The method for reconstructing chromosomal conformation through informatics

• Project/Area Number: 23710230
• Research Category: Grant-in-Aid for Young Scientists (B)
• Allocation Type: Multi-year Fund
• Research Field: System genome science
• Research Institution: The University of Tokyo
• Principal Investigator: NAKATO Ryuichiro 東京大学, 分子細胞生物学研究所, 助教 (60583044)
• Project Period (FY): 2011 – 2012
• Project Status: Completed (Fiscal Year 2012)
• Budget Amount: ¥4,550,000 (Direct Cost: ¥3,500,000、Indirect Cost: ¥1,050,000); Fiscal Year 2012: ¥2,470,000 (Direct Cost: ¥1,900,000、Indirect Cost: ¥570,000); Fiscal Year 2011: ¥2,080,000 (Direct Cost: ¥1,600,000、Indirect Cost: ¥480,000)
• Keywords: ゲノム情報学 / ChIP-seq 法 / データ可視化 / ChIP-seq法 / 転写解析 / クロマチン構造解析 / ゲノム機能解析 / ChIP-seq / 3C

Research Abstract

We have developed a cost-effective and time-efficient program DROMPA for ChIP-seq analysis. DROMPA can visualize a protein-binding map, which can reduce the total cost for an analysis. By using DROMPA, we comprehensively investigated the cohesin binding sites for human B-cells. We found that a part of cohesin sites colocalize with an enhancer marker with tissue-specific manner, and such sites were lost for CdLS, that is caused by the loss of cohesin function.

Research Products

• [Journal Article] DROMPA: easy-to-handle peak calling and visualization software for the computational analysis and validation of ChIP-seq data (2013)
  • Author(s): Nakato, R., Itoh T., Shirahige K.
  • Journal Title: Genes to Cells Volume: 18
  • Peer Reviewed
• [Journal Article] PRDM14 Ensures Naive Pluripotency through Dual Regulation of Signaling and Epigenetic Pathways in Mouse Embryonic Stem Cells (2013)
  • Author(s): Yamaji M., Ueda J., Hayashi K., Ohta H., Yabuta Y., Kurimoto K., Nakato R., Yamada Y., Shirahige K., Saitou M.
  • Journal Title: Cell Stem Cell Volume: 12 Pages: 368-382
  • Peer Reviewed
• [Journal Article] Eukaryotic replisome components cooperate to process histones during chromosome replication (2013)
  • Author(s): Foltman M., Evrin C., De Piccoli G., Jones R.C., Edmondson R.D., Katou Y., Nakato R., Shirahige K., Labib K.
  • Journal Title: Cell Rep Volume: 3 Pages: 892-904
  • Peer Reviewed
• [Journal Article] DROMPA: easy‐to‐handle peak calling and visualization software for the computational analysis and validation of ChIP‐seq data (2013)
  • Author(s): Ryuichiro Nakato
  • Journal Title: Genes to Cells Volume: 18 Issue: 7 Pages: 589-601
  • DOI: 10.1111/gtc.12058
  • Peer Reviewed
• [Journal Article] Telomere-binding protein Taz1 controls global replication timing through its localization near late replication origins in fission yeast (2012)
  • Author(s): Tazumi A., Fukuura M., Nakato R., Kishimoto A., Takenaka T., Ogawa S.,Song J.H., Takahashi T.S., Nakagawa T., Shirahige K., Masukata H.
  • Journal Title: Genes Dev Volume: 26 Pages: 2050-2062
  • Peer Reviewed
• [Journal Article] HDAC8 mutations in Cornelia de Lange syndrome affect the cohesin acetylation cycle (2012)
  • Author(s): Deardorff M.A., Bando M., Nakato, R.(他39名)
  • Journal Title: Nature Volume: 489 Pages: 313-317
  • Peer Reviewed
• [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., Nakato, R., Shirahige, K., and Labib, K.
  • Journal Title: Molecular Cell Volume: 45 Pages: 696-704
  • Peer Reviewed
• [Journal Article] Telomere-binding proteins play roles in control of replication timing (2012)
  • Author(s): Tazumi, A., Masukata, H.
  • Journal Title: Cell Cycle Volume: 11(24) Issue: 18 Pages: 4492-4493
  • DOI: 10.1101/gad.194282.112
  • Peer Reviewed
• [Journal Article] The inheritance of histone modifications depends upon the location in the chromosome in Saccharomyces cerevisiae (2011)
  • Author(s): Masumoto H., Nakato, R., Kanemaki M., Shirahige K., Hachinohe M.
  • Journal Title: PLoS ONE Volume: 6
  • Peer Reviewed
• [Journal Article] Origin Association of Sld3, Sld7, and Cdc45Proteins Is a Key Step for Determination of Origin-Firing Timing (2011)
  • Author(s): Tanaka S., Nakato R., Katou Y., Shirahige K., Araki H.
  • Journal Title: Current Biol Volume: 21 Pages: 2055-2063
  • Peer Reviewed
• [Journal Article] Origin association of Sld3, Sld7, and Cdc45 proteins is a key step for determination of origin-firing timing (2011)
  • Author(s): Tanaka, S., Nakano, R., Katou, Y., Shirahige, K. and Araki, H.
  • Journal Title: Curr. Biol Volume: 21 Issue: 24 Pages: 2055-2063
  • DOI: 10.1016/j.cub.2011.11.038
  • Peer Reviewed
• [Journal Article] The inheritance of histone modifications depends upon the location in the chromosome in Saccharomyces cerevisiae (2011)
  • Author(s): Masumoto H, Nakato, R., Kanemaki M, Shirahige K, Hachinohe M.
  • Journal Title: PLoS ONE Volume: 6 Issue: 12 Pages: e28980-e28980
  • DOI: 10.1371/journal.pone.0028980
  • Peer Reviewed
• [Book] 実験医学 (2012)
  • Author(s): 中戸隆一郎, 伊藤武彦, 白髭克彦, 次世代シークエンサーによる染色体構造解析
  • Publisher: 羊土社
• [Remarks]
  • URL: http://www.iam.u-tokyo.ac.jp/chromosomeinformatics/rnakato/drompa/
• [Remarks] DROMPA webiste
  • URL: http://www.iam.u-tokyo.ac.jp/chromosomeinformatics/rnakato/drompa/