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Theories of fluctuation and regulation of eukaryotic gene switches

Research Project

Project/Area Number 24244068
Research Category

Grant-in-Aid for Scientific Research (A)

Allocation TypeSingle-year Grants
Section一般
Research Field Biophysics/Chemical physics
Research InstitutionNagoya University

Principal Investigator

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

Co-Investigator(Renkei-kenkyūsha) TERADA Tomoki  名古屋大学, 大学院工学研究科, 准教授 (20420367)
CHIKENJI George  名古屋大学, 大学院工学研究科, 助教 (10420366)
Research Collaborator WANG Jin  New York州立大
Project Period (FY) 2012-04-01 – 2015-03-31
Project Status Completed (Fiscal Year 2014)
Budget Amount *help
¥38,350,000 (Direct Cost: ¥29,500,000、Indirect Cost: ¥8,850,000)
Fiscal Year 2014: ¥13,260,000 (Direct Cost: ¥10,200,000、Indirect Cost: ¥3,060,000)
Fiscal Year 2013: ¥12,870,000 (Direct Cost: ¥9,900,000、Indirect Cost: ¥2,970,000)
Fiscal Year 2012: ¥12,220,000 (Direct Cost: ¥9,400,000、Indirect Cost: ¥2,820,000)
Keywordsゲノム分子動力学 / 遺伝子スイッチの非断熱揺らぎ / 遺伝子制御ネットワーク理論 / クロマチン構造 / 国際情報交換アメリカ / 非断熱揺らぎ / 遺伝子制御ネットワーク / ゲノムMD / 遺伝子ネットワーク
Outline of Final Research Achievements

Principles of eukaryotic gene expression were studied theoretically by developing statistical mechanical and computational models of gene expression. By using a statistical mechanical model, stochastic behavior of genes was analyzed with the "eddy" current representation of probability flow, and importance of multiple stages of non-adiabatic fluctuations, i.e., super-non-adiabatic fluctuations, was shown. Methods of genome-scale simulation of chromosome structure and movement (genome-MD) were developed and applied to budding yeast and human nuclei. Genome-MD revealed correlatin between spatial distribution and transcriptional activity of genes in budding yeast nucleus. Fluctuations and transitions in expression dynamics of embryonic stem cells were examined theoretically and effects of super-non-adiabatic fluctuations were analyzed.

Report

(4 results)
  • 2014 Annual Research Report   Final Research Report ( PDF )
  • 2013 Annual Research Report
  • 2012 Annual Research Report
  • Research Products

    (25 results)

All 2015 2014 2013 2012 Other

All Journal Article (7 results) (of which Peer Reviewed: 7 results,  Open Access: 2 results) Presentation (13 results) (of which Invited: 12 results) Book (2 results) Remarks (3 results)

  • [Journal Article] Coupling of Lever Arm Swing and Biased Brownian Motion in Actomyosin2014

    • Author(s)
      Nie, QM., Togashi, A., Sasaki, TN., Takano, M., Sasai, M., Terada, TP
    • Journal Title

      PLoS Comput Biol

      Volume: 10 Issue: 4 Pages: e1003552-e1003552

    • DOI

      10.1371/journal.pcbi.1003552

    • NAID

      120005476003

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Folding pathway of a multidomain protein depends on its topology of domain connectivity2014

    • Author(s)
      Takashi Inanami, Tomoki P. Terada, and Masaki Sasai
    • Journal Title

      Proc. Natl. Acad. Sci. USA

      Volume: 111 Issue: 45 Pages: 15969-15974

    • DOI

      10.1073/pnas.1406244111

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Conformational flexibility of loops of myosin enhances global bias in the actin-myosin interaction landscape2014

    • Author(s)
      Qing-Miao Nie, Masaki Sasai, and Tomoki P. Terada
    • Journal Title

      Phys. Chem. Chem. Phys.

      Volume: 16 Issue: 14 Pages: 6441-6447

    • DOI

      10.1039/c3cp54464h

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Eddy current and coupled landscapes for nonadiabatic and nonequilibrium complex system dynamics2013

    • Author(s)
      Kun Zhang, Masaki Sasai, Jin Wang
    • Journal Title

      Proc. Natl. Acad. Sci. USA

      Volume: 110 Issue: 37 Pages: 14930-14935

    • DOI

      10.1073/pnas.1305604110

    • NAID

      120005476002

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Time scales in epigenetic dynamics and phenotypic heterogeneity of embryonic stem cells2013

    • Author(s)
      Masaki Sasai, Yudai Kawabata, Koh Makishi, Kazuhito Itoh, and Tomoki P. Terada
    • Journal Title

      PLoS Comp. Biol.

      Volume: 9 Issue: 12 Pages: e1003380-e1003380

    • DOI

      10.1371/journal.pcbi.1003380

    • NAID

      120005476001

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Entropic mechanism of allosteric communication in conformational transitions of dihydrofolate reductase2013

    • Author(s)
      Tomoki P. Terada, Toru Kimura, and Masaki Sasai
    • Journal Title

      J. Phys. Chem. B

      Volume: 117 Issue: 42 Pages: 12864-12877

    • DOI

      10.1021/jp402071m

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Non-Brownian dynamics and strategy of amoeboid cell locomotion2012

    • Author(s)
      S. I. Nishimura, M. Ueda, and M. Sasai
    • Journal Title

      Phys. Rev. E

      Volume: 85 Issue: 4 Pages: 041909-041909

    • DOI

      10.1103/physreve.85.041909

    • NAID

      120005476000

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Presentation] Epigenetic dynamics of gene regulation2015

    • Author(s)
      Masaki Sasai
    • Organizer
      Architecture, dynamics, and functionality of molecular biosystems
    • Place of Presentation
      Okazaki
    • Year and Date
      2015-03-30 – 2015-03-31
    • Related Report
      2014 Annual Research Report
    • Invited
  • [Presentation] 蛋白質機能発現の動的エネルギーランドスケープ理論2015

    • Author(s)
      笹井理生
    • Organizer
      第359回 CBI学会研究講演会
    • Place of Presentation
      東京大学
    • Year and Date
      2015-02-24
    • Related Report
      2014 Annual Research Report
    • 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 Annual Research Report
  • [Presentation] Dynamical energy landscape view of actomyosin motors2014

    • Author(s)
      Masaki Sasai, Qing-Miao Nie, and Tomoki P. Terada
    • Organizer
      The 7th Korea-Japan Seminars on Biomolecular Sciences
    • Place of Presentation
      Seoul
    • Year and Date
      2014-11-26 – 2014-11-28
    • Related Report
      2014 Annual Research 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 Annual Research Report
    • Invited
  • [Presentation] Computational Models for Chromatin Structure and Gene Expression2014

    • Author(s)
      Masaki Sasai, Naoko Tokuda, and Shin Fujishiro
    • Organizer
      The 2nd International Symposium of the Mathematics on Chromatin Live Dynamics
    • Place of Presentation
      広島大学
    • Related Report
      2013 Annual Research Report
    • Invited
  • [Presentation] Time scales in epigenetic dynamics and landscapes2013

    • Author(s)
      Masaki Sasai
    • Organizer
      Physical Principles and Underlying Mechanisms of Biomolecules and Materials
    • Place of Presentation
      Chinese Adademy of Science, Beijing
    • Related Report
      2013 Annual Research Report
    • Invited
  • [Presentation] Non-adiabatic gene switching and fluctuations in ES cells2013

    • Author(s)
      Masaki Sasai
    • Organizer
      Computational Methods for Bio and Complex Systems
    • Place of Presentation
      Korea Institute for Advanced Study, Seoul
    • Related Report
      2013 Annual Research Report
    • Invited
  • [Presentation] Epigenetic dynamics of eukaryotic cells2013

    • Author(s)
      Masaki Sasai
    • Organizer
      35th Annual International Conference of the IEEE Engineering of Medicine and Biology Society
    • Place of Presentation
      Osaka International Convention Center
    • Related Report
      2013 Annual Research Report
    • Invited
  • [Presentation] Fluctuating dynamics of 3D genome organization2013

    • Author(s)
      Masaki Sasai
    • Organizer
      The 2nd KIAS Conference on Subcellular Dynamics
    • Place of Presentation
      Korea Institute for Advanced Study, Seoul for Advanced Study, Seoul
    • Related Report
      2013 Annual Research Report
    • Invited
  • [Presentation] Slow dynamics of chromatins and non-adiabatic gene switches2012

    • Author(s)
      M. Sasai
    • Organizer
      Characterizing Landscapes: From Biomolecules to Cellular Networks
    • Place of Presentation
      Telluride, Colorado
    • Related Report
      2012 Annual Research Report
    • Invited
  • [Presentation] Revisiting the consistency principle of protein conformational change2012

    • Author(s)
      M. Sasai
    • Organizer
      12th KIAS Conference on Protein Structure and Function
    • Place of Presentation
      Seoul
    • Related Report
      2012 Annual Research Report
    • Invited
  • [Presentation] Heterogeneous dynamics and fluctuations in biomolecular networks2012

    • Author(s)
      M. Sasai
    • Organizer
      RIKEN Quantitative Biology Center Inaugural Symposium
    • Place of Presentation
      Kobe
    • Related Report
      2012 Annual Research Report
    • Invited
  • [Book] Chapter 21, Coarse-Grained Modeling of Biomolecules2015

    • Author(s)
      Naoko Tokuda and Masaki Sasai
    • Total Pages
      20
    • Publisher
      Taylor & Francis Books
    • Related Report
      2014 Annual Research Report
  • [Book] 生体分子のつくるシステム 「ゲノム系計算科学(計算科学講座第7巻)」2013

    • Author(s)
      笹井理生、寺田智樹
    • Total Pages
      27
    • Publisher
      共立出版
    • Related Report
      2012 Annual Research Report
  • [Remarks] http://www.tbp.cse.nagoya-u.ac.jp/HM_project.html

    • Related Report
      2014 Annual Research Report
  • [Remarks] 科研費プロジェクト

    • URL

      http://www.tbp.cse.nagoya-u.ac.jp/HM_project.html

    • Related Report
      2013 Annual Research Report
  • [Remarks] 科研費プロジェクト

    • URL

      http://www.tbp.cse.nagoya-u.ac.jp/HM_project.html

    • Related Report
      2012 Annual Research Report

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Published: 2013-05-15   Modified: 2019-07-29  

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