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Genome structural dynamics and transcription regulation

Research Project

Project/Area Number 26610130
Research Category

Grant-in-Aid for Challenging Exploratory Research

Allocation TypeMulti-year Fund
Research Field Biological physics/Chemical physics/Soft matter physics
Research InstitutionNagoya University

Principal Investigator

SASAI Masaki  名古屋大学, 工学研究科, 教授 (30178628)

Project Period (FY) 2014-04-01 – 2018-03-31
Project Status Completed (Fiscal Year 2017)
Budget Amount *help
¥3,640,000 (Direct Cost: ¥2,800,000、Indirect Cost: ¥840,000)
Fiscal Year 2016: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000)
Fiscal Year 2015: ¥1,170,000 (Direct Cost: ¥900,000、Indirect Cost: ¥270,000)
Fiscal Year 2014: ¥1,170,000 (Direct Cost: ¥900,000、Indirect Cost: ¥270,000)
Keywordsクロマチン / ゲノム / 分子動力学 / 転写制御 / 相分離 / 分子動力学計算
Outline of Final Research Achievements

Genome is not an abstract sequence of alphabet but a physical entity confined in the nucleus. We developed a computational method to simulate the three-dimensional structure and movement of genomes. We consider chromosomes as heteropolymers, which are comprised of local chromatin regions having various different physical properties; we assumed that those local properties are determined by the epigenetic histone marks of the corresponding regions. Simulations of human fibroblast and lymphoblastoid nuclei showed that the method developed in this project quantitatively reproduced the experimentally observed contact frequency between chromatin regions and nuclear lamina, Hi-C contact pattern data, contact frequency between chromatin regions and nucleoli, and compartmentalization of transcription active and inactive regions. Thus, the computational method developed in this project can be a platform for the systematic study of genome physics.

Report

(5 results)
  • 2017 Annual Research Report   Final Research Report ( PDF )
  • 2016 Research-status Report
  • 2015 Research-status Report
  • 2014 Research-status Report
  • Research Products

    (31 results)

All 2017 2016 2015 2014 Other

All Int'l Joint Research (2 results) Journal Article (7 results) (of which Int'l Joint Research: 1 results,  Peer Reviewed: 7 results,  Open Access: 6 results,  Acknowledgement Compliant: 2 results) Presentation (20 results) (of which Int'l Joint Research: 11 results,  Invited: 14 results) Book (2 results)

  • [Int'l Joint Research] State University of New York(米国)

    • Related Report
      2017 Annual Research Report
  • [Int'l Joint Research] State University of New York(米国)

    • Related Report
      2015 Research-status Report
  • [Journal Article] Role of ATP hydrolysis in cyanobacterial circadian oscillator2017

    • Author(s)
      S. Das, T. P. Terada, & M. Sasai
    • Journal Title

      Scientific Reports

      Volume: 7 Issue: 1

    • DOI

      10.1038/s41598-017-17717-z

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Heterogeneous spatial distribution of transcriptional activity in budding yeast nuclei2017

    • Author(s)
      N. Tokuda & M. Sasai
    • Journal Title

      Biophysical Journal

      Volume: 112 Issue: 3 Pages: 491-504

    • DOI

      10.1016/j.bpj.2016.11.3201

    • Related Report
      2016 Research-status Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Cooperativity and modularity in protein folding2016

    • Author(s)
      M. Sasai, G. Chikenji, & T. P. Terada
    • Journal Title

      Biophysics and Physicobiology

      Volume: 13 Issue: 0 Pages: 281-293

    • DOI

      10.2142/biophysico.13.0_281

    • NAID

      130005284044

    • ISSN
      2189-4779
    • Related Report
      2016 Research-status Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Liquid-like behavior of chromatin2016

    • Author(s)
      Kazuhiro Maeshima, Satoru Ide, Kayo Hibino and Masaki Sasai
    • Journal Title

      Current Opinion in Genetics and Development

      Volume: 37 Pages: 36-45

    • DOI

      10.1016/j.gde.2015.11.006

    • NAID

      120005822509

    • Related Report
      2015 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] 真核細胞のルースな遺伝子制御とクロマチン動態2016

    • Author(s)
      笹井理生,寺田智樹
    • Journal Title

      生物物理

      Volume: 56 Pages: 106-108

    • NAID

      130005140932

    • Related Report
      2015 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Multiple coupled landscapes and non-diabatic dynamics with applications to self activating genes2015

    • Author(s)
      Cong Chen, Kun Zhang, Haidong Feng, Masaki Sasai and Jin Wang
    • Journal Title

      Phys. Chem. Chem. Phys.

      Volume: 17 Issue: 43 Pages: 29036-29044

    • DOI

      10.1039/c5cp04780c

    • Related Report
      2015 Research-status Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Effects of collective histone state dynamics on epigenetic landscape and kinetics of cell reprogramming2015

    • Author(s)
      S. S. Ashwin and Masaki Sasai
    • Journal Title

      Scientific Reports

      Volume: 5 Issue: 1

    • DOI

      10.1038/srep16746

    • NAID

      120005822508

    • Related Report
      2015 Research-status Report
    • Peer Reviewed / Open Access
  • [Presentation] Genome folding: Analogy to protein folding problems2017

    • Author(s)
      M. Sasai
    • Organizer
      The Third Korean-Polish Conference on "Protein Folding:Theoretical and Experimental Approaches"
    • Place of Presentation
      High-1 Resort, Korea
    • Year and Date
      2017-02-05
    • Related Report
      2016 Research-status Report
    • Int'l Joint Research / Invited
  • [Presentation] The 3D Genome Architecture and Transcriptional Regulation2017

    • Author(s)
      M. Sasai
    • Organizer
      Gordon Research Conference on Stochastic Physics in Biology
    • Place of Presentation
      Ventura, CA
    • Year and Date
      2017-01-08
    • Related Report
      2016 Research-status Report
    • Int'l Joint Research / Invited
  • [Presentation] Role of dynamical DNA methylation in gene regulation2017

    • Author(s)
      Masaki Sasai
    • Organizer
      International Conference on Biological Physics 2017
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research
  • [Presentation] The phase-separation principle of human genome architecture2017

    • Author(s)
      Shin Fujishiro
    • Organizer
      第55回日本生物物理学会年会
    • Related Report
      2017 Annual Research Report
    • Invited
  • [Presentation] The phase-separation principle of human genome folding2017

    • Author(s)
      Masaki Sasai
    • Organizer
      CSRC Workshop on DNA Chromosome Structure and Dynamics
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Physical bases of 3D genome organization2017

    • Author(s)
      Masaki Sasai
    • Organizer
      CDB Seminar
    • Related Report
      2017 Annual Research Report
    • Invited
  • [Presentation] Genome folding inferred from epigenome2016

    • Author(s)
      Shin Fujishiro, Masaki Sasai
    • Organizer
      第39回日本分子生物学会
    • Place of Presentation
      パシフィコ横浜
    • Year and Date
      2016-11-30
    • Related Report
      2016 Research-status Report
    • Invited
  • [Presentation] 3D Genome Architecture Inferred from Epigenome2016

    • Author(s)
      Shin Fujishiro, Masaki Sasai
    • Organizer
      The 3rd International Conference on Computational Science and Engineering
    • Place of Presentation
      Ho Chi Minh City, Vietnam
    • Year and Date
      2016-11-28
    • Related Report
      2016 Research-status Report
    • Int'l Joint Research / Invited
  • [Presentation] Mechanisms for the misregulated gene expression in the yku70 esc1 mutant of budding yeast.2016

    • Author(s)
      Naoko Tokuda, Masaki Sasai
    • Organizer
      第54回日本生物物理学会
    • Place of Presentation
      つくば国際会議場
    • Year and Date
      2016-11-25
    • Related Report
      2016 Research-status Report
    • Invited
  • [Presentation] Fluctuating Three-Dimensional Genome Architecture and Gene Regulation2016

    • Author(s)
      Masaki Sasai
    • Organizer
      Gordon Research Conference on Protein Folding Dynamics
    • Place of Presentation
      ガルベストン市、テキサス州
    • Year and Date
      2016-01-10
    • Related Report
      2015 Research-status Report
    • Int'l Joint Research / Invited
  • [Presentation] Chromatin Domains and Heterogeneous Transcription Activities2015

    • Author(s)
      N. Tokuda, S. Fujishiro and M. Sasai
    • Organizer
      International Symposium on Chromatin Structure, Dynamics and Function
    • Place of Presentation
      兵庫県淡路
    • Year and Date
      2015-08-23
    • Related Report
      2015 Research-status Report
    • Int'l Joint Research / Invited
  • [Presentation] Eukaryotic gene regulation and chromosome architecture2015

    • Author(s)
      Masaki Sasai
    • Organizer
      CSRC Workshop on Kinetics of Enzymes and Molecular Machines
    • Place of Presentation
      北京
    • Year and Date
      2015-08-18
    • Related Report
      2015 Research-status Report
    • Int'l Joint Research / Invited
  • [Presentation] Fluctuations and histone state dynamics on topology of epigenetic landscape2015

    • Author(s)
      Ashwin S. S. and Masaki Sasai
    • Organizer
      New Frontiers in Non-equilibrium Statistical Physics
    • Place of Presentation
      京都
    • Year and Date
      2015-08-17
    • Related Report
      2015 Research-status Report
    • Int'l Joint Research
  • [Presentation] Eddy current flow of probability in stochastic gene expression dynamics in eukaryotes2015

    • Author(s)
      Baswati Bhattacharyya and Masaki Sasai
    • Organizer
      New Frontiers in Non-equilibrium Statistical Physics
    • Place of Presentation
      京都
    • Year and Date
      2015-08-17
    • Related Report
      2015 Research-status Report
    • Int'l Joint Research
  • [Presentation] Eukaryotic chromatin folding and gene regulation2015

    • Author(s)
      Masaki Sasai
    • Organizer
      3rd International Workshop on Theoretical and Computational Physics
    • Place of Presentation
      ダラット市, ベトナム
    • Year and Date
      2015-07-27
    • Related Report
      2015 Research-status Report
    • Int'l Joint Research / Invited
  • [Presentation] A coarse grained model of chromosomes based on the Hi-C data2014

    • Author(s)
      Naoko Tokuda, Shin Fujishiro, Masaki Sasai
    • Organizer
      The 4D Nucleome 2014
    • Place of Presentation
      Hiroshima
    • Year and Date
      2014-12-17 – 2014-12-20
    • Related Report
      2014 Research-status Report
  • [Presentation] Are there transcriptionally inactive regions localized in a budding yeast nucleus?2014

    • Author(s)
      Naoko Tokuda, Shin Fujishiro, Masaki Sasai
    • Organizer
      第52回日本生物物理学会年会
    • Place of Presentation
      札幌
    • Year and Date
      2014-09-25 – 2014-09-27
    • Related Report
      2014 Research-status Report
  • [Presentation] Computational chromosome conformation sampling of human diploid genome2014

    • Author(s)
      Shin Fujishiro, Naoko Tokuda, Masaki Sasai
    • Organizer
      第52回日本生物物理学会年会
    • Place of Presentation
      札幌
    • Year and Date
      2014-09-25 – 2014-09-27
    • Related Report
      2014 Research-status Report
  • [Presentation] ゲノム立体構造の動力学シミュレーション2014

    • Author(s)
      笹井理生、徳田直子、藤城新
    • Organizer
      第14回日本蛋白質科学会年会
    • Place of Presentation
      横浜
    • Year and Date
      2014-06-25 – 2014-06-27
    • Related Report
      2014 Research-status Report
    • Invited
  • [Presentation] Fluctuating genome structure and gene regulation2014

    • Author(s)
      Masaki Sasai, Naoko Tokuda, Shin Fujishiro
    • Organizer
      8th IUPAP International Conference on Biological Physics
    • Place of Presentation
      Beijing
    • Year and Date
      2014-06-18 – 2014-06-22
    • Related Report
      2014 Research-status Report
    • Invited
  • [Book] Modeling of genomes, Chapter 9 in Coarse-Grained Modeling of Biomolecules2017

    • Author(s)
      Naoko Tokuda & Masaki Sasai
    • Total Pages
      36
    • Publisher
      CRC Press Taylor & Francis Group
    • ISBN
      1466576065
    • Related Report
      2017 Annual Research Report
  • [Book] Chapter 21, Coarse-Grained Modeling of Biomolecules2015

    • Author(s)
      Naoko Tokuda, Masaki Sasai
    • Total Pages
      20
    • Publisher
      Taylor & Francis Books
    • Related Report
      2014 Research-status Report

URL: 

Published: 2014-04-04   Modified: 2022-06-07  

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