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Study of genome maintenance / inheritance mechanism based on chromosome 4D structure analysis

Research Project

Project/Area Number 15H02369
Research Category

Grant-in-Aid for Scientific Research (A)

Allocation TypeSingle-year Grants
Section一般
Research Field Genome biology
Research InstitutionThe University of Tokyo

Principal Investigator

SHIRAHIGE KATSUHIKO  東京大学, 分子細胞生物学研究所, 教授 (90273854)

Co-Investigator(Kenkyū-buntansha) 須谷 尚史  東京大学, 分子細胞生物学研究所, 講師 (30401524)
Project Period (FY) 2015-04-01 – 2018-03-31
Project Status Completed (Fiscal Year 2017)
Budget Amount *help
¥43,420,000 (Direct Cost: ¥33,400,000、Indirect Cost: ¥10,020,000)
Fiscal Year 2017: ¥12,480,000 (Direct Cost: ¥9,600,000、Indirect Cost: ¥2,880,000)
Fiscal Year 2016: ¥12,480,000 (Direct Cost: ¥9,600,000、Indirect Cost: ¥2,880,000)
Fiscal Year 2015: ¥18,460,000 (Direct Cost: ¥14,200,000、Indirect Cost: ¥4,260,000)
Keywords染色体高次構造 / 細胞周期 / コンデンシン / コヒーシン / 機械学習 / 染色体 / 染色体構築原理 / 次世代シークエンサー / ゲノム維持
Outline of Final Research Achievements

For this study, we have introduced in situ Hi-C method to explore 3D and 4D structure of genome. Omics analysis pipeline that integrates Hi-C, ChIP-seq, Trasncriptome, and Genome sequence data has been developed and help us to visualize chromosome functional structures at various level. Using this pipeline, the transition of the high order structure of chromosome during cell cycle was captured. Notable achievements include 1) Condensin is important for re-annealing of single-stranded DNA generated during transcription, which activity is important for chromosome condensation, b) Two cohesin acetyltransferases (ESCO 1 and 2) in human function in different pathways. 1 induces sisterchromatids cohesion throughout the cell cycle, while 2 travels on chromosomes together with DNA helicase during replication, and this interaction with helicase prevent degradation of Esco2. c) Origin of DNA replication of the fission yeast genome is determined by three factors as revealed by machine learning.

Report

(4 results)
  • 2017 Annual Research Report   Final Research Report ( PDF )
  • 2016 Annual Research Report
  • 2015 Annual Research Report
  • Research Products

    (27 results)

All 2018 2017 2016 2015 Other

All Int'l Joint Research (3 results) Journal Article (16 results) (of which Int'l Joint Research: 6 results,  Peer Reviewed: 16 results,  Open Access: 14 results,  Acknowledgement Compliant: 8 results) Presentation (8 results) (of which Int'l Joint Research: 4 results,  Invited: 8 results)

  • [Int'l Joint Research] オックスフォード大学/クリック研究所(英国)

    • Related Report
      2017 Annual Research Report
  • [Int'l Joint Research] ペンシルバニア大学/フィラデルフィアこども病院(米国)

    • Related Report
      2017 Annual Research Report
  • [Int'l Joint Research] カロリンスカ研究所(スウェーデン)

    • Related Report
      2017 Annual Research Report
  • [Journal Article] DBTSS/DBKERO for integrated analysis of transcriptional regulation2018

    • Author(s)
      Suzuki Ayako、Kawano Shin、Mitsuyama Toutai、Suyama Mikita、Kanai Yae、Shirahige Katsuhiko、Sasaki Hiroyuki、Tokunaga Katsushi、Tsuchihara Katsuya、Sugano Sumio、Nakai Kenta、Suzuki Yutaka
    • Journal Title

      Nucleic Acids Research

      Volume: 46 Issue: (D1) Pages: D229-D238

    • DOI

      10.1093/nar/gkx1001

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Statistical Analysis and Quality Assessment of ChIP-seq Data with DROMPA.2018

    • Author(s)
      Nakato R, Shirahige K.
    • Journal Title

      Methods Mol Biol.

      Volume: 1672 Pages: 631-643

    • DOI

      10.1007/978-1-4939-7306-4_41

    • ISBN
      9781493973057, 9781493973064
    • Related Report
      2017 Annual Research Report
    • Peer Reviewed
  • [Journal Article] interleukin-11 induces and maintains progenitors of different cell lineages during Xenopus tadpole tail regeneration2017

    • Author(s)
      Tsujioka Hiroshi、Kunieda Takekazu、Katou Yuki、Shirahige Katsuhiko、Fukazawa Taro、Kubo Takeo
    • Journal Title

      Nature Comunications

      Volume: 8 Issue: 1 Pages: 495-495

    • DOI

      10.1038/s41467-017-00594-5

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] An In Vitro Human Liver Model by iPSC-Derived Parenchymal and Non-parenchymal Cells.2017

    • Author(s)
      Koui Y, Kido T, Ito T, Oyama H, Chen SW, Katou Y, Shirahige K, Miyajima A.
    • Journal Title

      Stem Cell Reports.

      Volume: 9 Issue: 2 Pages: 490-498

    • DOI

      10.1016/j.stemcr.2017.06.010

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Genome-Wide Target Analyses of Otx2 Homeoprotein in Postnatal Cortex2017

    • Author(s)
      Sakai Akiko、Nakato Ryuichiro、Ling Yiwei、Hou Xubin、Hara Norikazu、Iijima Tomoya、Yanagawa Yuchio、Kuwano Ryozo、Okuda Shujiro、Shirahige Katsuhiko、Sugiyama Sayaka
    • Journal Title

      Frontiers in Neuroscience

      Volume: 11 Pages: 307-307

    • DOI

      10.3389/fnins.2017.00307

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Rtt101-Mms1-Mms22 coordinates replication-coupled sister chromatid cohesion and nucleosome assembly2017

    • Author(s)
      Zhang J, Shi D, Li X, Ding L, Tang J, Liu C, Shirahige K, Cao Q, Lou H.
    • Journal Title

      EMBO Rep.

      Volume: 18 Issue: 8 Pages: 1294-1305

    • DOI

      10.15252/embr.201643807

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Decreased cohesion in the brain leads to defective synapse development and anxiety-related behavior2017

    • Author(s)
      Fujita Y, Masuda K, Bando M, Nakato R, Katou Y, Tanaka T, Nakayama M, Takao K, Miyakawa T, Tanaka T, Ago Y, Hashimoto H, Shirahige K, Yamashita T.
    • Journal Title

      J. Exp. Med.

      Volume: 印刷中 Issue: 5 Pages: 1431-1452

    • DOI

      10.1084/jem.20161517

    • Related Report
      2017 Annual Research Report 2016 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Cornelia de Lange syndrome and molecular implications of the cohesin complex: Abstracts from the 7th biennial scientific and educational symposium 2016.2017

    • Author(s)
      Kline AD, Krantz ID, Deardorff MA, Shirahige K, Dorsett D, Gerton JL, Wu M, Mehta D, Mills JA, Carrico CS, Noon S, Herrera PS, Horsfield JA, Bettale C, Morgan J, Huisman SA, Moss J, McCleery J, Grados M, Hansen BD, Srivastava S, Taylor-Snell E, Kerr LM, Katz O, Calof AL, Musio A, Egense A, Haaland RE.
    • Journal Title

      Am J Med Genet A.

      Volume: 173(5) Issue: 5 Pages: 1172-1185

    • DOI

      10.1002/ajmg.a.38161

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
  • [Journal Article] ChIP-seq Analysis of Condensin Complex in Cultured Mammalian Cells.2017

    • Author(s)
      Sakata T, Shirahige K, Sutani T.
    • Journal Title

      Methods Mol Biol.

      Volume: 1515 Pages: 257-271

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] ASBEL-TCF3 complex is required for the tumorigenicity of colorectal cancer cells.2016

    • Author(s)
      Taniue K, Kurimoto A, Takeda Y, Nagashima T, Okada-Hatakeyama M, Yuki K, Katsuhiko S, Akiyama T.
    • Journal Title

      Proc Natl Acad Sci U S A.

      Volume: 113 Issue: 45 Pages: 12739-12744

    • DOI

      10.1073/pnas.1605938113

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] MYU, a Target lncRNA for Wnt/c-Myc Signaling, Mediates Induction of CDK6 to Promote Cell Cycle Progression.2016

    • Author(s)
      Kawasaki Y, Komiya M, Matsumura K, Negishi L, Suda S, Okuno M, Yokota N, Osada T, Nagashima T, Hiyoshi M, Okada-Hatakeyama M, Kitayama J, Shirahige K, Akiyama T.
    • Journal Title

      Cell Rep.

      Volume: 16(10) Issue: 10 Pages: 2554-64

    • DOI

      10.1016/j.celrep.2016.08.015

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] ARCN1 Mutations Cause a Recognizable Craniofacial Syndrome Due to COPI-Mediated Transport Defects.2016

    • Author(s)
      Izumi K, Brett M, Nishi E, Drunat S, Tan ES, Fujiki K, Lebon S, Cham B, Masuda K, Arakawa M, Jacquinet A, Yamazumi Y, Chen ST, Verloes A, Okada Y, Katou Y, Nakamura T, Akiyama T, Gressens P, Foo R, Passemard S, Tan EC, El Ghouzzi V, Shirahige K.
    • Journal Title

      Am J Hum Genet.

      Volume: 99(2) Issue: 2 Pages: 451-9

    • DOI

      10.1016/j.ajhg.2016.06.011

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
  • [Journal Article] DNMT3A R882 mutants interact with polycomb proteins to block haematopoietic stem and leukaemic cell differentiation.2016

    • Author(s)
      Koya J, Kataoka K, Sato T, Bando M, Kato Y, Tsuruta-Kishino T, Kobayashi H, Narukawa K, Miyoshi H, Shirahige K, Kurokawa M.
    • Journal Title

      Nat Commun.

      Volume: 7 Issue: 1 Pages: 10924-10924

    • DOI

      10.1038/ncomms10924

    • Related Report
      2016 Annual Research Report 2015 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Recent advances in ChIP-seq analysis: from quality management to whole-genome annotation.2016

    • Author(s)
      Nakato R, Shirahige K.
    • Journal Title

      Brief Bioinform

      Volume: 12 Pages: 1-12

    • DOI

      10.1093/bib/bbw023

    • Related Report
      2016 Annual Research Report 2015 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
  • [Journal Article] Rif1 binds to G-quadruplexes and suppresses replication over long distances.2015

    • Author(s)
      Yutaka Kanoh, Seiji Matsumoto, Rino Fukatsu, Naoko Kakusho, Nobuaki Kono, Claire Renard-Guillet, Koji Masuda, Keisuke Iida, Kazuo Nagasawa, Katsuhiko Shirahige, and *Hisao Masai
    • Journal Title

      Nature Struct. Mol. Biol.

      Volume: 22 Issue: 11 Pages: 889-897

    • DOI

      10.1038/nsmb.3102

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
  • [Journal Article] The Deubiquitinating Enzyme USP7 Regulates Androgen Receptor Activity by Modulating Its Binding to Chromatin2015

    • Author(s)
      Shu-Ting Chen, Maiko Okada, Ryuichiro Nakato, Kosuke Izumi, Masashige Bando and Katsuhiko Shirahige
    • Journal Title

      Journal of Biological Chemistry

      Volume: 290 Issue: 35 Pages: 21713-21723

    • DOI

      10.1074/jbc.m114.628255

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Presentation] Transcriptional regulation by cohesin and its loader2017

    • Author(s)
      Katsuhiko Shirahige
    • Organizer
      第9回NAGOYAグローバルリトリート
    • Place of Presentation
      愛知健康プラザ、愛知県大府市
    • Year and Date
      2017-02-10
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Organization of 3D genome structure mediated by cohesin and CTCF2017

    • Author(s)
      Toyonari Sakata, Katsuhiko Shirahige
    • Organizer
      EMBO Workshop “Evolution in the Time of Genome Architecture”
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Analysis of human chromosome organization mediated by cohesin complex2017

    • Author(s)
      Toyonari Sakata, Katsuhiko Shirahige
    • Organizer
      Genetic Networks (GN) Workshop
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] コヒーシンと染色体の高次機能2017

    • Author(s)
      Toyonari Sakata, Katsuhiko Shirahige
    • Organizer
      第76回日本癌学会学術総会
    • Related Report
      2017 Annual Research Report
    • Invited
  • [Presentation] Genetic Link of Human Rare Diseases Identify Regulatory Mechanism of Transcription by Cohesin and its Loader2016

    • Author(s)
      Katsuhiko Shirahige
    • Organizer
      CIFAR Genetic Network Workshop
    • Place of Presentation
      カナダ、トロント
    • Year and Date
      2016-04-15
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] コヒーシンローダーNIPBLによる転写制御2016

    • Author(s)
      白髭克彦
    • Organizer
      第33回染色体ワークショップ 第14回核ダイナミクス研究会
    • Place of Presentation
      宮城県宮城郡松島町
    • Year and Date
      2016-01-13
    • Related Report
      2015 Annual Research Report
    • Invited
  • [Presentation] How cohesin and its loader regulate transcription? Clues from newly identi ed disease andin vitro reconstitution system2016

    • Author(s)
      Katsuhiko Shirahige
    • Organizer
      トロント大学のセミナー
    • Place of Presentation
      カナダ、トロント
    • Related Report
      2016 Annual Research Report
    • Invited
  • [Presentation] コヒーシンローダー、コヒーシンによる転写伸長制御2015

    • Author(s)
      白髭克彦
    • Organizer
      第23回 DNA複製・組換え・修復ワークショップ
    • Place of Presentation
      静岡県焼津市
    • Year and Date
      2015-10-19
    • Related Report
      2015 Annual Research Report
    • Invited

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Published: 2015-04-16   Modified: 2022-08-26  

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