High density simulation for transcriptional dynamics

2011 Fiscal Year Final Research Report

• Project/Area Number: 22700309
• Research Category: Grant-in-Aid for Young Scientists (B)
• Allocation Type: Single-year Grants
• Research Field: Bioinformatics/Life informatics
• Research Institution: The University of Tokyo
• Principal Investigator: OHTA Yoshihiro 東京大学, 先端科学技術研究センター, 特任助教 (80436592)
• Project Period (FY): 2010 – 2011
• Keywords: 転写 / シミュレーション / RNAPII / RNA / セルオートマトン

Research Abstract

RNA polymerase II(RNAPII) is the responsible motor protein for transcription. Here we studied the formulation and results of a cellular automaton model of the RNAPII dynamics of gene transcription that takes account the effect of the velocity change according to the gene position, such as occurs in introns and exons. It was found that the RNAPII molecules move as a free-flow state, though regions of reduced velocity do exist such as exons, as far as the time interval between nearest RNAPII molecules is larger than the time required for an RNAPII passing the exclusion length in the velocity reduction region.

Research Products

• [Journal Article] Severe dermatitis with loss of epidermal Langerhans cells in human and mouse zinc deficiency (2012)
  • Author(s): Kawamura T, Ogawa Y, Nakamura Y, Nakamizo S, Ohta Y, Nakano H, Kabashima K, Katayama I, Koizumi S, Kodama T, Nakao A, Shimada S
  • Journal Title: The Journal of Clinical Investigation Volume: 122(2) Pages: 722-732
  • DOI: DOI:10.1172/JCI58618
  • Peer Reviewed
• [Journal Article] Cellular-automaton model of the cooperative dynamics of RNA polymerase II during transcription in human cells (2011)
  • Author(s): Ohta Y, Kodama T, Ihara S
  • Journal Title: Physical Review E Volume: 84 Pages: 15
  • DOI: DOI:10.1103/PhysRevE.84.041922
  • Peer Reviewed
• [Journal Article] Epigenetically coordinated GATA2 binding is necessary for endothelium-specific endomucin expression (2011)
  • Author(s): Kanki Y, Kohro T, Jiang S, Tsutsumi S, Mimura I, Suehiro J, Wada Y, Ohta Y, Ihara S, Iwanari H, Naito M, Hamakubo T, Aburatani H, Kodama T, Minami T
  • Journal Title: The EMBO Journal Volume: 30 Pages: 2582-2595
  • DOI: DOI:10.1038/emboj.2011.173
  • Peer Reviewed
• [Journal Article] Proteomic analysis of native hepatocyte nuclear factor-4α(HNF4α) isoforms, phosphorylation status, and interactive cofactors (2011)
  • Author(s): Daigo K, Kawamura T, Ohta Y, Ohashi R, Katayose S, Tanaka T, Aburatani H, Naito M, Kodama T, Ihara S, Hamakubo T
  • Journal Title: The Journal of Biological Chemistry Volume: Vol.286, No.1 Pages: 674-686
  • DOI: DOI:10.1074/jbc.M110.154732
  • Peer Reviewed
• [Journal Article] Active RNA Polymerases : Mobile or Immobile Molecular Machines? (2010)
  • Author(s): Papantonis A, Larkin JD, Wada Y, Ohta Y, Ihara S, Kodama T, Cook PR
  • Journal Title: PLoS Biology Volume: Volume8, Issue7 Pages: e1000419
  • DOI: DOI:10.1371/journal.pbio.1000419
  • Peer Reviewed
• [Presentation] High Density Spatial and Temporal Simulation Reveals Transcriptional Dynamics (2011)
  • Author(s): Ohta, Yoshihiro
  • Organizer: The Pacific Symposium on Biocomputing(PSB) 2011
  • Place of Presentation: Kona, USA
  • Year and Date: 20110104-08