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Structural basis for establishment and maintenance of DNA methylation and histone H3K9me3

Planned Research

Project AreaMechanisms underlying replication of non-genomic codes that mediate plasticity and robustness for cellular inheritance
Project/Area Number 19H05741
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 InstitutionYokohama City University

Principal Investigator

Arita Kyohei  横浜市立大学, 生命医科学研究科, 教授 (40549648)

Project Period (FY) 2019-06-28 – 2024-03-31
Project Status Completed (Fiscal Year 2023)
Budget Amount *help
¥80,600,000 (Direct Cost: ¥62,000,000、Indirect Cost: ¥18,600,000)
Fiscal Year 2023: ¥13,130,000 (Direct Cost: ¥10,100,000、Indirect Cost: ¥3,030,000)
Fiscal Year 2022: ¥14,950,000 (Direct Cost: ¥11,500,000、Indirect Cost: ¥3,450,000)
Fiscal Year 2021: ¥16,770,000 (Direct Cost: ¥12,900,000、Indirect Cost: ¥3,870,000)
Fiscal Year 2020: ¥13,130,000 (Direct Cost: ¥10,100,000、Indirect Cost: ¥3,030,000)
Fiscal Year 2019: ¥22,620,000 (Direct Cost: ¥17,400,000、Indirect Cost: ¥5,220,000)
Keywords構造生物学 / DNA維持メチル化 / UHRF1 / DNMT1 / DPPA3 / 非ゲノム情報複製 / cryo-EM / X線結晶構造解析 / Cryo-EM / 非ゲノム情報 / DNAメチル化 / ヒストン修飾 / ユビキチン化 / クライオ電子顕微鏡 / DNA複製 / クロマチン
Outline of Research at the Start

DNAメチル化やヒストンH3K9のメチル化(H3K9me3)は、クロマチンの構造変換を制御する遺伝子発現抑制的な非ゲノム情報である。これらの非ゲノム情報が発生・分化過程でどのように確立し、そして多細胞形質体を維持するために体細胞分裂後にどのように複製されていくのかは不明な点が多い。本研究では、非ゲノム情報による遺伝子発現抑制の確立と複製にかかる構造基盤として、ユビキチン化された複製因子PAF15とSETDB1によるDNA維持メチル化とH3K9me3の確立・複製に注目し、それぞれの分子機構を構造生物学的な観点から明らかにする。

Outline of Final Research Achievements

The aim of this study was to establish a structural basis for the replication of non-genome, especially DNA methylation and H3K9me3. Regarding H3K9me3, we established the preparation of ubiquitinated SETDB1, which is an enzymatically activated form. Cryo-EM analysis revealed a novel activation mechanism of the maintenance methyltransferase DNMT1 in DNA maintenance methylation. The structural basis for the inhibition of UHRF1 function by the maternal factor DPPA3 was elucidated using solution NMR. As a developmental study, a combination of computational science and structural biology was used to search for functional inhibitors of UHRF1, and compounds that inhibit binding to LIG1 were successfully identified. These findings led to the proposal of a novel regulatory mechanism for replication of the non-genome.

Academic Significance and Societal Importance of the Research Achievements

本研究成果は、非ゲノム情報であるDNAメチル化の維持機構を構造生物学的に明らかにして、DNAメチル化が個体の生涯を通して維持される生物学的に重要な分子機構の理解につながった。また、DNAメチル化の異常がもたらすがんの薬剤開発に向けて、DNA維持メチル化因子UHRF1の機能阻害剤の探索に成功した。今後の抗がん剤開発につながる研究成果を得た。

Report

(6 results)
  • 2023 Annual Research Report   Final Research Report ( PDF )
  • 2022 Annual Research Report
  • 2021 Annual Research Report
  • 2020 Annual Research Report
  • 2019 Annual Research Report
  • Research Products

    (49 results)

All 2024 2023 2022 2021 2020 2019 Other

All Int'l Joint Research (3 results) Journal Article (11 results) (of which Int'l Joint Research: 8 results,  Peer Reviewed: 11 results,  Open Access: 8 results) Presentation (29 results) (of which Int'l Joint Research: 5 results,  Invited: 5 results) Remarks (6 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] CNRS(フランス)

    • Related Report
      2021 Annual Research Report
  • [Journal Article] Cryo-electron microscopy reveals the impact of the nucleosome dynamics on transcription activity2024

    • Author(s)
      Arita Kyohei
    • Journal Title

      The Journal of Biochemistry

      Volume: 175 Issue: 4 Pages: 383-385

    • DOI

      10.1093/jb/mvae004

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Cooperative DNA-binding activities of Chp2 are critical for its function in heterochromatin assembly2023

    • Author(s)
      Rahayu Anisa Fitri、Hayashi Aki、Yoshimura Yuriko、Nakagawa Reiko、Arita Kyohei、Nakayama Jun-ichi
    • Journal Title

      The Journal of Biochemistry

      Volume: 174 Issue: 4 Pages: 371-382

    • DOI

      10.1093/jb/mvad050

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed
  • [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] 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] 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] Preparation of the ubiquitination-triggered active form of SETDB1 in Escherichia coli for biochemical and structural analyses2021

    • Author(s)
      Funyu Tomoko、Kanemaru Yuka、Onoda Hiroki、Arita Kyohei
    • Journal Title

      The Journal of Biochemistry

      Volume: 170 Issue: 5 Pages: 655-662

    • DOI

      10.1093/jb/mvab087

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Crystal structure of inhibitor-bound human MSPL that can activate high pathogenic avian influenza2021

    • Author(s)
      Ohno Ayako、Maita Nobuo、Tabata Takanori、Nagano Hikaru、Arita Kyohei、Ariyoshi Mariko、Uchida Takayuki、Nakao Reiko、Ulla Anayt、Sugiura Kosuke、Kishimoto Koji、Teshima-Kondo Shigetada、Okumura Yuushi、Nikawa Takeshi
    • Journal Title

      Life Science Alliance

      Volume: 4 Issue: 6 Pages: e202000849-e202000849

    • DOI

      10.26508/lsa.202000849

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Structural dynamics of double-stranded DNA with epigenome modification2020

    • Author(s)
      Furukawa Ayako、Walinda Erik、Arita Kyohei、Sugase Kenji
    • Journal Title

      Nucleic Acids Research

      Volume: 49 Issue: 2 Pages: 1152-1162

    • DOI

      10.1093/nar/gkaa1210

    • NAID

      120006943328

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Serine 298 Phosphorylation in Linker 2 of UHRF1 Regulates Ligand-Binding Property of Its Tandem Tudor Domain2020

    • Author(s)
      Kori Satomi、Jimenji Tomohiro、Ekimoto Toru、Sato Miwa、Kusano Fumie、Oda Takashi、Unoki Motoko、Ikeguchi Mitsunori、Arita Kyohei
    • Journal Title

      Journal of Molecular Biology

      Volume: 432 Issue: 14 Pages: 4061-4075

    • DOI

      10.1016/j.jmb.2020.05.006

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Enhanced processivity of Dnmt1 by monoubiquitinated histone H32020

    • Author(s)
      Y. Mishima, L. Brueckner, S. Takahashi, T. Kawakami, J. Otani, A. Shinohara, K. Takeshita, R. G. Garvilles, M. Watanabe, N. Sakai, H. Takeshima, C. Nachtegael, A. Nishiyama, M. Nakanishi, K. Arita, K. Nakashima, H. Hojo, I. Suetake
    • Journal Title

      Genes Cells

      Volume: 25 Issue: 1 Pages: 22-32

    • DOI

      10.1111/gtc.12732

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Structure of PCNA in complex with DNMT1 PIP box reveals the basis for the molecular mechanism of the interaction.2019

    • Author(s)
      1.Jimenji T, Matsumura R, Kori S, Arita K.
    • Journal Title

      Biochem. Biophys. Res. Commun.

      Volume: 516 Issue: 2 Pages: 578-583

    • DOI

      10.1016/j.bbrc.2019.06.060

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed
  • [Presentation] Structural basis for activation mechanism of DNMT12023

    • Author(s)
      Kyohei Arita
    • Organizer
      The 2nd International Symposium on REPLICATION of NON GENOME
    • Related Report
      2023 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] DNMT1:ユビキチン化H3:DNA複合体構造によるDNA維持メチル化の活性化機構の解明2022

    • Author(s)
      菊地杏美香, 小野田浩宜, 山口幸佑, 郡聡実, 山形敦史, Defossez Pierre-Antoine, 有田恭平
    • Organizer
      第45回 日本分子生物学会年会
    • Related Report
      2022 Annual Research Report
  • [Presentation] ユビキチン化によるSETDB1の酵素活性化機構の解明2022

    • Author(s)
      舩生 智子、山形 敦史、有田 恭平
    • Organizer
      第45回分子生物学会年会
    • Related Report
      2022 Annual Research Report
  • [Presentation] USP7によるユビキチン化ヒストンH3の脱ユビキチン化機構の解明2022

    • Author(s)
      吉見 早恵 小野田 浩宜 加藤 修衣 山形 敦史 有田 恭平
    • Organizer
      第45回分子生物学会年会
    • Related Report
      2022 Annual Research Report
  • [Presentation] エピジェネティック修飾ヌクレオソームに対するUHRF1の相互作用様式の検証2022

    • Author(s)
      敷町 怜愛, 松澤 舜, 蛭田萌里, 小野田 浩宜, 山形敦史, 有田 恭平
    • Organizer
      第45回分子生物学会年会
    • Related Report
      2022 Annual Research Report
  • [Presentation] UHRF1によるマルチモノユビキチン化機構の構造生物学的研究2022

    • Author(s)
      蛭田 萌理, 松澤 舜, 敷町 怜愛, 有田 恭平
    • Organizer
      第45回分子生物学会年会
    • Related Report
      2022 Annual Research Report
  • [Presentation] DNA維持メチル化関連タンパク質の活性・クロマチン局在制御の構造基盤2022

    • Author(s)
      有田恭平
    • Organizer
      第45回日本分子生物学会年会
    • Related Report
      2022 Annual Research Report
    • Invited
  • [Presentation] DPPA3によるUHRF1のクロマチン局在阻害の構造基盤2022

    • Author(s)
      有田恭平
    • Organizer
      第95回日本生化学会年会
    • Related Report
      2022 Annual Research Report
    • Invited
  • [Presentation] Structural basis for activation of DNA methyltransferase.2022

    • Author(s)
      有田恭平
    • Organizer
      第15回日本エピジェネティクス研究会年会
    • Related Report
      2022 Annual Research Report
    • Invited
  • [Presentation] グアニン四重鎖によるDNMT1の活性阻害機構の解明2022

    • Author(s)
      菊地杏美香, 小野田浩宜, 山形敦史, 有田恭平
    • Organizer
      第15回 日本エピジェネティクス研究会年会
    • Related Report
      2022 Annual Research Report
  • [Presentation] 大腸菌内ユビキチン化システムによる活性型 SETDB1 の調製と評価2022

    • Author(s)
      舩生 智子、小野田 浩宜、山形 敦史、有田 恭平
    • Organizer
      第22回日本蛋白質科学会年会
    • Related Report
      2022 Annual Research Report
  • [Presentation] 母性因子Stellaと維持メチル化因子UHRF1のNMRを用いた相互作用解析2021

    • Author(s)
      畑圭一, 小沼剛, 杉村奎汰, 西山敦哉, 林剛介, 池上貴久, 中西真, 有田恭平
    • Organizer
      第44回分子生物学会年会
    • Related Report
      2021 Annual Research Report
  • [Presentation] マルチモノユビキチン化機構の解明に向けたエピジェネティック修飾ヌクレオソームの調製2021

    • Author(s)
      敷町怜愛, 松澤舜, 小野田浩宜, 有田恭平
    • Organizer
      第44回分子生物学会年会
    • Related Report
      2021 Annual Research Report
  • [Presentation] G-quadruplex構造によるDNMT1の活性阻害機構の解明2021

    • Author(s)
      菊地杏美香, 小野田浩宜, 山形敦史, 有田恭平
    • Organizer
      第44回分子生物学会年会
    • Related Report
      2021 Annual Research Report
  • [Presentation] ユビキチン化依存的なSETDB1の酵素活性化機構解明に向けた、大腸菌内ユビキチン化システムの構築とその評価2021

    • Author(s)
      舩生智子, 金丸由桂, 有田恭平
    • Organizer
      第44回分子生物学会年会
    • Related Report
      2021 Annual Research Report
  • [Presentation] USP7によるユビキチン化ヒストンH3の脱ユビキチン化機構の解明2021

    • Author(s)
      吉見早恵, 小野田浩宜, 山形敦史, 有田恭平
    • Organizer
      第44回分子生物学会年会
    • Related Report
      2021 Annual Research Report
  • [Presentation] DNAメチル化を制御する薬剤の開発:構造生物学と計算科学を組み合わせた維持メチル化因子UHRF1の機能阻害剤の探索2021

    • Author(s)
      郡聡実, 柴橋佑希, 浴本亨, 西山敦哉, 吉見早恵 ,長門石暁, 大田雅照, 津本浩平, 中西真, 池口満徳, 有田恭平
    • Organizer
      第44回日本分子生物学会年会
    • Related Report
      2021 Annual Research Report
  • [Presentation] 計算科学と構造生物学を組み合わせたスクリーニングによるDNAメチル化制御薬の開発2021

    • Author(s)
      郡聡実, 柴橋佑希, 浴本亨, 西山敦哉, 吉見早恵, 長門石暁, 大田雅照, 津本浩平, 中西真, 池口満徳, 有田恭平
    • Organizer
      第12回スクリーニング学研究会
    • Related Report
      2021 Annual Research Report
  • [Presentation] Development of UHRF1 inhibitor based on the structural study of the recognition of methylated DNA ligase 1 by UHRF12021

    • Author(s)
      Satomi Kori, Yuki Shibahashi, Toru Ekimoto, Atsuya Nishiyama, Sae Yoshimi, Satoru Nagatoishi, Masateru Ohta, Kouhei Tsumoto, Mitsunori Ikeguchi, and Kyohei Arita
    • Organizer
      PDBアジア地区50周年記念シンポジウム
    • Related Report
      2021 Annual Research Report
  • [Presentation] DNAメチル化制御薬の開発:維持メチル化因子UHRF1の機能阻害剤のリード化合物の同定2021

    • Author(s)
      郡聡実, 柴橋佑希, 浴本亨, 西山敦哉, 吉見早恵, 長門石暁, 大田雅照, 津本浩平, 中西真, 池口満徳, 有田恭平
    • Organizer
      第49回構造活性相関シンポジウム
    • Related Report
      2021 Annual Research Report
  • [Presentation] 構造生物学から見たDNAメチル化が複製されていく仕組み2021

    • Author(s)
      有田恭平
    • Organizer
      第14回日本エピジェネティクス研究会年会
    • Related Report
      2020 Annual Research Report
    • Invited
  • [Presentation] The proper timing phosphorylation of Ser298 selects UHRF1-binding partners2020

    • Author(s)
      Satomi Kori, Tomohiro Jimenji, Toru Ekimoto, Laure Ferry, Shohei Matano, Miwa Sato, Fumie Kusano, Motoko Unoki, Pierre-Antoine Defossez, Mitsunori Ikeguchi, Kyohei Arita
    • Organizer
      第14回日本エピジェネティクス研究会年会
    • Related Report
      2020 Annual Research Report
  • [Presentation] Structural basis for the switching of binding partners by Ser298 phosphorylation in UHRF12020

    • Author(s)
      Satomi Kori, Tomohiro Jimenji, Toru Ekimoto, Miwa Sato, Fumie Kusano, Takashi Oda, Motoko Unoki, Mitsunori Ikeguchi, Kyohei Arita
    • Organizer
      第20回蛋白質科学会年会
    • Related Report
      2020 Annual Research Report
  • [Presentation] Conserved phosphorylation in UHRF1-binding partners regulates its binding to the peptide binding groove of UHRF1 TTD domain2019

    • Author(s)
      Satomi Kori, Laure Ferry, Shohei Matano, Tomohiro Jimenji, Toru Ekimoti, Takashi Oda, Pierre-Antoine Defossez, Mitsunori Ikeguchi, Kyohei Arita
    • Organizer
      16th Conference of the Asian Crystallographic Association: AsCA2019
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Structural basis for recognition of DNMT1 PIP box by PCNA2019

    • Author(s)
      Tomohiro Jimenji, Satomi Kori, Kyohei Arita
    • Organizer
      16th Conference of the Asian Crystallographic Association: AsCA2019
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research
  • [Presentation] UHRF1によるヒストンH3のマルチプルモノユビキチン化機構2019

    • Author(s)
      松澤舜, 若月誠, 柴野歩実, 郡聡実, 古川亜矢子, 西村善文, 西山敦哉, 中西真, 有田恭平
    • Organizer
      第42回分子生物学会年会
    • Related Report
      2019 Annual Research Report
  • [Presentation] 複製因子PAF15のマルチプルモノユビキチン化シグナル形成機構2019

    • Author(s)
      柴野歩実, 松澤舜, 郡聡実, 西山敦哉, 中西真, 有田恭平
    • Organizer
      第42回分子生物学会年会
    • Related Report
      2019 Annual Research Report
  • [Presentation] Structural Study for Recognition of Ubiquitylated Histone H3 by DNA Methyltransferase2019

    • Author(s)
      Arita Kyohei, Ishiyama Satoshi, Nishiyama, Atsuya, Defossez, Pierre-Antoine, Nakanishi, Makoto
    • Organizer
      ECM32 32nd European Crystallographic Meeting
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Crystal structure of UHRF1:LIG1 complex revealed structural change of UHRF1 and the key residues for high affinity binding2019

    • Author(s)
      Satomi Kori, Laure Ferry, Shohei Matano, Noriyuki Kodera, Takashi Oda, Pierre-Antoine Defossez,Kyohei Arita
    • Organizer
      ECM32 32nd European Crystallographic Meeting
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research
  • [Remarks] 卵子形成に必須なタンパク質DPPA3によるUHRF1の 機能阻害の分子機構を解明

    • URL

      http://www.tsurumi.yokohama-cu.ac.jp/news/202211arita_nar.html

    • Related Report
      2022 Annual Research Report
  • [Remarks] 細胞運命を決定するタンパク質DNMT1の活性制御機構を解明

    • URL

      http://www.tsurumi.yokohama-cu.ac.jp/news/202211arita_natcommun.html

    • Related Report
      2022 Annual Research Report
  • [Remarks] 横浜市立大学 生命医科学研究科 構造生物学研究室 有田グループ

    • URL

      http://www-mls.tsurumi.yokohama-cu.ac.jp/xtal-mls/members/kyouhei/index.html

    • Related Report
      2021 Annual Research Report
  • [Remarks] メチル基1つでDNAの運動性が変わることを解明 ~運動性というDNA上の目印~

    • URL

      https://www.yokohama-cu.ac.jp/news/2020/202012arita.html

    • Related Report
      2020 Annual Research Report
  • [Remarks] リン酸化によるUHRF1の結合相手の制御の仕組みを解明

    • URL

      https://www.yokohama-cu.ac.jp/news/2020/202006arita.html

    • Related Report
      2020 Annual Research Report
  • [Remarks] DNA維持メチル化酵素の複製サイトへの呼び込みの仕組みの一端を解明

    • URL

      http://www.tsurumi.yokohama-cu.ac.jp/news/20190712_arita.html

    • Related Report
      2019 Annual Research Report

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Published: 2019-07-04   Modified: 2025-01-30  

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