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2012 Fiscal Year Final Research Report

The method for reconstructing chromosomal conformation through informatics

Research Project

  • PDF
Project/Area Number 23710230
Research Category

Grant-in-Aid for Young Scientists (B)

Allocation TypeMulti-year Fund
Research Field System genome science
Research InstitutionThe 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
Keywordsゲノム情報学 / ChIP-seq 法 / データ可視化
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

    (10 results)

All 2013 2012 2011 Other

All Journal Article (8 results) (of which Peer Reviewed: 8 results) Book (1 results) Remarks (1 results)

  • [Journal Article] DROMPA: easy-to-handle peak calling and visualization software for the computational analysis and validation of ChIP-seq data2013

    • 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 Cells2013

    • 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 replication2013

    • 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] Telomere-binding protein Taz1 controls global replication timing through its localization near late replication origins in fission yeast2012

    • 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 cycle2012

    • 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 kinases2012

    • 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] The inheritance of histone modifications depends upon the location in the chromosome in Saccharomyces cerevisiae2011

    • Author(s)
      Masumoto H., Nakato, R., Kanemaki M., Shirahige K., Hachinohe M.
    • Journal Title

      PLoS ONE

      Volume: 6 Pages: e28980

    • Peer Reviewed
  • [Journal Article] Origin Association of Sld3, Sld7, and Cdc45Proteins Is a Key Step for Determination of Origin-Firing Timing2011

    • Author(s)
      Tanaka S., Nakato R., Katou Y., Shirahige K., Araki H.
    • Journal Title

      Current Biol

      Volume: 21 Pages: 2055-2063

    • 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
    • Total Pages
      P976-982
    • Publisher
      羊土社
  • [Remarks]

    • URL

      http://www.iam.u-tokyo.ac.jp/chromosomeinformatics/rnakato/drompa/

URL: 

Published: 2014-09-25  

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