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2022 Fiscal Year Annual Research Report

細胞核・クロマチン構造のダイナミクスと遺伝子制御

Planned Research

Project AreaChromatin potential for gene regulation
Project/Area Number 18H05527
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
Keywordsクロマチン / エピジェネティクス / 遺伝子発現制御 / 転写調節 / ヒストン修飾
Outline of Annual Research Achievements

(1)遺伝子活性化に働くクロマチン構造と動態の解析:
遺伝子発現の無い状態から転写活性化が起こるモデル系として、ゼブラフィッシュ胚性ゲノム活性化(ZGA; zygotic genome activation)に着目し、DNA複製因子であるPCNAの生細胞イメージングを用いてクロマチン動態解析を進めた。ZGA前では特定のクロマチン構造をとらないと思われていたが、PCNAの局在は必ずしも均一でなく、ゲノムの領域に応じて複製タイミングが異なる可能性も示唆された。また、ZGA後には、初期複製と後期複製のドメインが検出され、クロマチンドメインの形成が確認できた。この複製タイミングとクロマチンドメイン形成が転写活性化のポテンシャルを制御する可能性も考えられた。
(2)遺伝子発現変動に働くクロマチン構造の解析:
RNAポリメラーゼIIの開始型に特異的なSer5ph-Mintbodyと伸長型に特異的なSer2ph-Mintbodyを同時に発現する細胞に、ヒストン修飾特異的Mintbodyや転写関連蛋白質を発現させ、ヒストン修飾や各転写関連蛋白質と転写の開始と伸長との関係を明らかにした。また、RNAポリメラーゼIIのサブユニットとSer5ph、Ser2phを比較すると、RNAポリメラーゼの集積はSer5phと類似していた。このことから、開始部位にはより多くの分子が集積していることが明らかになり、RNAポリメラーゼIIは開始クラスターを形成すると考えられた。
(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:
RNAポリメラーゼII Ser2ph-Mintbodyを発現するノックインマウスを作製した。また、筋芽細胞の分化過程でおこる特定のヒストン修飾の局在性変化を明らかにした。

Research Progress Status

令和4年度が最終年度であるため、記入しない。

Strategy for Future Research Activity

令和4年度が最終年度であるため、記入しない。

  • Research Products

    (28 results)

All 2023 2022 Other

All Int'l Joint Research (4 results) Journal Article (13 results) (of which Int'l Joint Research: 5 results,  Peer Reviewed: 13 results,  Open Access: 10 results) Presentation (6 results) (of which Int'l Joint Research: 5 results,  Invited: 6 results) Remarks (5 results)

  • [Int'l Joint Research] Hubrecht Institute(オランダ)

    • Country Name
      NETHERLANDS
    • Counterpart Institution
      Hubrecht Institute
  • [Int'l Joint Research] Memorial Sloan Kettering Cencer Center/Colorado State University(米国)

    • Country Name
      U.S.A.
    • Counterpart Institution
      Memorial Sloan Kettering Cencer Center/Colorado State University
  • [Int'l Joint Research] Lausanne University(スイス)

    • Country Name
      SWITZERLAND
    • Counterpart Institution
      Lausanne University
  • [Int'l Joint Research] Cambridge University(英国)

    • Country Name
      UNITED KINGDOM
    • Counterpart Institution
      Cambridge University
  • [Journal Article] Epigenetic plasticity safeguards heterochromatin configuration in mammals2023

    • Author(s)
      Fukuda Kei、Shimi Takeshi、Shimura Chikako、Ono Takao、Suzuki Takehiro、Onoue Kenta、Okayama Satoko、Miura Hisashi、Hiratani Ichiro、Ikeda Kazuho、Okada Yasushi、Dohmae Naoshi、Yonemura Shigenobu、Inoue Azusa、Kimura Hiroshi、Shinkai Yoichi
    • Journal Title

      Nucleic Acids Research

      Pages: gkad387

    • DOI

      10.1093/nar/gkad387

    • Peer Reviewed / Open Access
  • [Journal Article] Actin filaments accumulated in the nucleus and remain in the vicinity of condensing chromosomes during prophase in zebrafish early embryo2023

    • Author(s)
      Oda Haruka、Sato Yuko、Kawashima Shigehiro A.、Fujiwara Yusuke、Palfy Mate、Wu Edlyn、Vastenhouw Nadine L.、Kanai Motomu、Kimura Hiroshi
    • Journal Title

      Biology Open

      Volume: 12 Pages: bio059783.

    • DOI

      10.1242/bio.059783

    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Live-cell tracking of γ-H2AX kinetics reveals the distinct modes of ATM and DNA-PK in the immediate response to DNA damage2023

    • Author(s)
      Trakarnphornsombat Watanya、Kimura Hiroshi
    • Journal Title

      Journal of Cell Science

      Volume: 136 Pages: jcs.260698

    • DOI

      10.1242/jcs.260698

    • Peer Reviewed / Open Access
  • [Journal Article] Dense and Acidic Organelle-Targeted Visualization in Living Cells: Application of Viscosity-Responsive Fluorescence Utilizing Restricted Access to Minimum Energy Conical Intersection2023

    • Author(s)
      Adachi Junya、Oda Haruka、Fukushima Toshiaki、Lestari Beni、Kimura Hiroshi、Sugai Hiroka、Shiraki Kentaro、Hamaguchi Rei、Sato Kohei、Kinbara Kazushi
    • Journal Title

      Analytical Chemistry

      Volume: 95 Pages: 5196~5204

    • DOI

      10.1021/acs.analchem.2c04133

    • Peer Reviewed / Open Access
  • [Journal Article] Nanog organizes transcription bodies2023

    • Author(s)
      Kuznetsova Ksenia、Chabot Noemie M.、Ugolini Martino、Wu Edlyn、Lalit Manan、Oda Haruka、Sato Yuko、Kimura Hiroshi、Jug Florian、Vastenhouw Nadine L.
    • Journal Title

      Current Biology

      Volume: 33 Pages: 164~173.e5

    • DOI

      10.1016/j.cub.2022.11.015

    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] The role of H3K9me3 in oral squamous cell carcinoma2023

    • Author(s)
      Tanaka Misako、Harada Hiroyuki、Kimura Hiroshi
    • Journal Title

      Biochemical and Biophysical Research Communications

      Volume: 640 Pages: 56~63

    • DOI

      10.1016/j.bbrc.2022.11.102

    • Peer Reviewed / Open Access
  • [Journal Article] Transient Methionine Deprivation Triggers Histone Modification and Potentiates Differentiation of Induced Pluripotent Stem Cells2022

    • Author(s)
      Ozawa Hiroki、Kambe Azusa、Hibi Kodai、Murakami Satoshi、Oikawa Akira、Handa Tetsuya、Fujiki Katsunori、Nakato Ryuichiro、Shirahige Katsuhiko、Kimura Hiroshi、Shiraki Nobuaki、Kume Shoen
    • Journal Title

      Stem Cells

      Volume: 41 Pages: 271~286

    • DOI

      10.1093/stmcls/sxac082

    • Peer Reviewed
  • [Journal Article] STREAMING-tag system reveals spatiotemporal relationships between transcriptional regulatory factors and transcriptional activity2022

    • Author(s)
      Ohishi Hiroaki、Shimada Seiru、Uchino Satoshi、Li Jieru、Sato Yuko、Shintani Manabu、Owada Hitoshi、Ohkawa Yasuyuki、Pertsinidis Alexandros、Yamamoto Takashi、Kimura Hiroshi、Ochiai Hiroshi
    • Journal Title

      Nature Communications

      Volume: 13 Pages: 7672

    • DOI

      10.1038/s41467-022-35286-2

    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Single-cell profiling of transcriptome and histone modifications with EpiDamID2022

    • Author(s)
      Rang Franka J.、de Luca Kim L.、de Vries Sandra S.、Valdes-Quezada Christian、Boele Ellen、Nguyen Phong D.、Guerreiro Isabel、Sato Yuko、Kimura Hiroshi、Bakkers Jeroen、Kind Jop
    • Journal Title

      Molecular Cell

      Volume: 82 Pages: 1956~1970.e14

    • DOI

      10.1016/j.molcel.2022.03.009

    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Nucleoplasmic lamin C rapidly accumulates at sites of nuclear envelope rupture with BAF and cGAS2022

    • Author(s)
      Kono Yohei、Adam Stephen A.、Sato Yuko、Reddy Karen L.、Zheng Yixian、Medalia Ohad、Goldman Robert D.、Kimura Hiroshi、Shimi Takeshi
    • Journal Title

      Journal of Cell Biology

      Volume: 221 Pages: jcb.202201024

    • DOI

      10.1083/jcb.202201024

    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Superfluid helium nanoscope insert with millimeter working range2022

    • Author(s)
      Kamiya Naoki、Kuramoto Kazuki、Takishima Kento、Yumoto Tatsuya、Oda Haruka、Shimi Takeshi、Kimura Hiroshi、Matsushita Michio、Fujiyoshi Satoru
    • Journal Title

      Review of Scientific Instruments

      Volume: 93 Pages: 103703~103703

    • DOI

      10.1063/5.0107395

    • Peer Reviewed / Open Access
  • [Journal Article] Intra Q-body: an antibody-based fluorogenic probe for intracellular proteins that allows live cell imaging and sorting2022

    • Author(s)
      Dai Yancen、Sato Yuko、Zhu Bo、Kitaguchi Tetsuya、Kimura Hiroshi、Ghadessy Farid J.、Ueda Hiroshi
    • Journal Title

      Chemical Science

      Volume: 13 Pages: 9739~9748

    • DOI

      10.1039/d2sc02355e

    • Peer Reviewed / Open Access
  • [Journal Article] Euchromatin factors HULC and Set1C affect heterochromatin organization and mating-type switching in fission yeast Schizosaccharomyces pombe2022

    • Author(s)
      Esquivel-Chavez Alfredo、Maki Takahisa、Tsubouchi Hideo、Handa Testuya、Kimura Hiroshi、Haber James E.、Thon Genevieve、Iwasaki Hiroshi
    • Journal Title

      Genes & Genetic Systems

      Volume: 97 Pages: 123~138

    • DOI

      10.1266/ggs.22-00012

    • Peer Reviewed
  • [Presentation] クロマチン修飾と転写の生細胞ダイナミクス2023

    • Author(s)
      木村 宏
    • Organizer
      第4回ゲノム生物物理学セミナー
    • Invited
  • [Presentation] Dynamics of chromatin organization and transcription in early zebrafish embryos2023

    • Author(s)
      Hiroshi Kimura
    • Organizer
      RIKEN BDR Symposium 2023
    • Int'l Joint Research / Invited
  • [Presentation] Dynamics of histone RNA polymerase II modifications in living cells2022

    • Author(s)
      Hiroshi Kimura
    • Organizer
      EMBO Workshop “Nuclear structure and dynamics”
    • Int'l Joint Research / Invited
  • [Presentation] Dynamics of histone and RNA polymerase II modifications in living cells2022

    • Author(s)
      Hiroshi Kimura
    • Organizer
      Japan-UK Regulation through Chromatin Conference 2022
    • Int'l Joint Research / Invited
  • [Presentation] Histone modification dynamics during transcription activation in living cells and embryos2022

    • Author(s)
      Hiroshi Kimura
    • Organizer
      Gordon Research Conference “Chromatin Structure and Function: Chromatin Modifications, RNA and Metabolism”
    • Int'l Joint Research / Invited
  • [Presentation] Chromatin domain organization and dynamics in zebrafish embryos as revealed by live-cell imaging2022

    • Author(s)
      Hiroshi Kimura
    • Organizer
      EMBO Workshop “Awakening of the genome: The maternal-to-zygotic transition”
    • Int'l Joint Research / Invited
  • [Remarks] 東工大 木村研究室

    • URL

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

  • [Remarks] 東工大 細胞制御工学研究センター

    • URL

      http://www.rcb.iir.titech.ac.jp/index.html

  • [Remarks] 新学術領域「遺伝子制御の基盤となるクロマチンポテンシャル」

    • URL

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

  • [Remarks] リサーチマップ 木村宏

    • URL

      https://researchmap.jp/hiroshikimura

  • [Remarks] ORCID Hiroshi Kimura

    • URL

      https://orcid.org/0000-0003-0854-083X

URL: 

Published: 2023-12-25  

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