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Elucidating the 3D Genome Landscape

Research Project

Project/Area Number 17K15050
Research Category

Grant-in-Aid for Young Scientists (B)

Allocation TypeMulti-year Fund
Research Field System genome science
Research InstitutionKochi University (2023)
The University of Tokyo (2018-2022)
Hiroshima University (2017)

Principal Investigator

Sugawara Takeshi  高知大学, データサイエンスセンター, 特任講師 (60713005)

Project Period (FY) 2017-04-01 – 2024-03-31
Project Status Completed (Fiscal Year 2023)
Budget Amount *help
¥4,160,000 (Direct Cost: ¥3,200,000、Indirect Cost: ¥960,000)
Fiscal Year 2020: ¥910,000 (Direct Cost: ¥700,000、Indirect Cost: ¥210,000)
Fiscal Year 2019: ¥910,000 (Direct Cost: ¥700,000、Indirect Cost: ¥210,000)
Fiscal Year 2018: ¥910,000 (Direct Cost: ¥700,000、Indirect Cost: ¥210,000)
Fiscal Year 2017: ¥1,430,000 (Direct Cost: ¥1,100,000、Indirect Cost: ¥330,000)
Keywordsゲノム構造変化 / 数理モデル / データ駆動 / ゲノム構造 / 数理モデリング / シミュレーション / クロマチン動態 / 染色体構造 / モデリング / 準安定構造 / 3Dゲノム地形 / 核内染色体構造 / データ駆動型数理モデリング / 細胞周期・細胞分化
Outline of Final Research Achievements

The initial plan aimed to quantify genome structural landscapes using a data-driven modeling approach with bulk Hi-C data, and to comprehensively describe genome structural changes accompanying cell cycle and cell differentiation. However, due to difficulties in sampling, the methodological direction was reconsidered. The newly proposed method utilizes single-cell Hi-C data and generative models to visualize genome 3D structural changes dependent on the cell cycle in detail. This approach compensates for the scarcity of data and uniquely extracts dynamic information from static data. Consequently, this development has advanced genome structure estimation to a new phase, and the progress was presented at academic conferences. In the future, the method is planned to be applied to the analysis of genome structural transitions during cell differentiation, indicating potential expansion into new research areas.

Academic Significance and Societal Importance of the Research Achievements

本研究は、Hi-Cデータ駆動型モデリング手法を用いてゲノム構造地形を定量化し、細胞状態変化に伴うゲノム構造変化を統一的に記述する点で学術的意義がある。細胞周期や細胞分化に伴うゲノム構造変化の数理的枠組みを細胞集団データから提案することを目指したが、サンプリングの困難さから軌道修正を行った。新提案手法は、単一細胞データと生成モデルを用いてゲノム3次元構造変化を詳細に可視化し、データ数の少なさを生成モデルで補う点に萌芽性があり、静的データから動的情報を抽出する手法にも独創性がある。この手法は他の単一細胞データ解析にも応用可能で、遺伝子動態やゲノム構造の多様性の解析に貢献し、社会的意義も大きい。

Report

(8 results)
  • 2023 Annual Research Report   Final Research Report ( PDF )
  • 2022 Research-status Report
  • 2021 Research-status Report
  • 2020 Research-status Report
  • 2019 Research-status Report
  • 2018 Research-status Report
  • 2017 Research-status Report
  • Research Products

    (12 results)

All 2024 2023 2022 2021 2020 2019 2017

All Journal Article (7 results) (of which Int'l Joint Research: 1 results,  Peer Reviewed: 6 results,  Open Access: 5 results) Presentation (5 results) (of which Int'l Joint Research: 1 results,  Invited: 1 results)

  • [Journal Article] Chemophoresis engine: A general mechanism of ATPase-driven cargo transport2022

    • Author(s)
      Takeshi Sugawara, Kunihiko Kaneko
    • Journal Title

      PLoS Computational Biology

      Volume: 18 Issue: 7 Pages: e1010324-e1010324

    • DOI

      10.1371/journal.pcbi.1010324

    • Related Report
      2022 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Chemophoresis Engine: Universal Principle of ATPase-driven Cargo Transport2021

    • Author(s)
      Sugawara Takeshi、Kaneko Kunihiko
    • Journal Title

      bioRxiv

      Volume: -

    • DOI

      10.1101/2021.10.15.463834

    • Related Report
      2021 Research-status Report
    • Open Access
  • [Journal Article] PHi-C: deciphering Hi-C data into polymer dynamics2020

    • Author(s)
      Shinkai Soya、Nakagawa Masaki、Sugawara Takeshi、Togashi Yuichi、Ochiai Hiroshi、Nakato Ryuichiro、Taniguchi Yuichi、Onami Shuichi
    • Journal Title

      NAR Genomics and Bioinformatics

      Volume: 2 Issue: 2

    • DOI

      10.1093/nargab/lqaa020

    • Related Report
      2019 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Microrheology for Hi-C Data Reveals the Spectrum of the Dynamic 3D Genome Organization2020

    • Author(s)
      Soya Shinkai, Takeshi Sugawara, Hisashi Miura, Ichiro Hiratani, Shuichi Onami
    • Journal Title

      Biophysical Journal

      Volume: 118 Issue: 9 Pages: 2220-2228

    • DOI

      10.1016/j.bpj.2020.02.020

    • Related Report
      2019 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Spindle pole body movement is affected by glucose and ammonium chloride in fission yeast2019

    • Author(s)
      Ito H, Sugawara T, Shinkai S, Mizukawa S, Kondo A, Senda H, Sawai K, Ito K, Suzuki S, Takaine M, Yoshida S, Imamura H, Kitamura K, Namba T, Tate SI, Ueno M
    • Journal Title

      Biochem Biophys Res Commun

      Volume: 511 Issue: 4 Pages: 820-825

    • DOI

      10.1016/j.bbrc.2019.02.128

    • Related Report
      2018 Research-status Report
    • Peer Reviewed
  • [Journal Article] Physical properties of the chromosomes and implications for development2017

    • Author(s)
      Sugawara Takeshi、Kimura Akatsuki
    • Journal Title

      Development, Growth & Differentiation

      Volume: 59 Issue: 5 Pages: 405-414

    • DOI

      10.1111/dgd.12363

    • Related Report
      2017 Research-status Report
    • Peer Reviewed
  • [Journal Article] Reduction in chromosome mobility accompanies nuclear organization during early embryogenesis in Caenorhabditis elegans2017

    • Author(s)
      Arai Ritsuko、Sugawara Takeshi、Sato Yuko、Minakuchi Yohei、Toyoda Atsushi、Nabeshima Kentaro、Kimura Hiroshi、Kimura Akatsuki
    • Journal Title

      Scientific Reports

      Volume: 7 Issue: 1 Pages: 3631-3631

    • DOI

      10.1038/s41598-017-03483-5

    • Related Report
      2017 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Presentation] 液滴-遺伝子相互作用の現象論モデル2024

    • Author(s)
      菅原武志
    • Organizer
      日本物理学会2024年春季大会
    • Related Report
      2023 Annual Research Report
  • [Presentation] 生成モデルを用いた3Dゲノム動態予測2024

    • Author(s)
      菅原武志
    • Organizer
      日本物理学会2024年春季大会
    • Related Report
      2023 Annual Research Report
  • [Presentation] べん毛モーター時系列テ゛ータ解析とエントロピー生成率(EPR)推定2023

    • Author(s)
      菅原武志
    • Organizer
      新学術領域研究「情報物理学でひもとく生命の秩序と設計原理 」第7回領域会議
    • Related Report
      2023 Annual Research Report
  • [Presentation] 液滴誘導型細胞内走化性の理論2023

    • Author(s)
      菅原武志
    • Organizer
      第61日本生物物理学会年会
    • Related Report
      2023 Annual Research Report
  • [Presentation] Chemophoresis engine: Theory of cargo transports using ATP hydrolysis2017

    • Author(s)
      Takeshi Sugawara, Kunihiko Kaneko
    • Organizer
      ON Workshop: Sensors, Motors and Behaviors at the Origin of Life
    • Related Report
      2017 Research-status Report
    • Int'l Joint Research / Invited

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Published: 2017-04-28   Modified: 2025-01-30  

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