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Statistical physics of dynamical transitions in ES cells

Research Project

Project/Area Number 23654147
Research Category

Grant-in-Aid for Challenging Exploratory Research

Allocation TypeMulti-year Fund
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州立大学, Stony Brook校, 准教授
Project Period (FY) 2011-04-28 – 2015-03-31
Project Status Completed (Fiscal Year 2014)
Budget Amount *help
¥3,510,000 (Direct Cost: ¥2,700,000、Indirect Cost: ¥810,000)
Fiscal Year 2013: ¥650,000 (Direct Cost: ¥500,000、Indirect Cost: ¥150,000)
Fiscal Year 2012: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000)
Fiscal Year 2011: ¥1,560,000 (Direct Cost: ¥1,200,000、Indirect Cost: ¥360,000)
Keywords遺伝子ネットワーク / ES細胞 / 揺らぎ / 国際情報交換アメリカ / 国際情報交流アメリカ
Outline of Final Research Achievements

Much interest has been focused on the mechanism and biological meaning of large flucutuation of gene expression pattern observed in mouse embryonic stem cells (mESC). In this study, six genes including core genes to maintain pluripotency in mESC were selected and a theoretical model of the regulatory network among those six genes was constructed. Dynamical behavior of the network was analyzed by performing stochastic simulations, which led to the hypothesis that the slow conformational fluctuation of chromatins around gene loci explains the observed large fluctuation of gene expression pattern in mESC.

Report

(5 results)
  • 2014 Annual Research Report   Final Research Report ( PDF )
  • 2013 Research-status Report
  • 2012 Research-status Report
  • 2011 Research-status Report
  • Research Products

    (22 results)

All 2015 2014 2013 2012 Other

All Journal Article (6 results) (of which Peer Reviewed: 6 results,  Open Access: 2 results) Presentation (13 results) (of which Invited: 11 results) Book (2 results) Remarks (1 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] 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 Research-status 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 Research-status 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 Research-status Report
    • Peer Reviewed
  • [Journal Article] Dynamical modeling of 3D genome organization in interphase budding yeast2012

    • Author(s)
      N. Tokuda, T. P. Terada, and M. Sasai
    • Journal Title

      Biophys. J.

      Volume: Vol.102, No.2 Issue: 2 Pages: 296-304

    • DOI

      10.1016/j.bpj.2011.12.005

    • Related Report
      2011 Research-status 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 Research-status 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
      北京
    • Related Report
      2013 Research-status 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
      ソウル
    • Related Report
      2013 Research-status 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
      大阪
    • Related Report
      2013 Research-status 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 Research-status 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, Korea
    • Related Report
      2012 Research-status Report
    • Invited
  • [Presentation] Heterogeneous dynamics and fluctuations in biomolecular networks2012

    • Author(s)
      M. Sasai
    • Organizer
      RIKEN Quantitative Biology Center Inaugural Symposium "Towards Whole-Cell Modeling"
    • Place of Presentation
      Kobe
    • Related Report
      2012 Research-status Report
    • Invited
  • [Presentation] Epigenetic switches and network transitions2012

    • Author(s)
      M. Sasai
    • Organizer
      2012 March Meeting of the American Physical Society(招待講演)
    • Place of Presentation
      Boston, USA
    • Related Report
      2011 Research-status Report
  • [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 Research-status Report
  • [Remarks] http://www.tbp.cse.nagoya-u.ac.jp/HM_project.html

    • Related Report
      2014 Annual Research Report

URL: 

Published: 2011-08-05   Modified: 2019-07-29  

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