Research and development of biological information platform for ChIP-seq analysis using next generation sequencer

• Project/Area Number: 21687001
• Research Category: Grant-in-Aid for Young Scientists (A)
• Allocation Type: Single-year Grants
• Research Field: Genetics/Genome dynamics
• Research Institution: Tokyo Institute of Technology
• Principal Investigator: ITOH Takehiko 東京工業大学, 大学院・生命理工学研究科, 教授 (90501106)
• Project Period (FY): 2009 – 2011
• Project Status: Completed (Fiscal Year 2011)
• Budget Amount: ¥27,430,000 (Direct Cost: ¥21,100,000、Indirect Cost: ¥6,330,000); Fiscal Year 2011: ¥7,280,000 (Direct Cost: ¥5,600,000、Indirect Cost: ¥1,680,000); Fiscal Year 2010: ¥7,280,000 (Direct Cost: ¥5,600,000、Indirect Cost: ¥1,680,000); Fiscal Year 2009: ¥12,870,000 (Direct Cost: ¥9,900,000、Indirect Cost: ¥2,970,000)
• Keywords: バイオインフォマティクス / ChIP-seq解析 / ChIP-seq法

Research Abstract

We developed a new algorithm for ChIP-seq analysis using next generation sequencer(i. e. Solexa/SOLiD) and targeted genome information, which can be picked up protein binding sites cyclopaedically and quantitatively from the entire genome.

Research Products

• [Journal Article] Replisome stability at defective DNA replication forks is independent of S phase checkpoint kinases (2012)
  • Author(s): De Piccoli G, Katou Y, Itoh T, et al
  • Journal Title: Mol Cell Volume: 45(5) Pages: 696-704
  • Peer Reviewed
• [Journal Article] Replisome stability at defective DNA replication forks is independent of S phase checkpoint kinases (2012)
  • Author(s): De Piccoli G, 他
  • Journal Title: Mol Cell. Volume: 45 Pages: 696-704
  • Peer Reviewed
• [Journal Article] Chromosome length influences replication-induced topological stress Nature (2011)
  • Author(s): A. Kegel, H. B. Lindroos, T. Kanno, K. Jeppsson, L. Strom, Y. Katou, T. Itoh, K. Shirahige, et al
  • Volume: 471(7338)
  • Pages: 392-6
  • Peer Reviewed
• [Journal Article] ATP Hydrolysis Is Required for Relocating Cohesin from Sites Occupied by Its Scc2/4 Loading Complex Curr (2011)
  • Author(s): B. Hu, T. Itoh, A. Mishra, Y. Katoh, K-L. Chan, W. Upcher, C. Godlee, M. B. Roig, K. Shirahige, and K. Nasmyth
  • Journal Title: Biol Volume: 21(1) Pages: 12-24
  • Peer Reviewed
• [Journal Article] Chromosome length influences replication-induced topological stress. (2011)
  • Author(s): Kegel A, Betts-Lindroos H, Kanno T, Jeppsson K, Strom L, Katou Y, Itoh T, Shirahige K, Sjogren C.
  • Journal Title: Nature Volume: 471(7338) Pages: 392-6
  • Peer Reviewed
• [Journal Article] Histone and TK0471/TrmBL2 form a novel heterogeneous genome architecture in the hyperthermophilic archaeon Thermococcus kodakarensis (2010)
  • Author(s): H. Maruyama, M. Shin, T. Oda, R. Matsumi, R. L. Ohniwa, T. Itoh, K. Shirahige, T. Imanaka, H. Atomi, S. H. Yoshimura, and K. Takeyasu
  • Journal Title: Mol Biol Cell
  • NAID: 120002871160
  • Peer Reviewed
• [Journal Article] A positively charged channel within the Smc1/Smc3 hinge required for sister chromatid cohesion EMBO (2010)
  • Author(s): A. Kurze, K. A. Michie, S. E. Dixon, A. Mishra, T. Itoh, S. Khalid, L. Strmecki, K. Shirahige, C. H. Hearing, J. Lowe, and K Nasmyth
  • Peer Reviewed