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Finding 3D co-localization of genomic elements from HiC data

Research Project

Project/Area Number 15K16089
Research Category

Grant-in-Aid for Young Scientists (B)

Allocation TypeMulti-year Fund
Research Field Life / Health / Medical informatics
Research InstitutionNational Institute of Advanced Industrial Science and Technology

Principal Investigator

Saito Yutaka  国立研究開発法人産業技術総合研究所, 人工知能研究センター, 研究員 (60721496)

Project Period (FY) 2015-04-01 – 2017-03-31
Project Status Completed (Fiscal Year 2016)
Budget Amount *help
¥2,860,000 (Direct Cost: ¥2,200,000、Indirect Cost: ¥660,000)
Fiscal Year 2016: ¥1,950,000 (Direct Cost: ¥1,500,000、Indirect Cost: ¥450,000)
Fiscal Year 2015: ¥910,000 (Direct Cost: ¥700,000、Indirect Cost: ¥210,000)
Keywordsゲノム3D構造 / エピゲノム / HiC/3C / ゲノム3次元構造 / HiC / 3C / 共局在遺伝子 / バイオインフォマティクス
Outline of Final Research Achievements

We developed Cosearge, a bioinformatics method for finding 3D co-localization of genomic elements from HiC data. We applied Cosearge to HiC data from embryonic stem cells, and detected a number of novel co-localized genes distinct from topologically associated domains proposed in existing studies. In particular, we found that SOX2 and DNA damage response genes are co-localized in embryonic stem cells.

Report

(3 results)
  • 2016 Annual Research Report   Final Research Report ( PDF )
  • 2015 Research-status Report
  • Research Products

    (10 results)

All 2017 2016 2015

All Journal Article (3 results) (of which Peer Reviewed: 3 results,  Open Access: 3 results,  Acknowledgement Compliant: 3 results) Presentation (7 results) (of which Int'l Joint Research: 1 results)

  • [Journal Article] Epigenetic silencing of V(D)J recombination is a major determinant for selective differentiation of mucosal-associated invariant t cells from induced pluripotent stem cells.2017

    • Author(s)
      Yutaka Saito, Chie Sugimoto, Toutai Mituyama and Hiroshi Wakao
    • Journal Title

      PLoS One

      Volume: 12 Issue: 3 Pages: e0174699-e0174699

    • DOI

      10.1371/journal.pone.0174699

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Brief Exposure to Small Molecules Allows Induction of Mouse Embryonic Fibroblasts into Neural Crest-like Precursors2017

    • Author(s)
      高山祐三、若林珠実、櫛笥博子、齋藤裕、渋谷陽一郎、芝田晋介、赤松和土、岡野栄之、木田泰之
    • Journal Title

      FEBS Letters

      Volume: 591 Issue: 4 Pages: 590-602

    • DOI

      10.1002/1873-3468.12572

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Detection of differentially methylated regions from bisulfite-seq data by hidden Markov models incorporating genome-wide methylation level distributions2015

    • Author(s)
      Yutaka Saito, and Toutai Mituyama
    • Journal Title

      BMC Genomics

      Volume: 16(Suppl 12) Issue: S12

    • DOI

      10.1186/1471-2164-16-s12-s3

    • Related Report
      2015 Research-status Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Presentation] iPS細胞からの自然免疫型T細胞分化誘導の分子機序の統合的解析2016

    • Author(s)
      若尾 宏, 杉本 智恵, 光山 統泰, 齋藤 裕
    • Organizer
      第39回 日本分子生物学会年会 (MBSJ 2016)
    • Place of Presentation
      パシフィコ横浜(神奈川県)
    • Year and Date
      2016-11-30
    • Related Report
      2016 Annual Research Report
  • [Presentation] 薬剤によるマウス胎児線維芽細胞(MEFs)からの神経堤細胞の分化誘導法の開発2016

    • Author(s)
      若林 玲実, 高山 祐三, 櫛笥 博子, 渋谷 陽一郎, 齋藤 裕, 赤松 和土, 芝田 晋介, 岡野 栄之, 木田 泰之
    • Organizer
      第39回 日本分子生物学会年会 (MBSJ 2016)
    • Place of Presentation
      パシフィコ横浜(神奈川県)
    • Year and Date
      2016-11-30
    • Related Report
      2016 Annual Research Report
  • [Presentation] ワークフローの紹介 (BS-seq)2016

    • Author(s)
      齋藤 裕
    • Organizer
      Galaxy Workshop Tokyo 2016
    • Place of Presentation
      東京大学先端科学技術研究センター(東京都)
    • Related Report
      2016 Annual Research Report
  • [Presentation] ゲノム3次元構造データに基づく共局在遺伝子の網羅的探索2015

    • Author(s)
      齋藤 裕,光山 統泰
    • Organizer
      第38回 日本分子生物学会年会,第88回 日本生化学会大会,合同大会 (BMB 2015)
    • Place of Presentation
      神戸ポートアイランド(兵庫県)
    • Year and Date
      2015-12-01
    • Related Report
      2015 Research-status Report
  • [Presentation] Detection of differentially methylated regions from bisulfite-seq data by hidden Markov models incorporating genome-wide methylation level distributions2015

    • Author(s)
      Yutaka Saito, and Toutai Mituyama
    • Organizer
      The 26th International Conference on Genome Informatics (GIW/InCoB 2015)
    • Place of Presentation
      MIRAIKAN (Tokyo, Japan)
    • Year and Date
      2015-09-09
    • Related Report
      2015 Research-status Report
    • Int'l Joint Research
  • [Presentation] ゲノム3次元構造データに基づく共局在遺伝子の網羅的探索2015

    • Author(s)
      齋藤 裕,光山 統泰
    • Organizer
      NGS現場の会 第四回研究会
    • Place of Presentation
      つくば国際会議場(茨城県)
    • Year and Date
      2015-07-01
    • Related Report
      2015 Research-status Report
  • [Presentation] ワークフローの紹介 (BS-seq)2015

    • Author(s)
      齋藤 裕
    • Organizer
      Galaxy Workshop Tokyo 2015
    • Place of Presentation
      東京大学先端科学技術研究センター(東京都)
    • Year and Date
      2015-04-28
    • Related Report
      2015 Research-status Report

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Published: 2015-04-16   Modified: 2018-03-22  

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