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Molecular Mechanisms for Regulation of Genomic Stability via DNA Methylation

Research Project

Project/Area Number 19H03153
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypeSingle-year Grants
Section一般
Review Section Basic Section 43010:Molecular biology-related
Research InstitutionThe University of Tokyo

Principal Investigator

Nishiyama Atsuya  東京大学, 医科学研究所, 准教授 (50378840)

Co-Investigator(Kenkyū-buntansha) 有田 恭平  横浜市立大学, 生命医科学研究科, 教授 (40549648)
Project Period (FY) 2019-04-01 – 2023-03-31
Project Status Completed (Fiscal Year 2022)
Budget Amount *help
¥17,160,000 (Direct Cost: ¥13,200,000、Indirect Cost: ¥3,960,000)
Fiscal Year 2022: ¥3,640,000 (Direct Cost: ¥2,800,000、Indirect Cost: ¥840,000)
Fiscal Year 2021: ¥4,160,000 (Direct Cost: ¥3,200,000、Indirect Cost: ¥960,000)
Fiscal Year 2020: ¥4,550,000 (Direct Cost: ¥3,500,000、Indirect Cost: ¥1,050,000)
Fiscal Year 2019: ¥4,810,000 (Direct Cost: ¥3,700,000、Indirect Cost: ¥1,110,000)
KeywordsDNAメチル化 / DNA複製 / 岡崎フラグメント / ADPリボシル化 / UHRF1 / LIG1 / ゲノム安定性 / ヒストン / PARP1 / HPF1 / LIG3 / ラギング鎖 / DNMT1
Outline of Research at the Start

ゲノム上には30万箇所を超えるDNAメチル化部位が存在し、遺伝子発現の抑制やゲノム安定性の維持に重要な役割を果たしている。しかしDNAメチル化による転写抑制のメカニズムが詳細に解析されている一方、DNAメチル化がゲノム安定性を保証するメカニズムについては明らかでない。申請者は、これまで試験管内染色体複製系を用いてDNAメチル化維持の分子機構の解明に取り組んできた。本研究では、これまでの研究成果を基にDNAメチル化がゲノム安定性を制御する分子機構の解明を目指す。

Outline of Final Research Achievements

This study focused on the interaction between the E3 ubiquitin ligase UHRF1, an important regulator of DNA methylation, and the DNA ligase LIG1, which is responsible for Okazaki fragment linkage, to clarify its significance and regulatory mechanism. First, we performed a detailed analysis of Okazaki fragment linkage using a cell-free system derived from Xenopus egg extracts and found that its dysregulation induces ADP-ribosylation by PARP1/HPF1 to activate the backup mechanism, the LIG3/XRCC1 pathway. We also showed that LIG1 binding of UHRF1, along with its previously reported interaction with PCNA, is important for the efficient linkage of the Okazaki fragment.

Academic Significance and Societal Importance of the Research Achievements

本研究は、まず岡崎フラグメント連結のバックアップ機構として働くLIG3/XRCC1経路がPARP1/HPF1によるヒストンH3ADPリボシル化を介して活性化することを明らかにし報告した。また、DNAメチル化制御因子UHRF1がLIG1との相互作用を介して岡崎フラグメント連結を制御することを示す実験結果を得ている。PARP1やDNAメチル化酵素の阻害剤は、抗がん剤としても注目されており、上記の研究成果は、染色体安定性を制御する新たな分子機構の発見にとどまらず、新たなDNAメチル化阻害剤やPARP1阻害剤開発の重要な分子基盤となることが期待される。

Report

(5 results)
  • 2022 Annual Research Report   Final Research Report ( PDF )
  • 2021 Annual Research Report
  • 2020 Annual Research Report
  • 2019 Annual Research Report
  • Research Products

    (28 results)

All 2023 2022 2021 2020 2019 Other

All Int'l Joint Research (6 results) Journal Article (8 results) (of which Int'l Joint Research: 5 results,  Peer Reviewed: 7 results,  Open Access: 6 results) Presentation (11 results) (of which Int'l Joint Research: 2 results,  Invited: 8 results) Remarks (3 results)

  • [Int'l Joint Research] CNRS(フランス)

    • Related Report
      2022 Annual Research Report
  • [Int'l Joint Research] ミュンヘン大学(ドイツ)

    • Related Report
      2022 Annual Research Report
  • [Int'l Joint Research] ロックフェラー大学(米国)

    • Related Report
      2022 Annual Research Report
  • [Int'l Joint Research] Ludwig-Maximilians-University Munchen(ドイツ)

    • Related Report
      2021 Annual Research Report
  • [Int'l Joint Research] University of Kansas(米国)

    • Related Report
      2020 Annual Research Report
  • [Int'l Joint Research] Ludwig-Maximilians-Universit Munich(ドイツ)

    • Related Report
      2019 Annual Research Report
  • [Journal Article] The termination of UHRF1-dependent PAF15 ubiquitin signaling is regulated by USP7 and ATAD52023

    • Author(s)
      Miyashita Ryota、Nishiyama Atsuya、Qin Weihua、Chiba Yoshie、Kori Satomi、Kato Norie、Konishi Chieko、Kumamoto Soichiro、Kozuka-Hata Hiroko、Oyama Masaaki、Kawasoe Yoshitaka、Tsurimoto Toshiki、Takahashi Tatsuro S、Leonhardt Heinrich、Arita Kyohei、Nakanishi Makoto
    • Journal Title

      eLife

      Volume: 12 Pages: 79013-79013

    • DOI

      10.7554/elife.79013

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Structural basis for the unique multifaceted interaction of DPPA3 with the UHRF1 PHD finger.2022

    • Author(s)
      Hata K, Kobayashi N, Sugimura K, Qin W, Haxholli D, Chiba Y, Yoshimi S, Hayashi G, Onoda H, Ikegami T, Mulholland CB, Nishiyama A, Nakanishi M, Leonhardt H, Konuma T, Arita K
    • Journal Title

      Nucleic Acids Res.

      Volume: 50 Issue: 21 Pages: 12527-12542

    • DOI

      10.1093/nar/gkac1082

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Structural basis for activation of DNMT12022

    • Author(s)
      Kikuchi A, Onoda H, Yamaguchi K, Kori S, Matsuzawa S, Chiba Y, Tanimoto S, Yoshimi S, Sato H, Yamagata A, Shirouzu M, Adachi N, Sharif J, Koseki H, Nishiyama A, Nakanishi M, Defossez PA, Arita K
    • Journal Title

      Nat Commun.

      Volume: 13 (1) Issue: 1 Pages: 1-11

    • DOI

      10.1038/s41467-022-34779-4

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Navigating the DNA methylation landscape of cancer2021

    • Author(s)
      Nishiyama Atsuya、Nakanishi Makoto
    • Journal Title

      Trends in Genetics

      Volume: 37 Issue: 11 Pages: 1012-1027

    • DOI

      10.1016/j.tig.2021.05.002

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed
  • [Journal Article] HPF1-dependent PARP activation promotes LIG3-XRCC1-mediated backup pathway of Okazaki fragment ligation2021

    • Author(s)
      Kumamoto Soichiro、Nishiyama Atsuya、Chiba Yoshie、Miyashita Ryota、Konishi Chieko、Azuma Yoshiaki、Nakanishi Makoto
    • Journal Title

      Nucleic Acids Research

      Volume: - Issue: 9 Pages: 5003-5016

    • DOI

      10.1093/nar/gkab269

    • Related Report
      2021 Annual Research Report 2020 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Structure-based screening combined with computational and biochemical analyses identified the inhibitor targeting the binding of DNA Ligase 1 to UHRF12021

    • Author(s)
      Kori Satomi、Shibahashi Yuki、Ekimoto Toru、Nishiyama Atsuya、Yoshimi Sae、Yamaguchi Kosuke、Nagatoishi Satoru、Ohta Masateru、Tsumoto Kouhei、Nakanishi Makoto、Defossez Pierre-Antoine、Ikeguchi Mitsunori、Arita Kyohei
    • Journal Title

      Bioorg Med Chem

      Volume: 52 Pages: 116500-116500

    • DOI

      10.1016/j.bmc.2021.116500

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Two distinct modes of DNMT1 recruitment ensure stable maintenance DNA methylation2020

    • Author(s)
      A. Nishiyama, C. Mulholland, S. Bultmann, S. Kori, A. Endo, Y. Saeki, W. Qin, C. Trummer, Y. Chiba, H. Yokoyama, S. Kumamoto, T. Kawakami, H. Hojo, G. Nagae, H. Aburatani, K. Tanaka, K. Arita, H. Leonhardt, M. Nakanishi
    • Journal Title

      Nat. Commun.

      Volume: 11 Issue: 1 Pages: 1222-1222

    • DOI

      10.1038/s41467-020-15006-4

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] DNA維持メチル化機構を制御するユビキチンシグナル2020

    • Author(s)
      西山敦哉
    • Journal Title

      Farumashia

      Volume: 56 Issue: 1 Pages: 36-40

    • DOI

      10.14894/faruawpsj.56.1_36

    • NAID

      130007779037

    • ISSN
      0014-8601, 2189-7026
    • Related Report
      2019 Annual Research Report
  • [Presentation] The termination of UHRF1-dependent PAF15 ubiquitin signaling is regulated by USP7 and ATAD52022

    • Author(s)
      西山敦哉
    • Organizer
      第15回エピジェネティクス研究会年会
    • Related Report
      2022 Annual Research Report
    • Invited
  • [Presentation] DNAメチル化継承の分子機構2022

    • Author(s)
      西山敦哉
    • Organizer
      日本遺伝学会第94回大会シンポジウムA
    • Related Report
      2022 Annual Research Report
    • Invited
  • [Presentation] DNMT1-DNA架橋によって誘導されるSUMOシグナルとその制御機構2022

    • Author(s)
      西山 敦哉, 谷本 翔汰, 千葉 祥恵, 遠藤 彬則, 佐伯 泰, 中西 真
    • Organizer
      第95回日本生化学会大会
    • Related Report
      2022 Annual Research Report
  • [Presentation] USP7とATAD5はUHRF1依存的なPAF15ユビキチンシグナルを制御する2022

    • Author(s)
      西山 敦哉 宮下 諒太 千葉 祥恵 郡 聡実 加藤 修衣 河添 好孝 秦 裕子 尾山 大明 高橋 達郎 有田 恭平 中西 真
    • Organizer
      第45回分子生物学会年会
    • Related Report
      2022 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] DNAメチル化と岡崎フラグメント連結をリンクする分子機構2021

    • Author(s)
      隈本宗一郎、西山敦哉、千葉祥恵、宮下諒太、小西知恵子、東義明、中西真
    • Organizer
      日本遺伝学会第93回大会
    • Related Report
      2021 Annual Research Report
    • Invited
  • [Presentation] Molecular mechanism of DNMT1-DNA cross-link repair2021

    • Author(s)
      Atsuya Nishiyama, Akinori Endoh, Yoshie Chiba, Chieko Konishi, Ayane Kaketani, Tomomi Nagatani, Yasushi, Saeki, Makoto Nakanishi
    • Organizer
      The 80th Annual Meeting of the Japanese Cancer Association
    • Related Report
      2021 Annual Research Report
    • Invited
  • [Presentation] DNAメチル化制御因子PAF15ユビキチン化の制御機構2021

    • Author(s)
      宮下諒太, 西山敦哉, 秦 裕子, 尾山 大明, 千葉 祥恵, 中西 真
    • Organizer
      第94回日本生化学会大会
    • Related Report
      2021 Annual Research Report
    • Invited
  • [Presentation] DNA複製に伴う岡崎フラグメント連結を保証する分子機構2020

    • Author(s)
      西山 敦哉, 隈本 宗一郎, 千葉 祥恵, 中西 真
    • Organizer
      第93回日本生化学会大会
    • Related Report
      2020 Annual Research Report
    • Invited
  • [Presentation] DNMT1のメチル化部位への局在を保証する2つの異なる分子機構2019

    • Author(s)
      西山 敦哉, Christopher B. Mulholland, Sebastian Bultmann, 郡 聡実, 遠藤 彬則, 千葉 祥恵, 隈本 宗一郎, 佐伯 泰, 有田 恭平, Heinrich Leonhardt, 中西 真
    • Organizer
      42nd MBSJ, Symposium ” Crosstalk between epigenome replication, genome stability, and chromatin organization ”
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] The LIG3/XRCC1 complex ensures Okazaki fragment ligation in the absence of LIG12019

    • Author(s)
      隈本 宗一郎、西山 敦哉、千葉 祥恵、中西 真
    • Organizer
      第37回染色体ワークショップ・第18回核ダイナミクス研究会
    • Related Report
      2019 Annual Research Report
  • [Presentation] Molecular mechanism of Okazaki fragment ligation2019

    • Author(s)
      隈本 宗一郎、西山 敦哉、千葉 祥恵、中西 真
    • Organizer
      第42回日本分子生物学会
    • Related Report
      2019 Annual Research Report
  • [Remarks] DNAメチル化制御因子PAF15のUSP7とATAD5を介した 不活性化の分子機構を解明

    • URL

      https://non-genome.com/activities/3214/

    • Related Report
      2022 Annual Research Report
  • [Remarks] 岡崎フラグメントの連結を堅牢に保証する分子メカニズム

    • URL

      https://non-genome.com/activities/2121/

    • Related Report
      2021 Annual Research Report 2020 Annual Research Report
  • [Remarks] 細胞記憶継承をDNA複製と協調するメカニズムの解明

    • URL

      https://www.ims.u-tokyo.ac.jp/imsut/jp/about/press/page_00056.html

    • Related Report
      2019 Annual Research Report

URL: 

Published: 2019-04-18   Modified: 2024-01-30  

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