• Search Research Projects
  • Search Researchers
  • How to Use
  1. Back to previous page

Regulation of gene expression and chromatin dynamics in living cells

Research Project

Project/Area Number 15370073
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypeSingle-year Grants
Section一般
Research Field Molecular biology
Research InstitutionKyoto University

Principal Investigator

KIMURA Hiroshi  Kyoto University, Graduate School of Medicine, Fellowship, 医学研究科, 研究員(科学技術振興)(常勤形態) (30241392)

Project Period (FY) 2003 – 2004
Project Status Completed (Fiscal Year 2004)
Budget Amount *help
¥15,500,000 (Direct Cost: ¥15,500,000)
Fiscal Year 2004: ¥4,400,000 (Direct Cost: ¥4,400,000)
Fiscal Year 2003: ¥11,100,000 (Direct Cost: ¥11,100,000)
Keywordstranscription / chromatin / gene expression regulation / living cells / nucleus / cell biology / molecular biology / histone / 細胞 / FRAP / GFP / ヌクレオソーム / 遺伝子発現 / 染色体
Research Abstract

In eukaryotic nuclei, DNA is wrapped around an octamer containing two copies of core histones, H2A, H2B, H3, and H4, making nucleosomes, the fundamental units of chromatin. Lines of evidence indicate that nucleosomes in living cells are not static but their components undergo exchanges associated with the chromatin functions like gene activation and centromere formation. However, the mechanisms regulating the histone dynamics are not well understood. We first investigated the effects of overexpressed histone chaperones like Nap1 and Asf1 on the mobility of hisones tagged with the green fluorescent protein(GFP) ; however, only little effects were observed. We then established an in vitro system that allows the assembly and exchange of histones in intact chromatin using permeabilized cells. GFP-H2A and H2B-GFP are incorporated into euchromatin by exchange independently of DNA replication, and H3-GFP is assembled into replicated chromatin, as found in living cells. Purifying the cellular factors assisting the exchange of H2A/H2B, we identified protein phosphatase 2C γ-subtype (PP2Cγ/PPM1G) as a histone chaperone that binds specifically to the H2A/H2B dimer. When the expression of PP2Cγ was suppressed to <5% of the normal level using RNAi, the mobility of GFP-H2A and H2B-GFP was significantly reduced, suggesting the function of PP2Cγ as a factor mediating H2A/H2B exchange. In contrast, Nap1-specific siRNA had little effects on the mobility ; however, this may be because the low level of suppression was only achieved down to 10〜20% and Napi is abundantly present in cells. We also found that the bacterially-expressed and purified PP2Cγ dephosphorylated histones in vitro. These results suggest a link between the exchange and dephosphorylation mediated by a single polypeptide, possibly counteracting the phosphorylation involved in the regulation of gene expression.

Report

(3 results)
  • 2004 Annual Research Report   Final Research Report Summary
  • 2003 Annual Research Report
  • Research Products

    (36 results)

All 2005 2004 2003 Other

All Journal Article (23 results) Book (6 results) Publications (7 results)

  • [Journal Article] Histone dynamics in living cells revealed by photobleaching2005

    • Author(s)
      Hiroshi Kimura
    • Journal Title

      DNA Repair (印刷中)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2004 Final Research Report Summary
  • [Journal Article] Functional region of CENP-H interacts with the Nuf2 complex that localizes to centromere during mitosis.2005

    • Author(s)
      Yoshikazu Mikami et al.
    • Journal Title

      Molecular and Cellular Biology 25(5)

      Pages: 1958-1970

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2004 Annual Research Report 2004 Final Research Report Summary
  • [Journal Article] The ORCl cycle in human cells.I.Cell cycle-regulated oscillation of human ORCl2005

    • Author(s)
      Yasutoshi Tatsumi et al.
    • Journal Title

      Journal of Biological Chemistry 278(42)

      Pages: 41528-41534

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2004 Final Research Report Summary
  • [Journal Article] The ORC1 cycle in human cells. I. Cell cycle-regulated oscillation of human ORC1.2005

    • Author(s)
      Yasutoshi Tatsumi et al.
    • Journal Title

      Journal of Biological Chemistry 278(42)

      Pages: 41528-41534

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2004 Final Research Report Summary
  • [Journal Article] The functional organization of mitochondrial genomes inhuman cells.2004

    • Author(s)
      Franscisco J.Iborra et al.
    • Journal Title

      BMC Biology 2(1)

      Pages: 9-9

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2004 Final Research Report Summary
  • [Journal Article] Manipulation of alternative splicing by a newly developed inhibitor of Clks.2004

    • Author(s)
      Michiko Muraki et al.
    • Journal Title

      Journal of Biological Chemistry 279(23)

      Pages: 24246-24254

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2004 Annual Research Report 2004 Final Research Report Summary
  • [Journal Article] Measuring histone and polymerase dynamics in living cells.2004

    • Author(s)
      Hiroshi Kimura et al.
    • Journal Title

      Methods in Enzymology 375(24)

      Pages: 381-393

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2004 Annual Research Report 2004 Final Research Report Summary
  • [Journal Article] TNFα-induced ATF3 expression is bidirectionally regulated by the JNK and ERK pathways in vascular endotherial cells2004

    • Author(s)
      Koichi Inoue et al.
    • Journal Title

      Genes to Cells 9(1)

      Pages: 59-70

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2004 Final Research Report Summary
  • [Journal Article] フォトブリーチング法による蛍光標識タンパク質の細胞内動態解析(2):生細胞を用いた解析と定量化2004

    • Author(s)
      木村 宏
    • Journal Title

      実験医学 22(12)

      Pages: 1851-1856

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2004 Final Research Report Summary
  • [Journal Article] フォトブリーチング法による蛍光標識タンパク質の細胞内動態解析(1):固定細胞を用いた条件設定2004

    • Author(s)
      木村 宏
    • Journal Title

      実験医学 22(12)

      Pages: 1739-1745

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2004 Annual Research Report 2004 Final Research Report Summary
  • [Journal Article] The functional organization of mitochondrial genomes in human cells.2004

    • Author(s)
      Franscisco J.Iborra et al.
    • Journal Title

      BMC Biology 2(1)

      Pages: 9-9

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2004 Annual Research Report 2004 Final Research Report Summary
  • [Journal Article] Measuring histone and polymerase dynamics in living cells2004

    • Author(s)
      Hiroshi Kimura et al.
    • Journal Title

      Methods in Enzymology 375(24)

      Pages: 381-393

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2004 Final Research Report Summary
  • [Journal Article] TNFα-induced ATF3 expression is bidirectionally regulated by the JNK and ERK pathways in vascular endotherial cells.2004

    • Author(s)
      Koichi Inoue et al.
    • Journal Title

      Genes to Cells 9(1)

      Pages: 59-70

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2004 Final Research Report Summary
  • [Journal Article] Measuring the kinetics of fluorescent proteins in living cells using photobleaching. II. Approaches for quantitative analysis.2004

    • Author(s)
      Hiroshi Kimura
    • Journal Title

      Experimental Medicine 22(12)

      Pages: 1851-1856

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2004 Final Research Report Summary
  • [Journal Article] Measuring the kinetics of fluorescent proteins in living cells using photobleaching. I. Setting up the conditions using fixed cells.2004

    • Author(s)
      Hiroshi Kimura
    • Journal Title

      Experimental Medicine 22(12)

      Pages: 1739-1745

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2004 Final Research Report Summary
  • [Journal Article] フォトブリーチング法による蛍光標識タンパク質の細胞内動態解析(2):生細胞を用いた解析と定量化2004

    • Author(s)
      木村 宏
    • Journal Title

      実験医学 22(13)

      Pages: 1851-1856

    • Related Report
      2004 Annual Research Report
  • [Journal Article] HAMLET interacts with histones and chromatin in tumor cell nuclei2003

    • Author(s)
      Caroline Duringer et al.
    • Journal Title

      Journal of Biological Chemistry 278(43)

      Pages: 42131-42135

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2004 Final Research Report Summary
  • [Journal Article] 時間軸にわたる染色体機能の変化2003

    • Author(s)
      木村 宏
    • Journal Title

      医学のあゆみ 208(10)

      Pages: 890-894

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2004 Final Research Report Summary
  • [Journal Article] 細胞核構造と機能のストカスティックな制御2003

    • Author(s)
      木村 宏
    • Journal Title

      生物物理 43(5)

      Pages: 234-239

    • NAID

      110001151674

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2004 Final Research Report Summary
  • [Journal Article] HAMLET interacts with histones and chromatin in tumor cell nuclei.2003

    • Author(s)
      Caroline Duringer et al.
    • Journal Title

      Journal of Biological Chemistry 278(48)

      Pages: 42131-42135

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2004 Final Research Report Summary
  • [Journal Article] Dynamic organization of chromosome structure and function during cell cycle.2003

    • Author(s)
      Hiroshi Kimura
    • Journal Title

      Journal of Clinical and Experimental Medicine (IGAKU NO AYUMI) 208(10)

      Pages: 890-894

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2004 Final Research Report Summary
  • [Journal Article] Stochastic regulation of nuclear structure and function.2003

    • Author(s)
      Hiroshi Kimura
    • Journal Title

      Biophysics 43(5)

      Pages: 234-239

    • NAID

      110001151674

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2004 Final Research Report Summary
  • [Journal Article] Histone dynamics in living cells revealed by photobleaching.

    • Author(s)
      Hiroshi Kimura
    • Journal Title

      RNA Repair (in press)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2004 Final Research Report Summary
  • [Book] Nuclear Dynamics (tentative title)2005

    • Author(s)
      Hiroshi Kimura et al.
    • Publisher
      Springer Verlag Tokyo(出版予定)
    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2004 Final Research Report Summary
  • [Book] Nuclear Dynamics(Ed. Kunio Takeyasu and Kyosuke Nagata)(tentative title)2005

    • Author(s)
      Hiroshi Kimura et al.
    • Publisher
      Springer-Verlag Tokyo(to be published)
    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2004 Final Research Report Summary
  • [Book] クロマチン・染色体実験プロトコール(押村光雄・平岡泰/編)2004

    • Author(s)
      木村 宏
    • Total Pages
      231
    • Publisher
      羊土社
    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2004 Annual Research Report 2004 Final Research Report Summary
  • [Book] 細胞核のダイナミクス(竹安邦夫・米田悦啓/編)2004

    • Author(s)
      木村 宏
    • Total Pages
      204
    • Publisher
      シュプリンガー・フェアラーク東京
    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2004 Final Research Report Summary
  • [Book] Protocols for chromatin and chromosomes(Ed. Mitsuo Oshimura and Yasushi Hiraoka)2004

    • Author(s)
      Hiroshi Kimura
    • Publisher
      Yodosha
    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2004 Final Research Report Summary
  • [Book] Nuclear Dynamics(Ed. Kunio Takeyasu and Yoshihiro Yoneda)2004

    • Author(s)
      Hiroshi Kimura
    • Publisher
      Springer-Verlag Tokyo
    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2004 Final Research Report Summary
  • [Publications] Yasutoshi Tatsumi: "The ORC1 cycle in human cells : I. Cell cycle-regulated oscillation of human ORC1"Journal of Biological Chemistry. 278(42). 41528-41534 (2003)

    • Related Report
      2003 Annual Research Report
  • [Publications] Caroline Duringer: "HAMLET interacts with histones and chromatin in tumor cell nuclei"Journal of Biological Chemistry. 278(43). 42131-42135 (2003)

    • Related Report
      2003 Annual Research Report
  • [Publications] Hiroshi Kimura: "Measuring histone and polymerase dynamics in living cells"Methods in Enzymology. 375. 381-393 (2004)

    • Related Report
      2003 Annual Research Report
  • [Publications] Michiko Muraki: "Manipulation of alternative splicing by a newly developed inhibitor of Clks"Journal of Biological Chemistry. (in press). (2004)

    • Related Report
      2003 Annual Research Report
  • [Publications] 木村 宏: "細胞核構造と機能のストカスティックな制御"生物物理. 43(5). 234-239 (2003)

    • Related Report
      2003 Annual Research Report
  • [Publications] 木村 宏: "時間軸にわたる染色体機能の変化"医学のあゆみ. 208(10). 890-894 (2004)

    • Related Report
      2003 Annual Research Report
  • [Publications] 竹安邦夫, 米田悦啓(編者): "細胞核のダイナミクス"シュプリンガー・フェアラーク東京(仮題)(印刷中). (2004)

    • Related Report
      2003 Annual Research Report

URL: 

Published: 2003-04-01   Modified: 2016-04-21  

Information User Guide FAQ News Terms of Use Attribution of KAKENHI

Powered by NII kakenhi