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Regulation of Enhanceosome by Cohesin

Research Project

Project/Area Number 20H05686
Research Category

Grant-in-Aid for Scientific Research (S)

Allocation TypeSingle-year Grants
Review Section Broad Section G
Research InstitutionThe University of Tokyo

Principal Investigator

Shirahige Katsuhiko  東京大学, 定量生命科学研究所, 教授 (90273854)

Co-Investigator(Kenkyū-buntansha) 須谷 尚史  東京大学, 定量生命科学研究所, 准教授 (30401524)
中戸 隆一郎  東京大学, 定量生命科学研究所, 准教授 (60583044)
Project Period (FY) 2020-08-31 – 2025-03-31
Project Status Completed (Fiscal Year 2024)
Budget Amount *help
¥197,340,000 (Direct Cost: ¥151,800,000、Indirect Cost: ¥45,540,000)
Fiscal Year 2024: ¥30,940,000 (Direct Cost: ¥23,800,000、Indirect Cost: ¥7,140,000)
Fiscal Year 2023: ¥37,700,000 (Direct Cost: ¥29,000,000、Indirect Cost: ¥8,700,000)
Fiscal Year 2022: ¥38,610,000 (Direct Cost: ¥29,700,000、Indirect Cost: ¥8,910,000)
Fiscal Year 2021: ¥42,510,000 (Direct Cost: ¥32,700,000、Indirect Cost: ¥9,810,000)
Fiscal Year 2020: ¥47,580,000 (Direct Cost: ¥36,600,000、Indirect Cost: ¥10,980,000)
Keywords染色体ループ / コヒーシン / 転写伸長反応 / 転写開始複合体 / 転写の一時停止 / 染色体構築 / 染色体動態制御 / SMC複合体 / 転写制御 / ゲノム高次構造 / 染色体高次構造 / 染色体動態 / エンハンソソーム / リモデリング複合体 / ヒストン密度 / in vitro転写系 / ATPase / コヒーシンローダー / prefab
Outline of Research at the Start

コヒーシンは真核細胞の染色体高次構造制御において中心的な役割を果たすタンパク質複合体であり、近年、ATP依存的にDNAにループ構造を導入するモーター活性を有することが示されてきている。その役割は、発生・分化制御やがん悪性化において重要な役割を果たすことが示唆される。一部のエンハンサーDNA上には「液-液相分離」に支配される不定形で動的な巨大タンパク質ネットワークが形成されていると報告されているが、本研究は、エンハンソソームによる転写伸長制御反応を特にコヒーシンに焦点を当てて分子的に理解すること、その生理的意義を明らかにすることを目的とする。

Outline of Final Research Achievements

This study analyzed the role of cohesin in regulating transcription elongation and revealed that cohesin has two distinct functions near the transcription start site. One is to promote enhancer-promoter interactions and positively regulate the formation of the transcription initiation complex; the other is to stabilize the paused state of RNA polymerase II (Pol II). Using a mathematical model, we demonstrated that gene expression changes observed upon cohesin depletion can be quantitatively explained by the combined effects of these two functions. This work highlights the dual role of cohesin in transcriptional regulation and its contribution to RNA quality control, providing important insights into the mechanisms of gene expression regulation. These findings may have potential applications in disease research and drug development.

Academic Significance and Societal Importance of the Research Achievements

本研究で、コヒーシンを中心とするSMC複合体が染色体立体構造を介し多段階の転写制御を担うことを解明した。特にPol IIのpausing保持と転写開始複合体形成促進という機構が示され、コヒーシン欠損RNAの品質管理上の欠陥も判明した。エンハンサー欠損がRNA品質に影響する初の証左である。さらにコヒーシン欠損は膀胱がんや急性骨髄性白血病でも高頻度に認められ、本成果は病態解明と新規治療戦略の基盤構築に寄与すると期待される。

Assessment Rating
Ex-post Assessment

A-: 一部十分ではなかったが、概ね期待どおりの成果があった

Assessment Rating
Interim Assessment

A: 順調に研究が進展しており、期待どおりの成果が見込まれる

Report

(11 results)
  • 2025 Ex-post Assessment (Comments) ( PDF )
  • 2024 Annual Research Report   Final Research Report ( PDF )
  • 2023 Annual Research Report
  • 2022 Abstract (Interim Assessment) ( PDF )   Annual Research Report   Interim Assessment (Comments) ( PDF )
  • 2021 Annual Research Report
  • 2020 Abstract ( PDF )   Comments on the Screening Results ( PDF )   Annual Research Report
  • Research Products

    (34 results)

All 2025 2024 2023 2022 2021 2020 Other

All Int'l Joint Research (10 results) Journal Article (17 results) (of which Int'l Joint Research: 7 results,  Peer Reviewed: 15 results,  Open Access: 15 results) Presentation (7 results) (of which Int'l Joint Research: 5 results,  Invited: 7 results)

  • [Int'l Joint Research] カロリンスカ研究所(スウェーデン)

    • Related Report
      2024 Annual Research Report
  • [Int'l Joint Research] フランシス クリック研究所(英国)

    • Related Report
      2024 Annual Research Report
  • [Int'l Joint Research] CIB(スペイン)

    • Related Report
      2024 Annual Research Report
  • [Int'l Joint Research] The Azrieli Faculty of Medicine(イスラエル)

    • Related Report
      2024 Annual Research Report
  • [Int'l Joint Research] Children's Hospital of Philadelphia(米国)

    • Related Report
      2022 Annual Research Report
  • [Int'l Joint Research] カロリンスカ研究所(スウェーデン)

    • Related Report
      2022 Annual Research Report
  • [Int'l Joint Research] Center for Biological Research(スペイン)

    • Related Report
      2022 Annual Research Report
  • [Int'l Joint Research] Children's Hospital of Philadelphia(米国)

    • Related Report
      2021 Annual Research Report
  • [Int'l Joint Research] カロリンスカ研究所(スウェーデン)

    • Related Report
      2021 Annual Research Report
  • [Int'l Joint Research] Center for Biological Research(スペイン)

    • Related Report
      2021 Annual Research Report
  • [Journal Article] Regulation of pericentromeric DNA loop size via Scc2-cohesin interaction2025

    • Author(s)
      Nguyen Sao Anh、Sakata Toyonori、Shirahige Katsuhiko、Sutani Takashi
    • Journal Title

      iScience

      Volume: 28 Issue: 5 Pages: 112322-112322

    • DOI

      10.1016/j.isci.2025.112322

    • Related Report
      2024 Annual Research Report
  • [Journal Article] A common molecular mechanism underlying Cornelia de Lange and CHOPS syndromes2025

    • Author(s)
      Sakata Toyonori、Tei Shoin、Izumi Kosuke、Krantz Ian D.、Bando Masashige、Shirahige Katsuhiko
    • Journal Title

      Current Biology

      Volume: 35 Issue: 6 Pages: 1353-1363

    • DOI

      10.1016/j.cub.2025.01.044

    • Related Report
      2024 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Biallelic variants in GTF3C5, a regulator of RNA polymerase III-mediated transcription, cause a multisystem developmental disorder2024

    • Author(s)
      Iwata-Otsubo Aiko、Skraban Cara M.、Yoshimura Atsunori、Sakata Toyonori、,,,Shirahige Katsuhiko、Izumi Kosuke
    • Journal Title

      Human Genetics

      Volume: 143 Issue: 3 Pages: 437-453

    • DOI

      10.1007/s00439-024-02656-3

    • Related Report
      2024 Annual Research Report
  • [Journal Article] Context-dependent perturbations in chromatin folding and the transcriptome by cohesin and related factors2023

    • Author(s)
      Nakato Ryuichiro、Sakata Toyonori、Wang Jiankang、Nagai Luis Augusto Eijy、Nagaoka Yuya、Oba Gina Miku、Bando Masashige、Shirahige Katsuhiko
    • Journal Title

      Nature Communications

      Volume: 14 Issue: 1 Pages: 5647-5647

    • DOI

      10.1038/s41467-023-41316-4

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Mesenchymal loss of p53 alters stem cell capacity and models human soft tissue sarcoma traits.2023

    • Author(s)
      Sorimachi Y, Kobayashi H, Shiozawa Y, Koide S, Nakato R, Shimizu Y, Okamura T, Shirahige K, Iwama A, Goda N, Takubo K, Takubo K.
    • Journal Title

      Stem Cell Reports

      Volume: S2213-6711(23) Issue: 5 Pages: 00097-8

    • DOI

      10.1016/j.stemcr.2023.03.009

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Cell cycle-dependent gene networks for cell proliferation activated by nuclear CK2α complexes2023

    • Author(s)
      Homma Miwako Kato、Nakato Ryuichiro、Niida Atsushi、Bando Masashige、Fujiki Katsunori、Yokota Naoko、Yamamoto So、Shibata Takeshi、Takagi Motoki、Yamaki Junko、Kozuka-Hata Hiroko、Oyama Masaaki、Shirahige Katsuhiko、Homma Yoshimi
    • Journal Title

      Life Science Alliance

      Volume: 7 Issue: 1 Pages: e202302077-e202302077

    • DOI

      10.26508/lsa.202302077

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] EVI1 exerts distinct roles in AML via ERG and cyclin D1 promoting a chemoresistant and immune-suppressive environment2023

    • Author(s)
      Masamoto Yosuke、Chiba Akira、Mizuno Hideaki、Hino Toshiya、Hayashida Hiroki、Sato Tomohiko、Bando Masashige、Shirahige Katsuhiko、Kurokawa Mineo
    • Journal Title

      Blood Advances

      Volume: 7 Issue: 8 Pages: 1577-1593

    • DOI

      10.1182/bloodadvances.2022008018

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Transient Methionine Deprivation Triggers Histone Modification and Potentiates Differentiation of Induced Pluripotent Stem Cells.2023

    • Author(s)
      Ozawa H, Kambe A, Hibi K, Murakami S, Oikawa A, Handa T, Fujiki K, Nakato R, Shirahige K, Kimura H, Shiraki N, Kume S
    • Journal Title

      Stem Cells.

      Volume: 41(3) Issue: 3 Pages: 271-286

    • DOI

      10.1093/stmcls/sxac082

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] The Epigenetic Legacy of Maternal Protein Restriction: Renal Ptger1 DNA Methylation Changes in Hypertensive Rat Offspring2023

    • Author(s)
      Jia Huijuan、Miyoshi Moe、Li Xuguang、Furukawa Kyohei、Otani Lila、Shirahige Katsuhiko、Miura Fumihito、Ito Takashi、Kato Hisanori
    • Journal Title

      Nutrients

      Volume: 15 Issue: 18 Pages: 3957-3957

    • DOI

      10.3390/nu15183957

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] HSF1 phosphorylation establishes an active chromatin state via the TRRAP TIP60 complex and promotes tumorigenesis2022

    • Author(s)
      Fujimoto Mitsuaki、Takii Ryosuke、Matsumoto Masaki、Okada Mariko、Nakayama Keiich I.、Nakato Ryuichiro、Fujiki Katsunori、Shirahige Katsuhiko、Nakai Akira
    • Journal Title

      Nature Communications

      Volume: 13 Issue: 1 Pages: 4355-4355

    • DOI

      10.1038/s41467-022-32034-4

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Cohesin-dependent chromosome loop extrusion is limited by transcription and stalled replication forks.2022

    • Author(s)
      Jeppsson K, Sakata T, Nakato R, Milanova S, Shirahige K, Bjorkegren C.
    • Journal Title

      Sci Adv.

      Volume: 8(23) Issue: 23

    • DOI

      10.1126/sciadv.abn7063

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Large-scale multi-omics analysis suggests specific roles for intragenic cohesin in transcriptional regulation.2022

    • Author(s)
      Wang J, Bando M, Shirahige K, Nakato R.
    • Journal Title

      Nat Commun

      Volume: 13(1) Issue: 1 Pages: 3218-3218

    • DOI

      10.1038/s41467-022-30792-9

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Highly rigid H3.1/H3.2-H3K9me3 domains set a barrier for cell fate reprogramming in trophoblast stem cells2022

    • Author(s)
      Hada M, Miura H, Tanigawa A, Matoba S, Inoue K, Ogonuki N, Hirose M, Watanabe N, Nakato R, Fujiki K, Hasegawa A, Sakashita A, Okae H, Miura K, Shikata D, Arima T, Shirahige K, Hiratani I, Ogura A.
    • Journal Title

      Genes Dev

      Volume: 36 Issue: 1-2 Pages: 84-102

    • DOI

      10.1101/gad.348782.121

    • Related Report
      2022 Annual Research Report 2021 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Pericentromeric noncoding RNA changes DNA binding of CTCF and inflammatory gene expression in senescence and cancer2021

    • Author(s)
      Kenichi Miyata, Yoshinori Imai, Satoshi Hori, Mika Nishio, Tze Mun Loo, Ryo Okada, Liying Yang, Tomoyoshi Nakadai, et. al.
    • Journal Title

      Proc Natl Acad Sci U S A

      Volume: 118 Issue: 35

    • DOI

      10.1073/pnas.2025647118

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Checkpoint-mediated DNA polymerase ε exonuclease activity curbing counteracts resection-driven fork collapse.2021

    • Author(s)
      Pellicano G, Al Mamun M, Jurado-Santiago D, Villa-Hernandez S, Yin X, Giannattasio M, Lanz MC, Smolka MB, Yeeles J, Shirahige K, Garcia-Diaz M, Bermejo R.
    • Journal Title

      Mol Cell.

      Volume: 81(13) Issue: 13 Pages: 2778-2792

    • DOI

      10.1016/j.molcel.2021.04.006

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Bioinformatical dissection of fission yeast DNA replication origins2020

    • Author(s)
      Koji Masuda, Claire Renard-Guillet, Katsuhiko Shirahige, Takashi Sutani
    • Journal Title

      Open Biol .

      Volume: Volume 10Issue 7 Issue: 7 Pages: 200052-200052

    • DOI

      10.1098/rsob.200052

    • 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
  • [Presentation] Transcriptional Dysregulation in Cohesinopathy2024

    • Author(s)
      KATSUHIKO SHIRAHIGE
    • Organizer
      SMC complexes:Orchestrating Diverse Genome Functions
    • Related Report
      2024 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Basic principles of transcription studied through rare diseases (Key Note lecture)2024

    • Author(s)
      KATSUHIKO SHIRAHIGE
    • Organizer
      Conference of Advanced Computing and Imaging in Biomedicine
    • Related Report
      2024 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Is Cohesin Really Necessary for Transcription?2023

    • Author(s)
      Katsuhiko Shirahige
    • Organizer
      ロッテルダム大学 セミナー
    • Related Report
      2023 Annual Research Report
    • Invited
  • [Presentation] Is Cohesin Really Necessary for Transcription?2023

    • Author(s)
      Katsuhiko Shirahige
    • Organizer
      CdLS Meeting (イタリア シエナ)
    • Related Report
      2023 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Is Cohesin Really Necessary for Transcription?2023

    • Author(s)
      Katsuhiko Shirahige
    • Organizer
      ウィーン大学セミナー
    • Related Report
      2023 Annual Research Report
    • Invited
  • [Presentation] Is Cohesin Really Necessary for Transcription?2023

    • Author(s)
      Katsuhiko Shirahige
    • Organizer
      Cohesinopathy Symposium (スペイン ザラゴザ)
    • Related Report
      2023 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Is Cohesin Really Necessary for Transcription?2023

    • Author(s)
      Katsuhiko Shirahige
    • Organizer
      生命ダイナミクスシンポジウム(台湾大学)
    • Related Report
      2023 Annual Research Report
    • Int'l Joint Research / Invited

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Published: 2020-09-07   Modified: 2026-03-16  

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