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A novel approach for the understanding of basic structure and behavior of human chromosomes

Research Project

Project/Area Number 22221009
Research Category

Grant-in-Aid for Scientific Research (S)

Allocation TypeSingle-year Grants
Research Field Genome biology
Research InstitutionThe University of Tokyo

Principal Investigator

SHIRAHIGE Katsuhiko  東京大学, 分子細胞生物学研究所, 教授 (90273854)

Co-Investigator(Kenkyū-buntansha) 伊藤 武彦  東京工業大学, 生命理工学研究科, 教授 (90501106)
広田 亨  公益財団法人がん研究会, 部長 (50421368)
須谷 尚史  東京大学, 分子細胞生物学研究所, 助教 (30401524)
Project Period (FY) 2010-04-01 – 2015-03-31
Project Status Completed (Fiscal Year 2014)
Budget Amount *help
¥224,510,000 (Direct Cost: ¥172,700,000、Indirect Cost: ¥51,810,000)
Fiscal Year 2014: ¥40,820,000 (Direct Cost: ¥31,400,000、Indirect Cost: ¥9,420,000)
Fiscal Year 2013: ¥39,780,000 (Direct Cost: ¥30,600,000、Indirect Cost: ¥9,180,000)
Fiscal Year 2012: ¥40,170,000 (Direct Cost: ¥30,900,000、Indirect Cost: ¥9,270,000)
Fiscal Year 2011: ¥40,820,000 (Direct Cost: ¥31,400,000、Indirect Cost: ¥9,420,000)
Fiscal Year 2010: ¥62,920,000 (Direct Cost: ¥48,400,000、Indirect Cost: ¥14,520,000)
Keywords染色体 / ゲノム構造 / 染色体構造 / 染色体機能 / 転写 / 次世代シークエンサー / タンパクプロファイル解析 / SMCタンパク / ゲノム / 染色体可視化 / ChIP-seq / 染色体動態 / ChIP-seq解析 / 染色体情報 / 染色体構築
Outline of Final Research Achievements

We have built up the informatics system to explore human chromosome dynamics by Next Generation Sequencer Based Technology. Then by using this technology we have analyzed chromosome behavior during cell cycle, aging, and in cell line established from developmental disease patient. Our main achievements can be summarized as follows. 1) Discovery of cohesin deacetylase and its function during cell cycle, 2) Identification of cohesin as an essential component that link chromosome high order structure and transcriptional elongation, 3) identification of condensin's role as a masker of R-loop during mitosis, and 4) Establishment of new chromosomal informatics system (DROMPA) to understand chromosome dynamics.

Assessment Rating
Verification Result (Rating)

A+

Assessment Rating
Result (Rating)

A: Progress in the research is steadily towards the initial goal. Expected research results are expected.

Report

(9 results)
  • 2015 Research Progress Assessment (Verification Result) ( PDF )
  • 2014 Annual Research Report   Final Research Report ( PDF )
  • 2013 Annual Research Report   Abstract(Research Progress Assessment) ( PDF )   Research Progress Assessment (Result) ( PDF )
  • 2012 Annual Research Report
  • 2011 Annual Research Report
  • 2010 Annual Research Report
  • Research Products

    (39 results)

All 2015 2014 2013 2012 2011 2010 Other

All Journal Article (24 results) (of which Peer Reviewed: 24 results,  Open Access: 4 results,  Acknowledgement Compliant: 5 results) Presentation (13 results) Remarks (2 results)

  • [Journal Article] Germline gain-of-function mutations in AFF4 cause a developmental syndrome functionally linking the super elongation complex and cohesin.2015

    • Author(s)
      Izumi K, Nakato R, Zhang Z, Edmondson AC, Noon S, Dulik MC, Rajagopalan R, Venditti CP, Gripp K, Samanich J, Zackai EH, Deardorff MA, Clark D, Allen JL, Dorsett D, Misulovin Z, Komata M, Bando M, Kaur M, Katou Y, Shirahige K*, Krantz ID*.
    • Journal Title

      Nature Genetics

      Volume: 47 Issue: 4 Pages: 338-338

    • DOI

      10.1038/ng.3229

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] The chromosomal association of the Smc5/6 complex depends on cohesion and predicts the level of sister chromatid entanglement.2014

    • Author(s)
      Jeppsson K, Carlborg KK, Nakato R, Berta DG, Lilienthal I, Kanno T, Lindqvist A, Brink MC, Dantuma NP, Katou Y, Shirahige K, Sjogren C.
    • Journal Title

      PLoS Genet.

      Volume: 10

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Histone variants enriched in oocytes enhance reprogramming to induced pluripotent stem cells.2014

    • Author(s)
      Shinagawa T, Takagi T, Tsukamoto D, Tomaru C, Huynh LM, Sivaraman P, Kumarevel T, Inoue K, Nakato R, Katou Y, Sado T, Takahashi S, Ogura A, Shirahige K, Ishii S.
    • Journal Title

      Cell Stem Cell.

      Volume: 14 Pages: 217-224

    • Related Report
      2014 Annual Research Report 2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] The maintenance of chromosome structure: positioning and functioning of SMC complexes.2014

    • Author(s)
      Jeppsson K, Kanno T, Shirahige K, Sjogren C.
    • Journal Title

      Nat Rev Mol Cell Biol.

      Volume: 15 Issue: 9 Pages: 601-614

    • DOI

      10.1038/nrm3857

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Chromatin immunoprecipitation protocol for mammalian cells.2014

    • Author(s)
      Komata M, Katou Y, Tanaka H, Nakato R, Shirahige K, Bando M.
    • Journal Title

      Methods Mol Biol.

      Volume: 1164 Pages: 33-38

    • DOI

      10.1007/978-1-4939-0805-9_4

    • ISBN
      9781493908042, 9781493908059
    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Design, Synthesis, and Biological Activity of NCC149 Derivatives as Histone Deacetylase 8-Selective Inhibitors.2014

    • Author(s)
      Suzuki T, Muto N, Bando M, Itoh Y, Masaki A, Ri M, Ota Y, Nakagawa H, Iida S, Shirahige K, Miyata N.
    • Journal Title

      ChemMedChem.

      Volume: 9 Issue: 3 Pages: 657-664

    • DOI

      10.1002/cmdc.201300414

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Inferring the choreography of parental genomes during fertilization from ultralarge-scale whole-transcriptome analysis.2014

    • Author(s)
      Park SJ, Komata M, Inoue F, Yamada K, Nakai K, Ohsugi M, Shirahige K.
    • Journal Title

      Genes Dev.

      Volume: 27 Issue: 24 Pages: 2736-2748

    • DOI

      10.1101/gad.227926.113

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Smc5/6-mediated regulation of replication progression contributes to chromosome assembly during mitosis in human cells.2014

    • Author(s)
      Gallego-Paez LM, Tanaka H, Bando M, Takahashi M, Nozaki N, Nakato R, Shirahige K*, Hirota T*.(Shared Corresponding Authors)
    • Journal Title

      Mol Biol Cell.

      Volume: 27 Issue: 2 Pages: 2736-2748

    • DOI

      10.1091/mbc.e13-01-0020

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Recurrent mutations in multiple components of the cohesin complex in myeloid neoplasms.2013

    • Author(s)
      Kon A, Yoshida K
    • Journal Title

      Nature Genet.

      Volume: 45 Issue: 10 Pages: 1232-1237

    • DOI

      10.1038/ng.2731

    • Related Report
      2013 Annual Research Report
    • 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)
      Nakato R, Itoh T, Shirahige K.
    • Journal Title

      Genes to Cells.

      Volume: 6月号 Pages: 1-13

    • Related Report
      2012 Annual Research Report
    • 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., Shirahige, K., and Saitou, M
    • Journal Title

      Cell Stem Cell

      Volume: 12 Issue: 3 Pages: 368-382

    • DOI

      10.1016/j.stem.2012.12.012

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Rapid Discovery of Highly Potent and Selective Inhibitors of Histone Deacetylase 8 Using Click Chemistry to Generate Candidate Libraries2012

    • Author(s)
      Takayoshi Suzuki, Yosuke Ota, Masaki Ri, Masashige Bando, Aogu Gotoh, Yukihiro Itoh, Hiroki Tsumoto, Prima R. Tatum, Tamio Mizukami, Hidehiko Nakagawa, Shinsuke Iida, Ryuzo Ueda, Katsuhiko Shirahige, and Naoki Miyata.
    • Journal Title

      J. Med. Chem.

      Volume: 55 Issue: 22 Pages: 9562-9575

    • DOI

      10.1021/jm300837y

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Cohesin acetylation promotes sister chromatid cohesion only in association with the replication machinery.2012

    • Author(s)
      Song J, Lafont A, Chen J, Wu FM, Shirahige K, Rankin S.
    • Journal Title

      J Biol Chem.

      Volume: 5;287(41) Issue: 41 Pages: 34325-36

    • DOI

      10.1074/jbc.m112.400192

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] HDAC8 mutations in Cornelia de Lange syndrome affect the cohesin acetylation cycle.2012

    • Author(s)
      Deardorff MA
    • Journal Title

      Nature

      Volume: 489(7415) Issue: 7415 Pages: 313-7

    • DOI

      10.1038/nature11316

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] The Prereplication Complex Recruits XEco2 to Chromatin to Promote Cohesin Acetylation in Xenopus Egg Extracts2012

    • Author(s)
      Torahiko L. Higashi
    • Journal Title

      Current Biology

      Volume: 22 Issue: 11 Pages: 977-988

    • DOI

      10.1016/j.cub.2012.04.013

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Origin association of Sld3, Sld7, and Cdc45 proteins is a key step for determination of origin-firing timing2011

    • 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

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Spoll-accessory proteins link double-strand break sites to the chromosome axis in early meiotic recombination2011

    • Author(s)
      Panizza S, Mendoza MA, Berlinger M, Huang L, Nicolas A, Shirahige K, Klein F
    • Journal Title

      Cell

      Volume: 146 Issue: 3 Pages: 372-383

    • DOI

      10.1016/j.cell.2011.07.003

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] The replication checkpoint protects fork stability by releasing trans cribed genes from nuclear pores2011

    • Author(s)
      Bermejo R, Capra T, Jossen R, Colosio A, Frattini C, Carotenuto W, Cocito A, Doksani Y, Klein H, Gomez-Gonzalez B, Aguilera A, Katou Y, Shirahige K, Foiani M
    • Journal Title

      Cell

      Volume: 146 Issue: 2 Pages: 233-246

    • DOI

      10.1016/j.cell.2011.06.033

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Chromosome length influences replication-induced topological stress2011

    • Author(s)
      A.Kegel, H.B.Lindroos, T.Kanno, K.Jeppsson, L.Strom, Y.Katou, T.Itoh, K.Shirahige, C.Sjogren
    • Journal Title

      Nature

      Volume: 471 Issue: 7338 Pages: 391-394

    • DOI

      10.1038/nature09791

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] ATP Hydrolysis Is Required for Relocating Cohesin from Sites Occupied by Its Scc2/4 Loading Complex2011

    • Author(s)
      B.Hu, T.Itoh, A.Mishra, Y.Katoh, K-L.Chan, W.Upcher, C.Godlee, M.B.Roig, K.Shirahige, K.Nasmyth
    • Journal Title

      Curr.Biol.

      Volume: 21 Issue: 1 Pages: 12-24

    • DOI

      10.1016/j.cub.2010.12.004

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] A direct role for cohesin in gene regulation and ecdysone response in Drosophila salivary glands.2010

    • Author(s)
      Pauli A, van Bemmel JG, Oliveira RA, Itoh T, Shirahige K, van, Steensel B, Nasmyth K.
    • Journal Title

      Curr Biol.

      Volume: 20 Pages: 1787-98

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] An Smc3 acetylation cycle is essential for establishment of sister chromatid cohesion.2010

    • Author(s)
      Beckouet F, Hu B, Roig MB, Sutani T, Komata M, Uluocak P, Katis VL, Shirahige K, Nasmyth K.
    • Journal Title

      Mol Cell.

      Volume: 39 Pages: 689-699

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Genome-wide DNA methylation analysis in cohesin mutant human cell Iines.2010

    • Author(s)
      Liu J, Zhang Z, Bando M, Itoh T, Deardorff MA, Li JR, Clark D, Kaur M, Tatsuro K, Kline AD, Chang C, Vega H, Jackson LG, Spinner NB, Shirahige K, Krantz ID.
    • Journal Title

      Nucleic Acids Res.

      Volume: 38 Pages: 5657-71

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Sororin mediates sister chromatid cohesion by antagonizing Wapl.2010

    • Author(s)
      Nishiyama T, Ladurner R, Schmitz J, Kreidl E, Schleiffer A, Bhaskara V, Bando M, Shirahige K, Hyman AA, Mechtler K, Peters JM.
    • Journal Title

      Cell.

      Volume: 143 Pages: 737-49

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Presentation] HDAC8 mutations in Cornelia de Lange Syndrome provide insight into the cohesin acetylation cycle2012

    • Author(s)
      白髭克彦
    • Organizer
      The Research Institute of Molecular Pathology in Vienna
    • Place of Presentation
      オーストリア・ウィーン
    • Related Report
      2012 Annual Research Report
  • [Presentation] HDAC8 mutations in Cornelia de Lange Syndrome provide insight into the cohesin acetylation cycle2012

    • Author(s)
      白髭克彦
    • Organizer
      The 13th International Conference on Systems Biology in Toronto
    • Place of Presentation
      カナダ・トロント
    • Related Report
      2012 Annual Research Report
  • [Presentation] ゲノムワイドアプローチ2012

    • Author(s)
      白髭克彦
    • Organizer
      第30回日本骨代謝学会学術集会
    • Place of Presentation
      東京都・新宿区
    • Related Report
      2012 Annual Research Report
  • [Presentation] Genome wide Localization Study of Acetylated Cohesin in Human2012

    • Author(s)
      白髭克彦
    • Organizer
      CdSL Foundation Scientific and Educational Symposia 2012
    • Place of Presentation
      アメリカ・シカゴ
    • Related Report
      2012 Annual Research Report
  • [Presentation] ゲノム学的手法による染色体構造解析、この10年のあゆみ2011

    • Author(s)
      白髭克彦
    • Organizer
      細胞システムコロキウム
    • Place of Presentation
      埼玉県和光市・理化学研究所(招待講演)
    • Year and Date
      2011-11-11
    • Related Report
      2011 Annual Research Report
  • [Presentation] Regulation of Cohesin Dynamics by acetylation and deacetylation2011

    • Author(s)
      白髭克彦
    • Organizer
      東工大生命GCOE国際シンポジウム
    • Place of Presentation
      東京工業大学(招待講演)
    • Year and Date
      2011-07-04
    • Related Report
      2011 Annual Research Report
  • [Presentation] Hdac8欠損型コヒーシン病に見られるコヒーシン代謝異常-コヒーシンアセチル化制御とその意義-2011

    • Author(s)
      白髭克彦
    • Organizer
      第5回日本エピジェネティクス研究会年会
    • Place of Presentation
      熊本大学(招待講演)
    • Related Report
      2011 Annual Research Report
  • [Presentation] Mecl is required for efficient replication fork pausing at Cohesin sites2011

    • Author(s)
      白髭克彦
    • Organizer
      EMBO Workshop
    • Place of Presentation
      フランス・モンペリエ(招待講演)
    • Related Report
      2011 Annual Research Report
  • [Presentation] Hadc8 is a cohesion deacetylase that is required for recycling of cohesion2011

    • Author(s)
      白髭克彦
    • Organizer
      国際シンポジウム「International Symposium on the Physicochemical Field for Genetic Activities)
    • Place of Presentation
      淡路夢舞台国際会議場(兵庫県)
    • Related Report
      2010 Annual Research Report
  • [Presentation] 転写調節因子としてのコヒーシン、コンデンシン

    • Author(s)
      白髭克彦
    • Organizer
      第14回がん・エピゲノム研究会
    • Place of Presentation
      宮城県・仙台市
    • Related Report
      2012 Annual Research Report
  • [Presentation] Transcriptional Regulation by SMC protein

    • Author(s)
      白髭克彦
    • Organizer
      London Research Institute (cancer research UK)
    • Place of Presentation
      イギリス・ロンドン
    • Related Report
      2012 Annual Research Report
  • [Presentation] Transcriptional regulation by condens in yeast and human cells

    • Author(s)
      白髭克彦
    • Organizer
      Symposium on Chromosome Biology
    • Place of Presentation
      イギリス・オックスフォード
    • Related Report
      2012 Annual Research Report
  • [Presentation] タンパク動態地図から知る生命機能

    • Author(s)
      白髭克彦
    • Organizer
      生命科学シンポジウム
    • Place of Presentation
      東京都・文京区
    • Related Report
      2012 Annual Research Report
  • [Remarks] 肥満と低身長が特徴の新たな希少遺伝病を発見   AFF4遺伝子が発育・体重増加をコントロール

    • URL

      http://www.iam.u-tokyo.ac.jp/pressrelease150304.html

    • Related Report
      2014 Annual Research Report
  • [Remarks] 染色体情報解析システムDROMPA

    • URL

      http://wwwiam.u-tokyo.ac.jp/cromosomeinformatics/rnakato/drompa/

    • Related Report
      2012 Annual Research Report

URL: 

Published: 2010-08-23   Modified: 2019-07-29  

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