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Elucidating the significance of chromatin modification in gene regulation by living cell imaging

Research Project

Project/Area Number 17H01417
Research Category

Grant-in-Aid for Scientific Research (A)

Allocation TypeSingle-year Grants
Section一般
Research Field Molecular biology
Research InstitutionTokyo Institute of Technology

Principal Investigator

Kimura Hiroshi  東京工業大学, 科学技術創成研究院, 教授 (30241392)

Project Period (FY) 2017-04-01 – 2021-03-31
Project Status Completed (Fiscal Year 2020)
Budget Amount *help
¥42,510,000 (Direct Cost: ¥32,700,000、Indirect Cost: ¥9,810,000)
Fiscal Year 2020: ¥10,790,000 (Direct Cost: ¥8,300,000、Indirect Cost: ¥2,490,000)
Fiscal Year 2019: ¥10,790,000 (Direct Cost: ¥8,300,000、Indirect Cost: ¥2,490,000)
Fiscal Year 2018: ¥10,790,000 (Direct Cost: ¥8,300,000、Indirect Cost: ¥2,490,000)
Fiscal Year 2017: ¥10,140,000 (Direct Cost: ¥7,800,000、Indirect Cost: ¥2,340,000)
Keywords遺伝子発現 / クロマチン / ヒストン修飾 / 転写制御 / 遺伝子発現制御 / 生細胞イメージング / エピジェネティクス / 転写調節 / 細胞分化 / ストレス応答 / 遺伝子 / 発現制御 / 発生・分化 / ゲノム / シグナル伝達
Outline of Final Research Achievements

Gene expression patterns exhibit dynamic changes as cells differentiate and respond to external signals. To understand the significance of histone modifications in transcriptional activation and inactivation, we conducted this study using a unique system for visualizing post-translational modifications in living cells. In transcriptional activation, we found that acetylation of histone H3 is important for heat shock stress-induced transcriptional activation. In addition, we showed how methylation of histone H3 and H4 accumulates during X-chromosome inactivation during mouse embryonic stem cell differentiation.

Academic Significance and Societal Importance of the Research Achievements

本研究では、刺激に応答した遺伝子活性化過程や発生・分化過程におけるクロマチン修飾の時空間的変化を明らかにした。クロマチン構造変化と転写の制御は遺伝子発現の根幹を成しており、単一細胞レベルでの生細胞計測を中心とした解析により、この制御機構の一端を解明することができた。この基盤研究の成果は、高効率な脱分化系・分化誘導系の確立や薬物動態評価等の基盤技術開発にも将来的につながると考えられ、再生医療、生殖医療、薬剤開発等にも広く波及効果を及ぼすと期待できる。

Report

(5 results)
  • 2020 Annual Research Report   Final Research Report ( PDF )
  • 2019 Annual Research Report
  • 2018 Annual Research Report
  • 2017 Annual Research Report
  • Research Products

    (55 results)

All 2021 2020 2019 2018 2017 Other

All Int'l Joint Research (13 results) Journal Article (22 results) (of which Int'l Joint Research: 12 results,  Peer Reviewed: 16 results,  Open Access: 17 results) Presentation (10 results) (of which Int'l Joint Research: 5 results,  Invited: 10 results) Remarks (9 results) Patent(Industrial Property Rights) (1 results)

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

    • Related Report
      2019 Annual Research Report
  • [Int'l Joint Research] University of Copenhagen(デンマーク)

    • 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] Curie Institute(フランス)

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

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

    • Related Report
      2018 Annual Research Report
  • [Int'l Joint Research] キュリー研究所(フランス)

    • Related Report
      2017 Annual Research Report
  • [Int'l Joint Research] フロリダ州立大学/コロラド州立大学(米国)

    • Related Report
      2017 Annual Research Report
  • [Int'l Joint Research] ケンブリッジ大学(英国)

    • Related Report
      2017 Annual Research Report
  • [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: - Issue: 5 Pages: 298-312

    • 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 Issue: 3

    • DOI

      10.15252/embr.202051989

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [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 Issue: 1 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] 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 Issue: 4

    • DOI

      10.1073/pnas.2019554118

    • 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] Chromatin integration labeling for mapping DNA-binding proteins and modifications with low input.2020

    • Author(s)
      Tetsuya Handa, Akihito Harada, Kazumitsu Maehara, Shoko Sato, Masaru Nakao, Naoki Goto, Hitoshi Kurumizaka, Yasuyuki Ohkawa, Hiroshi Kimura.
    • Journal Title

      Nat Protoc.

      Volume: 15 Issue: 10 Pages: 3334-3360

    • DOI

      10.1038/s41596-020-0375-8

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access
  • [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 Issue: 14

    • DOI

      10.1242/jcs.243444

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access / 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

      Nature Communications

      Volume: 11 Issue: 1 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 Issue: 38

    • DOI

      10.1126/sciadv.abc0330

    • Related Report
      2020 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

      Scientific Reports

      Volume: 9 Issue: 1 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] 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 Issue: 19

    • DOI

      10.1242/dev.179127

    • Related Report
      2019 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

      The Journal of Cell Biology

      Volume: 218 Issue: 2 Pages: 385-386

    • DOI

      10.1083/jcb.201811170

    • 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 Issue: 1 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] A chromatin integration labelling method enables epigenomic profiling with lower input2018

    • 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

      Nature Cell Biology

      Volume: 21 Issue: 2 Pages: 287-296

    • DOI

      10.1038/s41556-018-0248-3

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] NOTCH-mediated non-cell autonomous regulation of chromatin structure during senescence2018

    • Author(s)
      Parry AJ, Hoare M, Bihary D, Hansel-Hertsch R, Smith S, Tomimatsu K, Mannion E, Smith A, D'Santos P, Russel IA, Balasubramanian S, Kimura H, Samarajiwa SA, Narita M.
    • Journal Title

      Nat Commun

      Volume: 9 Issue: 1 Pages: 1840-1840

    • DOI

      10.1038/s41467-018-04283-9

    • Related Report
      2018 Annual Research Report 2017 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [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

    • ISBN
      9781493987658, 9781493987665
    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Nucleome Consortium2018

    • Author(s)
      TASHIRO Satoshi、KIMURA Hiroshi
    • Journal Title

      Seibutsu Butsuri

      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] 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] Transcription organizes euchromatin similar to an active microemulsion2018

    • Author(s)
      Hilbert Lennart、Sato Yuko、Kimura Hiroshi、J?licher Frank、Honigmann Alf、Zaburdaev Vasily、Vastenhouw Nadine
    • Journal Title

      bioRxiv

      Volume: - Pages: 234112-234112

    • DOI

      10.1101/234112

    • Related Report
      2018 Annual Research Report
    • Open Access / Int'l Joint Research
  • [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
  • [Journal Article] H3S10ph broadly marks early-replicating domains in interphase ESCs and shows reciprocal antagonism with H3K9me2.2018

    • Author(s)
      Chen CCL, Goyal P, Karimi MM, Abildgaard MH, Kimura H, Lorincz MC.
    • Journal Title

      Genome Res

      Volume: 28 Issue: 1 Pages: 37-51

    • DOI

      10.1101/gr.224717.117

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [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] 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] 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] クロマチン修飾ダイナミクスと転写制御2017

    • Author(s)
      木村宏
    • Organizer
      第40回日本分子生物学会年会
    • Related Report
      2017 Annual Research Report
    • Invited
  • [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 2019 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 2019 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 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
  • [Remarks] 東工大 木村宏 研究室

    • URL

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

    • Related Report
      2017 Annual Research Report
  • [Remarks] 東工大 細胞制御工学研究センター

    • URL

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

    • Related Report
      2017 Annual Research Report
  • [Remarks] 東工大 木村宏 研究者情報

    • URL

      http://t2r2.star.titech.ac.jp/cgi-bin/researcherinfo.cgi?q_researcher_content_number=CTT100673940#

    • Related Report
      2017 Annual Research Report
  • [Patent(Industrial Property Rights)] ヒストンH3トリメチル化リシン特異的モノクローナル抗体又はその抗原結合性断片2017

    • Inventor(s)
      木村 宏、佐藤優子、大井彰人、胡桃坂仁志、鯨井智也、他
    • Industrial Property Rights Holder
      東京工業大学
    • Industrial Property Rights Type
      特許
    • Industrial Property Number
      2017-111580
    • Filing Date
      2017
    • Related Report
      2017 Annual Research Report

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Published: 2017-04-28   Modified: 2022-03-29  

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