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The structural study of heterochromatin by cryo-EM

Research Project

Project/Area Number 16K18473
Research Category

Grant-in-Aid for Young Scientists (B)

Allocation TypeMulti-year Fund
Research Field Genome biology
Research InstitutionWaseda University

Principal Investigator

Machida Shinichi  早稲田大学, 理工学術院, 助教 (50732195)

Project Period (FY) 2016-04-01 – 2018-03-31
Project Status Completed (Fiscal Year 2017)
Budget Amount *help
¥4,030,000 (Direct Cost: ¥3,100,000、Indirect Cost: ¥930,000)
Fiscal Year 2017: ¥1,170,000 (Direct Cost: ¥900,000、Indirect Cost: ¥270,000)
Fiscal Year 2016: ¥2,860,000 (Direct Cost: ¥2,200,000、Indirect Cost: ¥660,000)
Keywordsエピジェネティクス / クロマチン / ヒストン / ヘテロクロマチン / HP1 / ヒストン修飾 / ヌクレオソーム / H3K9me3
Outline of Final Research Achievements

Heterochromatin functions as an important component for gene silencing and genome maintenance by the formation of condensed chromatin structures. The methylation of histone H3 at lysine 9 (H3K9me3) and its recognition by HP1 represent heterochromatin formation. However, it is unclear how HP1 folds chromatin containing H3K9me3 into condensed chromatin. In this study, we reconstituted H3K9me3 chromatin complexed with human HP1, and determined the structure of H3K9me3 chromatin complexed with HP1 by cryogenic electron microscopy.

Report

(3 results)
  • 2017 Annual Research Report   Final Research Report ( PDF )
  • 2016 Research-status Report
  • Research Products

    (15 results)

All 2018 2017 2016 Other

All Journal Article (11 results) (of which Int'l Joint Research: 1 results,  Peer Reviewed: 11 results,  Open Access: 8 results,  Acknowledgement Compliant: 4 results) Presentation (1 results) Remarks (3 results)

  • [Journal Article] Cryo-EM structure of the nucleosome containing the ALB1 enhancer DNA sequence2018

    • Author(s)
      Takizawa Yoshimasa、Tanaka Hiroki、Machida Shinichi、Koyama Masako、Maehara Kazumitsu、Ohkawa Yasuyuki、Wade Paul A.、Wolf Matthias、Kurumizaka Hitoshi
    • Journal Title

      Open Biology

      Volume: 8 Issue: 3 Pages: 170255-170255

    • DOI

      10.1098/rsob.170255

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Structural Basis of Heterochromatin Formation by Human HP12018

    • Author(s)
      Machida Shinichi、Takizawa Yoshimasa、Ishimaru Masakazu、Sugita Yukihiko、Sekine Satoshi、Nakayama Jun-ichi、Wolf Matthias、Kurumizaka Hitoshi
    • Journal Title

      Molecular Cell

      Volume: 69 Issue: 3 Pages: 385-397

    • DOI

      10.1016/j.molcel.2017.12.011

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed
  • [Journal Article] HP1との結合により形成される構成的なヘテロクロマチンの基盤となる構造2018

    • Author(s)
      町田晋一, 滝沢由政, Matthias Wolf, 胡桃坂仁志
    • Journal Title

      First Author's

      Volume: . Pages: 014

    • DOI

      10.7875/first.author.2018.014

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Phosphorylation of CBX2 controls its nucleosome-binding specificity2017

    • Author(s)
      Takayuki Kawaguchi, Shinichi Machida, Hitoshi Kurumizaka, Hideaki Tagami, Jun-ichi Nakayama
    • Journal Title

      The Journal of Biochemistry

      Volume: 162 Issue: 5 Pages: 343-355

    • DOI

      10.1093/jb/mvx040

    • NAID

      40021394855

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Histone H3 Methylated at Arginine 17 Is Essential for Reprogramming the Paternal Genome in Zygotes.2017

    • Author(s)
      Hatanaka Y, Tsusaka T, Shimizu N, Morita K, Suzuki T, Machida S, Satoh M, Honda A, Hirose M, Kamimura S, Ogonuki N, Nakamura T, Inoue K, Hosoi Y, Dohmae N, Nakano T, Kurumizaka H, Matsumoto K, Shinkai Y, Ogura A.
    • Journal Title

      Cell Rep

      Volume: 20(12) Issue: 12 Pages: 2756-2765

    • DOI

      10.1016/j.celrep.2017.08.088

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] SYCP3 regulates strand invasion activities of RAD51 and DMC12017

    • Author(s)
      Kobayashi Wataru、Hosoya Noriko、Machida Shinichi、Miyagawa Kiyoshi、Kurumizaka Hitoshi
    • Journal Title

      Genes to Cells

      Volume: 22 Issue: 9 Pages: 799-809

    • DOI

      10.1111/gtc.12513

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Xeroderma pigmentosum group C protein interacts with histones: regulation by acetylated states of histone H3.2017

    • Author(s)
      Kakumu E
    • Journal Title

      Genes Cells.

      Volume: 3 Issue: 3 Pages: 310-327

    • DOI

      10.1111/gtc.12479

    • Related Report
      2017 Annual Research Report 2016 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Influence of polynucleosome preparation methods on sedimentation velocity analysis of chromatin.2017

    • Author(s)
      Kujirai T, Machida S, Osakabe A, Kurumizaka H.
    • Journal Title

      J. Biochem.

      Volume: 161 Issue: 4 Pages: 381-388

    • DOI

      10.1093/jb/mvw081

    • NAID

      40021219908

    • Related Report
      2017 Annual Research Report 2016 Research-status Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Testis-Specific Histone Variant H3t Gene Is Essential for Entry into Spermatogenesis2017

    • Author(s)
      Ueda J., Harada A., Urahama T., Machida S., Maehara K., Hada M., Makino Y., Nogami J., Horikoshi N., Osakabe A., Taguchi H., Tanaka H., Tachiwana H., Yao T., Yamada M., Iwamoto T., Isotani A., Ikawa M., Tachibana T., Okada Y., Kimura H., Ohkawa Y., Kurumizaka H., Yamagata K.
    • Journal Title

      Cell Reports

      Volume: 18(3) Issue: 3 Pages: 593-600

    • DOI

      10.1016/j.celrep.2016.12.065

    • NAID

      120006957416

    • Related Report
      2016 Research-status Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Chromatin architecture may dictate the target site for DMC1, but not for RAD51, during homologous pairing2016

    • Author(s)
      Kobayashi W., Takaku M., Machida S., Tachiwana H., Maehara K., Ohkawa Y. and Kurumizaka H
    • Journal Title

      Scientific reports

      Volume: 6 Issue: 1 Pages: 24428-24428

    • DOI

      10.1038/srep24228

    • Related Report
      2016 Research-status Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Structural and biochemical analyses of monoubiquitinated human histones H2B and H42016

    • Author(s)
      Machida S, Sekine S, Nishiyama Y, Horikoshi N, Kurumizaka H.
    • Journal Title

      Open Biol.

      Volume: 6 Issue: 6 Pages: 160090-160090

    • DOI

      10.1098/rsob.160090

    • Related Report
      2016 Research-status Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Presentation] ヘテロクロマチンの立体構造解析2017

    • Author(s)
      町田晋一、滝沢由政、石丸雅一、関根慧、中山潤一、Matthias Wolf、胡桃坂仁志
    • Organizer
      第11回日本エピジェネティクス研究会年会
    • Related Report
      2017 Annual Research Report
  • [Remarks] 早稲田大学ホームページ

    • URL

      https://www.waseda.jp/top/news/56537

    • Related Report
      2017 Annual Research Report
  • [Remarks] 沖縄科学技術大学院大学ホームページ

    • URL

      https://www.oist.jp/ja/news-center/press-releases/32226

    • Related Report
      2017 Annual Research Report
  • [Remarks] 基礎生物学研究所ホームページ

    • URL

      http://www.nibb.ac.jp/press/2018/01/11.html

    • Related Report
      2017 Annual Research Report

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Published: 2016-04-21   Modified: 2019-03-29  

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