetylation catalyst system2021

    • 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

    • Related Report
      2020 Annual Research Report
    • 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

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Transcription organizes euchromatin via microphase separation2021

    • 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

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Variable immersion microscopy with a high numerical aperture2021

    • 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

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Visualizing transcription sites in living cells using a genetically encoded probe specific for the elongating form of RNA polymerase II2021

    • 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

    • Related Report
      2020 Annual Research Report
    • Open Access
  • [Journal Article] Discriminative feature of cells characterizes cell populations of interest by a small subset of genes2021

    • Author(s)
      Fujii Takeru、Maehara Kazumitsu、Fujita Masatoshi、Ohkawa Yasuyuki
    • Journal Title

      bioRxiv

      Volume: - Pages: 435089-435089

    • DOI

      10.1101/2021.03.12.435089

    • Related Report
      2020 Annual Research Report
    • Open Access
  • [Journal Article] Cohesin and condensin extrude DNA loops in a cell cycle-dependent manner2020

    • Author(s)
      Golfier Stefan、Quail Thomas、Kimura Hiroshi、Brugues Jan
    • Journal Title

      eLife

      Volume: 9

    • DOI

      10.7554/elife.53885

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Transcription-dependent cohesin repositioning rewires chromatin loops in cellular senescence2020

    • 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

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Single-molecule imaging reveals control of parental histone recycling by free histones during DNA replication2020

    • Author(s)
      Gruszka D. T.、Xie S.、Kimura H.、Yardimci H.
    • Journal Title

      Science Advances

      Volume: 6

    • DOI

      10.1126/sciadv.abc0330

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Histone modification dynamics as revealed by multicolor immunofluorescence-based single-cell analysis2020

    • 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

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Genome-wide kinetic properties of transcriptional bursting in mouse embryonic stem cells2020

    • 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

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Genomic Profiling by ALaP-Seq Reveals Transcriptional Regulation by PML Bodies through DNMT3A Exclusion2020

    • 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

    • Related Report
      2020 Annual Research Report
    • 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

    • Related Report
      2020 Annual Research Report 2019 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Modeling population size independent tissue epigenomes by ChIL-seq with single-thin sections2020

    • 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

    • Related Report
      2020 Annual Research Report
    • Open Access
  • [Journal Article] Live-cell imaging reveals the spatiotemporal organization of endogenous RNA polymerase II phosphorylation at a single gene2020

    • 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

    • Related Report
      2020 Annual Research Report
    • Open Access / Int'l Joint Research
  • [Journal Article] Subnuclear gene positioning through lamina association affects copper tolerance2020

    • 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

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Kinase inhibition profiles as a tool to identify kinases for specific phosphorylation sites2020

    • 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

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Coordinated demethylation of H3K9 and H3K27 is required for rapid inflammatory responses of endothelial cells2020

    • 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

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Histone modification dynamics as revealed by a multicolor immunofluorescence-based single-cell analysis2020

    • 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

    • Related Report
      2019 Annual Research Report
    • 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

    • Related Report
      2019 Annual Research Report
  • [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

    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research
  • [Journal Article] Comprehensive epigenome characterization reveals diverse transcriptional regulation across human vascular endothelial cells2019

    • 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

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] A genetically encoded probe for imaging nascent and mature HA-tagged proteins in vivo2019

    • 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

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Intrabody-based FRET probe to visualize endogenous histone acetylation2019

    • 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

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Incorporation and influence of Leishmania histone H3 in chromatin2019

    • 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

    • Related Report
      2019 Annual Research Report
    • 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

    • Related Report
      2019 Annual Research Report
    • 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

    • Related Report
      2019 Annual Research Report
    • 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 vivo2019

    • 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

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Effect of mycalolides isolated from a marine sponge Mycale aff. nullarosette on actin in living cells2019

    • 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

    • Related Report
      2019 Annual Research Report
    • 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

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Cell competition corrects noisy Wnt morphogen gradients to achieve robust patterning in the zebrafish embryo2019

    • 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

    • Related Report
      2019 Annual Research Report
    • 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

    • Related Report
      2019 Annual Research Report
    • 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

    • Related Report
      2019 Annual Research Report
    • 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

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Cohesin and condensin extrude loops in a cell-cycle dependent manner2019

    • Author(s)
      Golfier Stefan、Quail Thomas、Kimura Hiroshi、Brugues Jan
    • Journal Title

      bioRxiv

      Volume: - Pages: 821306-821306

    • DOI

      10.1101/821306

    • Related Report
      2019 Annual Research Report
    • Open Access / Int'l Joint Research
  • [Journal Article] Single-molecule imaging reveals control of parental histone recycling by free histones during DNA replication2019

    • Author(s)
      Gruszka Dominika T.、Xie Sherry、Kimura Hiroshi、Yardimci Hasan
    • Journal Title

      bioRxiv

      Volume: - Pages: 789578-789578

    • DOI

      10.1101/789578

    • Related Report
      2019 Annual Research Report
    • Open Access / Int'l Joint Research
  • [Journal Article] Transcription-driven cohesin repositioning rewires chromatin loops in cellular senescence2019

    • 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

    • Related Report
      2019 Annual Research Report
    • 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

    • Related Report
      2019 Annual Research Report
  • [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

    • Related Report
      2019 Annual Research Report
  • [Journal Article] Signs of biological activities of 28,000-year-old mammoth nuclei in mouse oocytes visualized by live-cell imaging2019

    • 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

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] A mosaic of old and young nucleoporins2019

    • Author(s)
      Shimi Takeshi、Kimura Hiroshi
    • Journal Title

      Journal of Cell Biology

      Volume: 218 Pages: 385-386

    • DOI

      10.1083/jcb.201811170

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] A chromatin integration labelling method enables epigenomic profiling with lower input2019

    • 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

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Heterochromatin suppresses gross chromosomal rearrangements at centromeres by repressing Tfs1/TFIIS-dependent transcription2019

    • 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

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Quantitative measurements of chromatin modification dynamics during zygotic genome activation2019

    • 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

    • Related Report
      2018 Annual Research Report
    • 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

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Modeling latent flows on single-cell data using the Hodge decomposition2019

    • Author(s)
      Maehara Kazumitsu、Ohkawa Yasuyuki
    • Journal Title

      bioRxiv

      Volume: - Pages: 592089-592089

    • DOI

      10.1101/592089

    • Related Report
      2018 Annual Research Report
    • Open Access
  • [Journal Article] Visualizing the Dynamics of Inactive X Chromosomes in Living Cells Using Antibody-Based Fluorescent Probes2018

    • 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

    • Related Report
      2018 Annual Research Report
    • 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

    • Related Report
      2018 Annual Research Report
  • [Journal Article] Nucleome Consortium2018

    • 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
    • Related Report
      2018 Annual Research Report
    • Open Access
  • [Journal Article] A genetically encoded probe for imaging HA-tagged protein translation, localization, and dynamics in living cells and animals2018

    • 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

    • Related Report
      2018 Annual Research Report
    • Open Access / Int'l Joint Research
  • [Journal Article] Coordinated demethylation of H3K9 and H3K27 is required for rapid inflammatory responses of endothelial cells2018

    • 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

    • Related Report
      2018 Annual Research Report
    • 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 surface2018

    • 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

    • Related Report
      2018 Annual Research Report
    • 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

    • Related Report
      2018 Annual Research Report
  • [Journal Article] 共焦点レーザー走査顕微鏡 iii. FRAP/FLIP2018

    • Author(s)
      木村 宏
    • Journal Title

      実験医学増刊

      Volume: 36 Pages: 50-51

    • Related Report
      2018 Annual Research Report
  • [Presentation] Tracking histone and RNA polymerase II modifications in living cells using genetically encoded probes2021

    • Author(s)
      Hiroshi Kimura
    • Organizer
      RIKEN BDR Symposium
    • Related Report
      2020 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Gene regulation and chromatin dynamics in living cells2020

    • Author(s)
      Hiroshi Kimura
    • Organizer
      The 79th of Annual Meeting of the Japanese Cancer Association
    • Related Report
      2020 Annual Research Report
    • 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
    • Related Report
      2020 Annual Research Report
    • Invited
  • [Presentation] Roles of histone acetylation and nuclear F-actin in zebrafish embryo development2020

    • Author(s)
      Hiroshi Kimura
    • Organizer
      Chromosome Dynamics - An international symposium on chromatin and chromosome stability
    • Related Report
      2019 Annual Research Report
    • 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
    • Related Report
      2019 Annual Research Report
    • Invited
  • [Presentation] Single-cell histone modification analysis: from live-cell imaging to epigenome profiling2019

    • Author(s)
      Hiroshi Kimura
    • Organizer
      Single Cell Omics Germany Workshop "Advances in single cell epigenomics 2019"
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Tracking RNA polymerase II and histone modification dynamics during the zygotic genome activation2019

    • Author(s)
      Hiroshi Kimura
    • Organizer
      第92回日本生化学会大会
    • Related Report
      2019 Annual Research Report
    • Invited
  • [Presentation] Chromatin modification dynamics during the activation and inactivation of transcription2019

    • Author(s)
      Hiroshi Kimura
    • Organizer
      Gordon Research Conference "Genome Architecture in Cell Fate and Disease"
    • Related Report
      2019 Annual Research Report
    • 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
    • Related Report
      2019 Annual Research Report
    • Invited
  • [Presentation] Modification-specific intracellular antibodies for monitoring histone modification in vivo2019

    • Author(s)
      Hiroshi Kimura
    • Organizer
      3rd Epigenetics and Bioengineering Conference (EpiBio 2019)
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research
  • [Presentation] A single-molecule localization approach to quantify the interaction between transcriptional machinery and chromatin structure2019

    • Author(s)
      Yuma Ito, Makio Tokunaga
    • Organizer
      第57回日本生物物理学会年会
    • Related Report
      2019 Annual Research Report
  • [Presentation] Chromatin integration labelling Technology for expanding multi-omics2019

    • Author(s)
      Yasuyuki Ohkawa
    • Organizer
      EMBO Symposia: Multi-Omics
    • Related Report
      2019 Annual Research Report
    • 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
    • Related Report
      2019 Annual Research Report
  • [Presentation] Histone H3.3 sub-variants are required for regulating skeletal muscle differentiation2019

    • Author(s)
      Yasuyuki Ohkawa
    • Organizer
      2018 Federation of American Societies for Experimental Biology (FASEB)
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Chromatin Integration Labeling- an Epigenomic Profiling for Single Cell Analysis2019

    • Author(s)
      Yasuyuki Ohkawa
    • Organizer
      Cell Symposium: Single Cells: Technology to Biology
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Chromatin modification dynamics during gene activation and inactivation in living cells2018

    • Author(s)
      Hiroshi Kimura
    • Organizer
      CSHL Meeting "Nuclear Organization & Function"
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Chromatin Modification Dynamics in Living Cells2018

    • Author(s)
      Hiroshi Kimura
    • Organizer
      Gordon Research Conference "Chromatin Structure and Function"
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Sensing Histone Modification and Transcription Dynamics in Living Cells2018

    • Author(s)
      Hiroshi Kimura
    • Organizer
      2nd Epigenetics and Bioengineering Conference
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Chromatin modification dynamics during gene activation in living cells and embryos2018

    • Author(s)
      Hiroshi Kimura
    • Organizer
      Joint Annual Meeting of JSDB 51st and JSCB 70th
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] A chromatin integration labeling method enables epigenomic profiling with lower input2018

    • 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
    • Related Report
      2018 Annual Research Report
    • 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
    • Related Report
      2018 Annual Research Report
    • 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
    • Related Report
      2018 Annual Research Report
    • Invited
  • [Presentation] Chromatin integration labeling (ChIL) technology: an immunoprecipitation-free method for low-input epigenomic profiling2018

    • Author(s)
      Hiroshi Kimura
    • Organizer
      IHEC Meeting 2018
    • Related Report
      2018 Annual Research Report
    • 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
    • Related Report
      2018 Annual Research Report
    • 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
    • Related Report
      2018 Annual Research Report
    • 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
    • Related Report
      2018 Annual Research Report
    • 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
    • Related Report
      2018 Annual Research Report
    • 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
    • Related Report
      2018 Annual Research Report
    • Invited
  • [Presentation] ChILT-an Epigenomic Profiling for Single Cell Analysis2018

    • Author(s)
      Yasuyuki Ohkawa
    • Organizer
      Gordon Research Conference"Chromatin Structure and Function"
    • Related Report
      2018 Annual Research Report
    • 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
    • Related Report
      2020 Annual Research Report
  • [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

    • Related Report
      2020 Annual Research Report
  • [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/

    • Related Report
      2020 Annual Research Report
  • [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

    • Related Report
      2020 Annual Research Report
  • [Remarks] 新学術領域「クロマチン潜在能」

    • URL

      http://www.nibb.ac.jp/potentia/

    • Related Report
      2020 Annual Research Report
  • [Remarks] 東工大 木村研

    • URL

      http://kimura-lab.bio.titech.ac.jp/

    • Related Report
      2019 Annual Research Report
  • [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/

    • Related Report
      2019 Annual Research Report
  • [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

    • Related Report
      2019 Annual Research Report
  • [Remarks] 東京工業大学 木村宏研究室

    • URL

      http://kimura-lab.bio.titech.ac.jp/

    • Related Report
      2018 Annual Research Report
  • [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/

    • Related Report
      2018 Annual Research Report
  • [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

    • Related Report
      2018 Annual Research Report

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Published: 2018-07-20   Modified: 2022-07-01  

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