Regulation of Gene Transcription Inferred From Transcription Factor Binding and Nucleosome Positioning

• Project/Area Number: 20300103
• Research Category: Grant-in-Aid for Scientific Research (B)
• Allocation Type: Single-year Grants
• Section: 一般
• Research Field: Bioinformatics/Life informatics
• Research Institution: Japan Atomic Energy Agency
• Principal Investigator: KONO Hidetoshi Japan Atomic Energy Agency, 量子ビーム応用研究部門, 研究主幹 (40291918)
• Co-Investigator(Renkei-kenkyūsha): MATSUMOTO Atsushi 日本原子力研究開発機構, 量子ビーム応用研究部門・生体分子シミュレーショングループ, 研究副主幹 (10399420)
• Project Period (FY): 2008 – 2010
• Project Status: Completed (Fiscal Year 2010)
• Budget Amount: ¥17,550,000 (Direct Cost: ¥13,500,000、Indirect Cost: ¥4,050,000); Fiscal Year 2010: ¥6,500,000 (Direct Cost: ¥5,000,000、Indirect Cost: ¥1,500,000); Fiscal Year 2009: ¥6,630,000 (Direct Cost: ¥5,100,000、Indirect Cost: ¥1,530,000); Fiscal Year 2008: ¥4,420,000 (Direct Cost: ¥3,400,000、Indirect Cost: ¥1,020,000)
• Keywords: バイオインフォマティクス / ヌクレオソーム / 転写 / 遺伝子発現 / 制御 / クロマチン / ヒストン修飾 / ゲノム / 生体生命情報 / タンパク質-核酸

Research Abstract

Gene Regulation is controlled by binding of regulator proteins to DNA and positioning of nucleosome structures. We have developed a method that can predict nucleosome positions based on the physico-chemical properties of DNA sequences. The predicted distributions of nucleosome positions around transcription start sites of yeast genes indicate that transcription patterns of the genes can be classified into five groups. In addition, GC content was highly correlated with the distribution of nucleosomes.

Research Products

• [Journal Article] DNAの水和水とダイナミクスの塩基配列依存症-DNA-タンパク質、DNA-低分子認識の理解に向けて- (2010)
  • Author(s): 米谷佳晃, 河野秀俊
  • Journal Title: メディカルバイオ 揺らぎと生体機能10月別冊 Pages: 66-71
• [Journal Article] A Generalized Conformational Energy Function of DNA Derived from Molecular Dynamics Simulations (2009)
  • Author(s): Yamasaki S., Terada T., Shimizu K., Kono H., Sarai A.
  • Journal Title: Nucleic Acids Res. 37
  • Peer Reviewed
• [Journal Article] Evaluation of DNA Intramolecular Interactions for Nucleosome Positioning in Yeast. (2009)
  • Author(s): Fernandez M., Fujii S., Kono H., Sarai, A.
  • Journal Title: Genome Informatics 23 Pages: 13-20
  • Peer Reviewed
• [Journal Article] Sequence dependencies of DNA deformability and hydration in the minor groove. (2009)
  • Author(s): Yonetani Y., Kono H.
  • Journal Title: Biophys J 97 Pages: 1138-47
  • Peer Reviewed
• [Journal Article] A Generalized Conformational Energy Function of DNA Derived from Molecular Dynamics Simulations. (2009)
  • Author(s): Yamasaki, S., Terada, T., Shimizu, K., Kono, H., Sarai, A.
  • Journal Title: Nucleic Acids Res. 37
  • Peer Reviewed
• [Journal Article] Evaluation of DNA Intramolecular Interactions for Nucleosome Positioning in Yeast (2009)
  • Author(s): Fernandez, M., Fujii, S., Kono, H., Sarai, A.
  • Journal Title: Genome Informatics 23 Pages: 13-20
  • Peer Reviewed
• [Presentation] Free energy profiles for nucleosome position changes (2011)
  • Author(s): Kono, H., Kanaeda, N., Ishida, H.
  • Organizer: Biophysical Society Annual Meeting
  • Place of Presentation: 米国、ボルチモア
  • Year and Date: 2011-03-06
• [Presentation] Free energy profiles for nucleosome position changes. (2011)
  • Author(s): Kono H., Kanaeda N., Ishida H.
  • Organizer: 55th Biophysical Society Annual Meeting
  • Place of Presentation: Baltimore, USA
• [Presentation] 構造バイオインフォマティクスと分子動力学計算による遺伝子発現制御メカニズムの理解 (2010)
  • Author(s): 河野秀俊
  • Organizer: 日本分子生物学会年会、日本生化学会大会合同大会
  • Place of Presentation: 神戸
  • Year and Date: 2010-12-08
• [Presentation] ヌクレオソームポジションにおける間接認識の役割 (2010)
  • Author(s): Fernandez, M., 藤井聡, 河野秀俊, 皿井明倫
  • Organizer: 日本蛋白質科学会年会
  • Place of Presentation: 札幌
  • Year and Date: 2010-06-16
• [Presentation] 構造バイオインフォマティクスと分子動力学計算による遺伝子発現制御メカニズムの理解 (2010)
  • Author(s): 河野秀俊
  • Organizer: 第33回日本分子生物学会年会第83回日本生科学会大会合同大会
  • Place of Presentation: 神戸(招待講演)
• [Presentation] 情報エントロピーを用いたタンパク質-DNA認識におけるindirect readoutの寄与の評価 (2010)
  • Author(s): 山崎智,河野秀俊,清水謙多郎,皿井明倫,寺田透
  • Organizer: 第10回日本蛋白質科学会年会
  • Place of Presentation: 札幌
• [Presentation] ヌクレオソームポジションにおける間接認識の役割 (2010)
  • Author(s): Fernandez M.,藤井聡,河野秀俊,皿井明倫
  • Organizer: 第10回日本蛋白質科学会年会
  • Place of Presentation: 札幌
• [Presentation] Evaluation of DNA Intramolecular Interactions for Nucleosome Positioning in Yeast. (2009)
  • Author(s): Fernandez, M., Fujii, S., Kono, H., Sarai, A.
  • Organizer: The 20th International Conference on Genome Informatics.
  • Place of Presentation: 横浜
  • Year and Date: 2009-12-16
• [Presentation] The free energy profile of a nucleosome core particle through the molecular dynamics simulation (2009)
  • Author(s): N.Kanaeda, H.Ishida, H.Kono
  • Organizer: 第47回日本生物物理学会年会
  • Place of Presentation: 徳島
  • Year and Date: 2009-10-30
• [Presentation] Structure-based Analysis of Cooperativity in Protein-DNA Recognition (2009)
  • Author(s): Tanaka A., Fujii S., Kono H., Sarai A.
  • Organizer: 第47回日本生物物理学会年会
  • Place of Presentation: 徳島
• [Presentation] Role of indirect readout in protein-DNA recognition assessed by a Bayesian approach (2009)
  • Author(s): Yamasaki S., Fukui K., Kono H., Shimizu K., Sarai A., Terada T.
  • Organizer: 第47回日本生物物理学会年会
  • Place of Presentation: 徳島
• [Presentation] タンパク質-DNA相互作用の認識塩基配列と非認識塩基配列による違い (2008)
  • Author(s): 徳久淳師,河野秀俊
  • Organizer: 第8回日本蛋白質科学会年会
  • Place of Presentation: 東京(日本)
• [Book] DNAの水和水とダイナミクスの塩基配列依存症-DNA-タンパク質、DNA-低分子認識の理解に向けて(揺らぎと生体機能10月別冊) (2010)
  • Author(s): 米谷佳晃,河野秀俊
  • Publisher: メディカルバイオ
• [Book] Chapter 13 Rotamer Libraries for Molecular Modeling and Design of Proteins (Protein Design and Engineering) (2009)
  • Author(s): 河野秀俊
  • Publisher: Park&Cochran, Taylor & Francis Group
• [Book] Chapter 13 Rotamer Libraries for Molecular Modeling and Design of Proteins (Protein Design and Engineering) (2009)
  • Author(s): Hidetoshi Kono
  • Total Pages: 12
  • Publisher: Taylor & Francis Group
• [Book] タンパク質とDNAの結合予測.実験医学増刊号(26) (2008)
  • Author(s): 皿井明倫,河野秀俊
  • Publisher: バイオデータベースとソフトウェア最前線
• [Remarks] ホームページ等