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Chromatin dynamics analysis using computer simulation

Planned Research

Project AreaDynamic chromatin structure and function
Project/Area Number 25116003
Research Category

Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)

Allocation TypeSingle-year Grants
Review Section Biological Sciences
Research InstitutionNational Institutes for Quantum and Radiological Science and Technology (2016-2017)
Japan Atomic Energy Agency (2013-2015)

Principal Investigator

Kono Hidetoshi  国立研究開発法人量子科学技術研究開発機構, 関西光科学研究所 量子生命科学研究部, グループリーダー(定常) (40291918)

Research Collaborator LI Zhenhai  
Project Period (FY) 2013-06-28 – 2018-03-31
Project Status Completed (Fiscal Year 2017)
Budget Amount *help
¥52,260,000 (Direct Cost: ¥40,200,000、Indirect Cost: ¥12,060,000)
Fiscal Year 2017: ¥9,360,000 (Direct Cost: ¥7,200,000、Indirect Cost: ¥2,160,000)
Fiscal Year 2016: ¥9,360,000 (Direct Cost: ¥7,200,000、Indirect Cost: ¥2,160,000)
Fiscal Year 2015: ¥9,360,000 (Direct Cost: ¥7,200,000、Indirect Cost: ¥2,160,000)
Fiscal Year 2014: ¥9,360,000 (Direct Cost: ¥7,200,000、Indirect Cost: ¥2,160,000)
Fiscal Year 2013: ¥14,820,000 (Direct Cost: ¥11,400,000、Indirect Cost: ¥3,420,000)
Keywordsヌクレオソーム / 分子動力学計算 / クロマチン / ヒストン / シミュレーション / 翻訳後修飾 / エピゲノム / 分子シミュレーション / アンサンブル / 生体生命情報学
Outline of Final Research Achievements

We studied impact of post-translational modifications of histones and histone variants on the structure and dynamics of mono-nucleosomes and poly-nucleosomes by integrating computer simulation and experimental data. We found that acetylation and methylation of H3 tails induce DNA dissociation from the histone core. We determined a novel nucleosome structure which is overlapping the typical 8-mer nucleosome and a 6-mer nucleosome which is missing one H2A-H2B heterodimer from the typical nucleosome. In addition, we found H4 tails play an important role in producing various packing forms of two nucleosomes, indicating that the way of the tail interactions yields a variety of chromatin conformations.

Report

(6 results)
  • 2017 Annual Research Report   Final Research Report ( PDF )
  • 2016 Annual Research Report
  • 2015 Annual Research Report
  • 2014 Annual Research Report
  • 2013 Annual Research Report
  • Research Products

    (52 results)

All 2018 2017 2016 2015 2014 2013 Other

All Int'l Joint Research (2 results) Journal Article (15 results) (of which Int'l Joint Research: 3 results,  Peer Reviewed: 15 results,  Open Access: 10 results,  Acknowledgement Compliant: 5 results) Presentation (35 results) (of which Int'l Joint Research: 12 results,  Invited: 14 results)

  • [Int'l Joint Research] ジャワハルラール・ネルー大学(インド)

    • Related Report
      2017 Annual Research Report
  • [Int'l Joint Research] コロラド大学/オハイオ州立大学/ロチェスター大学(米国)

    • Related Report
      2017 Annual Research Report
  • [Journal Article] Free energy profiles for unwrapping the outer superhelical turn of nucleosomal DNA2018

    • Author(s)
      Kono Hidetoshi、Sakuraba Shun、Ishida Hisashi
    • Journal Title

      PLOS Computational Biology

      Volume: 14 Issue: 3 Pages: e1006024-e1006024

    • DOI

      10.1371/journal.pcbi.1006024

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Crystal structure of the overlapping dinucleosome composed of hexasome and octasome2017

    • Author(s)
      Daiki Kato, Akihisa Osakabe, Yasuhiro Arimura, Yuka Mizukami, Naoki Horikoshi, Kazumi Saikusa, Satoko Akashi, Yoshifumi Nishimura, Sam-Yong Park, Jumpei Nogami, Kazumitsu Maehara, Yasuyuki Ohkawa, Atsushi Matsumoto, Hidetoshi Kono, Rintaro Inoue, Masaaki Sugiyama, Hitoshi Kurumizaka
    • Journal Title

      Science

      Volume: 356 Issue: 6334 Pages: 205-208

    • DOI

      10.1126/science.aak9867

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Predicting conformational ensembles and genome-wide transcription factor binding sites from DNA sequences2017

    • Author(s)
      Andrabi Munazah、... 、Kono Hidetoshi、Nussinov Ruth、Mizuguchi Kenji、Ahmad Shandar
    • Journal Title

      Scientific Reports

      Volume: 7 Issue: 1 Pages: 4071-4071

    • DOI

      10.1038/s41598-017-03199-6

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Covalent Modifications of Histone H3K9 Promote Binding of CHD32017

    • Author(s)
      Tencer Adam H.、....、Kono Hidetoshi、Poirier Michael G.、Musselman Catherine A.、Kutateladze Tatiana G.
    • Journal Title

      Cell Reports

      Volume: 21 Issue: 2 Pages: 455-466

    • DOI

      10.1016/j.celrep.2017.09.054

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Accessibility of the histone H3 tail in the nucleosome for binding of paired readers2017

    • Author(s)
      Gatchalian Jovylyn、Wang Xiaodong、Ikebe Jinzen、Cox Khan L.、Tencer Adam H.、Zhang Yi、Burge Nathaniel L.、Di Luo、Gibson Matthew D.、Musselman Catherine A.、Poirier Michael G.、Kono Hidetoshi、Hayes Jeffrey J.、Kutateladze Tatiana G.
    • Journal Title

      Nature Communications

      Volume: 8 Issue: 1 Pages: 1489-1489

    • DOI

      10.1038/s41467-017-01598-x

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] H4 Tails Potentially Produce the Diversity in the Orientation of Two Nucleosomes2017

    • Author(s)
      Ishida Hisashi、Kono Hidetoshi
    • Journal Title

      Biophysical Journal

      Volume: 113 Issue: 5 Pages: 978-990

    • DOI

      10.1016/j.bpj.2017.07.015

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed
  • [Journal Article] ヌクレオソーム中におけるヒストンテールの特性とアセチル化の影響2017

    • Author(s)
      池部仁善; 櫻庭俊; 河野秀俊
    • Journal Title

      日本生物物理学会誌

      Volume: 57 Pages: 095-095

    • NAID

      130005509480

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Spotting the difference in molecular dynamics simulations of biomolecules2016

    • Author(s)
      Sakuraba, S.; Kono, H.
    • Journal Title

      J. Chem. Phys.

      Volume: 145 Issue: 7 Pages: 074116-074116

    • DOI

      10.1063/1.4961227

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Distinct Roles of Histone H3 and H2A Tails in Nucleosome Stability2016

    • Author(s)
      Li, Z.; Kono, H.
    • Journal Title

      Scientific Reports

      Volume: 6 Issue: 1 Pages: 31437-31437

    • DOI

      10.1038/srep31437

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] H3 histone tail conformation within the nucleosome and the impact of K14 acetylation studied using enhanced sampling simulation2016

    • Author(s)
      J. Ikebe, S. Sakuraba and H. Kono,
    • Journal Title

      PLoS Computational Biology

      Volume: 12 Issue: 3 Pages: e1004788-e1004788

    • DOI

      10.1371/journal.pcbi.1004788

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Two arginine residues suppress the flexibility of nucleosomal DNA in the canonical nucleosome core.2015

    • Author(s)
      Kono H, Shirayama K, Arimura Y, Tachiwana H, Kurumizaka H.
    • Journal Title

      PLoS One

      Volume: 10 Issue: 3 Pages: e0120635-e0120635

    • DOI

      10.1371/journal.pone.0120635

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Intensity of diffracted X-rays from biomolecules with radiation damage caused by strong X-ray pulses2014

    • Author(s)
      Kai, T., Tokuhisa, A., Moribayashi, K., Fukuda, Y., Kono, H. & Go, N
    • Journal Title

      J. Phys. Soc. Jpn.

      Volume: 83 Issue: 9 Pages: 094301-094301

    • DOI

      10.7566/jpsj.83.094301

    • NAID

      210000133248

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Local Dynamics Coupled to Hydration Water Determines DNA-sequence Dependent Deformability2014

    • Author(s)
      H. Nakagawa, Y. Yonetani, K. Nakajima, S. Ohira-Kawamura, T.Kikuchi, Y. Inamura, M. Kataoka, H. Kono
    • Journal Title

      Physical Reiew E

      Volume: 90 Issue: 2 Pages: 022723-022723

    • DOI

      10.1103/physreve.90.022723

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Adaptive lambda square dynamics simulation: an efficient conformational sampling method for biomolecules2014

    • Author(s)
      Ikebe, J., Sakuraba, S. & Kono, H.
    • Journal Title

      Journal of Computational Chemistry

      Volume: 35 Issue: 1 Pages: 9-50

    • DOI

      10.1002/jcc.23462

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Dissociation Free-Energy Profiles of Specific and Nonspecific DNA-Protein Complexes2013

    • Author(s)
      Yonetani, Y. & Kono, H
    • Journal Title

      J Phys Chem B

      Volume: 117 Issue: 25 Pages: 7535-45

    • DOI

      10.1021/jp402664w

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Presentation] Mono- and Di- nucleosome Dynamics Studied by Molecular Modeling and Simulation2018

    • Author(s)
      Kono, H.
    • Organizer
      The 8th Taiwan-Japan Joint Meeting on Neutron and X-ray Scattering
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] スーパーコンピュータでみる分子の形と動き2018

    • Author(s)
      河野秀俊
    • Organizer
      一般公開シンポジウム、遺伝子研究の最前線
    • Related Report
      2017 Annual Research Report
  • [Presentation] Distinct Roles of H3 and H2A tails in linker DNA dynamics.2017

    • Author(s)
      Li, Z.; Ikebe, J.; Sakuraba, S.; Kono, H.
    • Organizer
      Biophysical Society 61th Annual Meeting
    • Place of Presentation
      New Orleans, Louisiana, USA (海外)
    • Year and Date
      2017-02-11
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research
  • [Presentation] THE FREE-ENERGY LANDSCAPE OF THE DI-NUCLEOSOME: A CRITICAL ROLE OF THE H4 TAILS FOR THE NUCLEOSOME-NUCLEOSOME CONFORMATION.2017

    • Author(s)
      Ishida, H.; Kono, H.
    • Organizer
      Biophysical Society 61th Annual Meeting
    • Place of Presentation
      New Orleans, Louisiana, USA (海外)
    • Year and Date
      2017-02-11
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research
  • [Presentation] アセチル化、メチル化によるヒストンH3テールの振る舞いの変化2017

    • Author(s)
      河野秀俊; Di, L.; 池部仁善; 櫻庭俊,
    • Organizer
      第34回染色体ワークショップ・第15回核ダイナミクス研究会
    • Place of Presentation
      千葉・木更津・かずさDNA(国内)
    • Year and Date
      2017-01-11
    • Related Report
      2016 Annual Research Report
  • [Presentation] Impact of post-translational modifications on the structure and dynamics of nucleosome2017

    • Author(s)
      Kono, H., Luo, D.
    • Organizer
      1st QST International Symposium"Quantum Life Science"
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Free energy analysis of the Nucleosome-Nucleosome interaction analyzed by Biomolecular Simulations2017

    • Author(s)
      Ishida, H.; Kono, H.
    • Organizer
      1st QST International Symposium"Quantum Life Science"
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Impact of Post-Translational Modifications on Histone H3 tail on Nucleosome Structure and Dynamics2017

    • Author(s)
      Kono, H.
    • Organizer
      EMBO Conference: The Nucleosome: From Atoms to Genomes
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Role of tails in intra-nucleosome and inter-nucleosomes2017

    • Author(s)
      Kono, H.
    • Organizer
      1st Munche-Japan mini-Symposium,Chromatin Structure and Function
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] ヒストンH3翻訳後修飾のヌクレオソーム動態に与える影響2017

    • Author(s)
      河野秀俊
    • Organizer
      第17回日本蛋白質科学会年会
    • Related Report
      2017 Annual Research Report
    • Invited
  • [Presentation] ヒストン翻訳後修飾はヌクレオソームの安定性を変える2017

    • Author(s)
      河野秀俊
    • Organizer
      第40回日本分子生物学会年会
    • Related Report
      2017 Annual Research Report
    • Invited
  • [Presentation] セントロメア特異的なクロマチン構造の解析2016

    • Author(s)
      鈴木翠; 立名和博昭; 滝沢由政; 松本淳; 河野秀俊; Wolf, M.; 胡桃坂仁志
    • Organizer
      第39回日本分子生物学会年会
    • Place of Presentation
      神奈川・横浜・パシフィコ横浜(国内)
    • Year and Date
      2016-11-30
    • Related Report
      2016 Annual Research Report
  • [Presentation] 特殊なヌクレオソームの立体構造解析2016

    • Author(s)
      加藤大貴; 越阪部晃永; 足立風水也; 水上優夏; 有村泰宏; 七種和美; 明石知子; 西村善文; 朴三用; 松本淳; 河野秀俊; 井上倫太郎; 杉山正明; 胡桃坂仁志
    • Organizer
      第39回日本分子生物学会年会
    • Place of Presentation
      神奈川・横浜・パシフィコ横浜(国内)
    • Year and Date
      2016-11-30
    • Related Report
      2016 Annual Research Report
  • [Presentation] 転写因子のアクティビィティは結合サイト及びその周辺領域のDNA特性の関係できまる2016

    • Author(s)
      河野秀俊
    • Organizer
      第16回日本蛋白質科学会年会
    • Place of Presentation
      福岡・福岡・福岡国際会議場(国内)
    • Year and Date
      2016-06-07
    • Related Report
      2016 Annual Research Report
    • Invited
  • [Presentation] Distinct Roles of Histone H3 and H2A Tails in Nucleosome Stability2016

    • Author(s)
      Li, Z.; Kono, H.
    • Organizer
      Chromatin Structure & Function, Gordon Conference
    • Place of Presentation
      Les Diablerets, Switzerland (海外)
    • Year and Date
      2016-05-22
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Impact of Histone Variant and Post-translational Modification on Nucleosome2016

    • Author(s)
      Kono, H., Ikebe, J., Sakuraba, S. and Ishida, H.
    • Organizer
      Biophysical Society 60th Annual Meeting
    • Place of Presentation
      Los Angeles Convention Center (Los Angels, CA, USA)
    • Year and Date
      2016-02-27
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Role of H3 and H2A Tails on Nucleosome Stability2016

    • Author(s)
      Kono, H.
    • Organizer
      Colorado Chromatin Meeting 2016
    • Place of Presentation
      Colorado State Univ., Colorado, USA (海外)
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Role of histone variant and histone tails within the nucleosome and the impact of H3 tail acetylation studied using enhanced sampling simulation2015

    • Author(s)
      Ikebe J, Li Z, Sakuraba S, Ishida H, Kono H.
    • Organizer
      4th International Symposium of the Mathematics on Chromatin Live Dynamics Hiroshima
    • Place of Presentation
      JMSアステールプラザ(広島県広島市)
    • Year and Date
      2015-12-07
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Impact on nucleosome dynamics via histone variants and post-translational modifications2015

    • Author(s)
      Kono, H.
    • Organizer
      スパコン「京」がひらく科学と社会; Supercomputational Life Science 2015 (SCLS 2015)
    • Place of Presentation
      東京大学本郷キャンパス(東京都文京区)
    • Year and Date
      2015-10-20
    • Related Report
      2015 Annual Research Report
    • Invited
  • [Presentation] Dynamics of nucleosomes and impact of acetylation2015

    • Author(s)
      Kono H, Ikebe J, Sakuraba S, Ishida H.
    • Organizer
      International Symposium on Chromatin Structure, Dynamics, and Function
    • Place of Presentation
      淡路夢舞台国際会議場(兵庫県淡路市)
    • Year and Date
      2015-08-23
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Differences in Dynamics among Nucleosomes with Distinct Histone Compositions2015

    • Author(s)
      Kono, H.
    • Organizer
      RIKEN Epigenetics in Kobe
    • Place of Presentation
      理研再生科学総合研究センター(神戸)
    • Year and Date
      2015-02-14
    • Related Report
      2014 Annual Research Report
    • Invited
  • [Presentation] Free Energy Profile for Nucleosomal DNA Unwrapping2015

    • Author(s)
      Kono, H., Sakuraba, S. & Ishida, H.
    • Organizer
      Biophysical Society 59th Annual Meeting
    • Place of Presentation
      米国 ボルチモア
    • Year and Date
      2015-02-07 – 2015-02-11
    • Related Report
      2014 Annual Research Report
  • [Presentation] Conformational sampling of unmodified and acetylated H3 histone tails on a nucleosome by all-atom model molecular dynamics simulations2015

    • Author(s)
      Ikebe, J., Sakuraba, S. & Kono, H.
    • Organizer
      Biophysical Society 59th Annual Meeting
    • Place of Presentation
      米国 ボルチモア
    • Year and Date
      2015-02-07 – 2015-02-11
    • Related Report
      2014 Annual Research Report
  • [Presentation] 生体分子MDの間違い探し2014

    • Author(s)
      櫻庭俊、河野秀俊
    • Organizer
      第28回分子シミュレーション討論会
    • Place of Presentation
      市民会館(仙台)
    • Year and Date
      2014-11-12 – 2014-11-14
    • Related Report
      2014 Annual Research Report
  • [Presentation] シミュレーションによる動的クロマチンダイナミクス2014

    • Author(s)
      河野秀俊
    • Organizer
      分子研研究会「細胞核内反応の分子化学」
    • Place of Presentation
      分子研(岡崎)
    • Year and Date
      2014-09-27
    • Related Report
      2014 Annual Research Report
    • Invited
  • [Presentation] ヌクレオソームにおけるH3ヒストンテールの構造アンサンブル2014

    • Author(s)
      河野秀俊、池部仁善
    • Organizer
      第14回日本蛋白質科学学会年会
    • Place of Presentation
      ワークピア横浜(横浜)
    • Year and Date
      2014-06-25 – 2014-06-27
    • Related Report
      2014 Annual Research Report
    • Invited
  • [Presentation] Understanding Protein-DNA Recognition by Structural Bioinformatics and Molecular Dynamics Simulation

    • Author(s)
      Kono, H.
    • Organizer
      Second BMIRC International Symposium on Advances in Bioinformatics and Medical Engineering
    • Place of Presentation
      Center of Iizuka Research and Development, Iizuka, Fukuoka
    • Related Report
      2013 Annual Research Report
    • Invited
  • [Presentation] 立体構造から探るタンパク質-DNA 認識機構

    • Author(s)
      河野秀俊
    • Organizer
      2013 年年会生命医薬情報学連合大会
    • Place of Presentation
      タワーホール船堀、東京
    • Related Report
      2013 Annual Research Report
    • Invited
  • [Presentation] Free Energy Profile for Nucleosomal DNA Unwrapping

    • Author(s)
      Kono, H., Yonetani, Y., Ikebe, J., Sakuraba, S. & Ishida, H.
    • Organizer
      第51回日本生物物理学会年会
    • Place of Presentation
      京都国際会館、京都
    • Related Report
      2013 Annual Research Report
    • Invited
  • [Presentation] Adaptive lambda square dynamics simulation: an efficient conformational sampling method for biomolecules

    • Author(s)
      Ikebe, J., Sakuraba, S. & Kono, H.
    • Organizer
      Biophysical Society 58th Annual Meeting
    • Place of Presentation
      San Francisco、米国
    • Related Report
      2013 Annual Research Report
  • [Presentation] DISSOCIATION FREE-ENERGY PROFILES OF SPECIFIC AND NON-SPECIFIC DNA-LACREPRESSOR COMPLEXES:ADAPTIVE BIASINGFORCE MOLECULAR DYNAMICS STUDY

    • Author(s)
      Kono, H. & Yonetani, Y.
    • Organizer
      Biophysical Society 58th Annual Meeting
    • Place of Presentation
      San Francisco、米国
    • Related Report
      2013 Annual Research Report
  • [Presentation] CENP-Aヌクレオソーム特異的なDNA構造の構造生物学的・生化学的解析

    • Author(s)
      Shirayama, K., Arimura, Y., Tachiwana, H., Kono, H. & Kurumizaka, H.
    • Organizer
      第86回日本生化学会大会
    • Place of Presentation
      パシフィコ横浜、横浜
    • Related Report
      2013 Annual Research Report
  • [Presentation] CENP-A ヌクレオソームにおける動的なDNA構造とその制御機構

    • Author(s)
      Arimura, Y., Osakabe, A., Shirayama, K., Takeda, Y., Miya, Y., Tachiwana, H., Kono, H. & Kurumizaka, H.
    • Organizer
      第36回日本分子生物学会年会
    • Place of Presentation
      神戸国際会議場、神戸
    • Related Report
      2013 Annual Research Report
  • [Presentation] H3ヒストンテールの構造とダイナミクス

    • Author(s)
      河野秀俊、池部仁善
    • Organizer
      第31回 染色体ワークショップ・第12回 核ダイナミクス研究会
    • Place of Presentation
      ホテルおかだ、神奈川
    • Related Report
      2013 Annual Research Report
  • [Presentation] Adaptive lambda square dynamics simulation: an efficient conformational sampling method for biomolecules

    • Author(s)
      Ikebe, J., Sakuraba, S. & Kono, H.
    • Organizer
      第51回日本生物物理学会年会
    • Place of Presentation
      京都国際会館、京都
    • Related Report
      2013 Annual Research Report

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Published: 2013-07-10   Modified: 2022-02-28  

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