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DNA-protein cross-links and chromatin remodeling

Planned Research

Project AreaCoupling of replication, repair and transcription, and their common mechanism of chromatin remodeling
Project/Area Number 22131010
Research Category

Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)

Allocation TypeSingle-year Grants
Review Section Biological Sciences
Research InstitutionHiroshima University

Principal Investigator

IDE HIROSI  広島大学, 理学(系)研究科(研究院), 教授 (30223126)

Co-Investigator(Renkei-kenkyūsha) NAKANO Toshiaki  広島大学, 大学院理学研究科, 助教 (10526122)
Project Period (FY) 2010-04-01 – 2015-03-31
Project Status Completed (Fiscal Year 2014)
Budget Amount *help
¥127,920,000 (Direct Cost: ¥98,400,000、Indirect Cost: ¥29,520,000)
Fiscal Year 2014: ¥23,530,000 (Direct Cost: ¥18,100,000、Indirect Cost: ¥5,430,000)
Fiscal Year 2013: ¥24,440,000 (Direct Cost: ¥18,800,000、Indirect Cost: ¥5,640,000)
Fiscal Year 2012: ¥26,390,000 (Direct Cost: ¥20,300,000、Indirect Cost: ¥6,090,000)
Fiscal Year 2011: ¥26,390,000 (Direct Cost: ¥20,300,000、Indirect Cost: ¥6,090,000)
Fiscal Year 2010: ¥27,170,000 (Direct Cost: ¥20,900,000、Indirect Cost: ¥6,270,000)
Keywordsゲノム損傷 / DNA複製 / 転写 / DNA修復 / クロマチンリモデリング
Outline of Final Research Achievements

In this study, we have assessed the biological effects and repair mechanism of DNA-protein cross-link (DPC) damage. DPCs inhibited the translocation of replicative helicases, showing a unique mechanism of replisome stalling. DPCs caused backup of RNA polymerases, resulting in error-prone transcription. We have established a novel method of DPC detection using fluorescence labeling, and analyzed the induction of genomic DPCs by aldehydes, ionizing radiation, and anticancer drugs and their repair. We also showed that knockdown of RUVBL2, an essential subunit of a chromatin remodeling complex INO80, conferred a moderate sensitivity to DPC-inducing agents, suggesting a role of the chromatin remodeling complex in homologous recombination.

Report

(6 results)
  • 2014 Annual Research Report   Final Research Report ( PDF )
  • 2013 Annual Research Report
  • 2012 Annual Research Report
  • 2011 Annual Research Report
  • 2010 Annual Research Report
  • Research Products

    (25 results)

All 2015 2014 2013 2012 2011 2010

All Journal Article (9 results) (of which Peer Reviewed: 9 results,  Open Access: 4 results,  Acknowledgement Compliant: 3 results) Presentation (15 results) (of which Invited: 5 results) Book (1 results)

  • [Journal Article] Induction of DNA-protein cross-links by ionizing radiation and their elimination from the genome2015

    • Author(s)
      Nakano T., Mitsusada Y., Salem A., Shoulkamy M., Sugimoto T., Hirayama R., Uzawa A., Furusawa Y., and Ide H.
    • Journal Title

      Mutation Research

      Volume: 771 Pages: 45-50

    • DOI

      10.1016/j.mrfmmm.2014.12.003

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Restriction-modification system with methyl-inhibited base excision and abasic-site cleavage activities2015

    • Author(s)
      Masaki Fukuyo, Toshiaki Nakano, Yingbiao Zhang, Yoshikazu Furuta, Ken Ishikawa, Miki Watanabe-Matsui, Hirokazu Yano, Takeshi Hamakawa, Hiroshi Ide, Ichizo Kobayashi
    • Journal Title

      Nucleic Acids Research

      Volume: Vol. 43, No. 5 Issue: 5 Pages: 2841-2852

    • DOI

      10.1093/nar/gkv116

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Synergistic enhancement of 5-fluorouracil cytotoxicity by deoxyuridine analogs in cancer cells2015

    • Author(s)
      Matsumoto Y., Rodriguez V., Whitford T.A., Beeharry N., Ide H., and Tomkinson A.E.
    • Journal Title

      Oncoscience

      Volume: 2 Pages: 272-284

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Depletion of RUVBL2 in human cells confers moderate sensitivity to anticancer agents2014

    • Author(s)
      Miyamoto-Matsubara M., Han Y., Ono K., Xie M., Salem A., Shoulkamy M., Nakano T., and Ide H.
    • Journal Title

      Journal of Cancer Science and Therapy

      Volume: 6 Issue: 11 Pages: 440-445

    • DOI

      10.4172/1948-5956.1000306

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Hypersensitivity of mouse NEIL1-knockdown cells to hydrogen peroxide during S phase2014

    • Author(s)
      Ryohei Yamamoto
    • Journal Title

      Journal of Radiation Research

      Volume: in press Issue: 4 Pages: 707-712

    • DOI

      10.1093/jrr/rru021

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Translocation and stability of replicative DNA helicases upon encountering DNA-protein cross-links2013

    • Author(s)
      Toshiaki Nakano
    • Journal Title

      Journal of Biological Chemistry

      Volume: 288 Issue: 7 Pages: 4649-4658

    • DOI

      10.1074/jbc.m112.419358

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Detection of DNA-protein crosslinks (DPCs) by novel direct fluorescence labeling methods: distinct stabilities of aldehyde and radiation-induced DPCs2012

    • Author(s)
      Mahmoud I. Shoulkamy, Toshiaki Nakano, Makiko Ohshima, Ryoichi Hirayama, Akiko Uzawa, Yoshiya Furusawa, Hiroshi Ide
    • Journal Title

      Nucleic Acids Research

      Volume: 40 Issue: 18 Pages: e143-e143

    • DOI

      10.1093/nar/gks601

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] T7 RNApolymerases backed up by covalently trapped proteins catalyze highly errorprone transcription2012

    • Author(s)
      Nakano T., Ouchi R., Kawazoe J., PackS. P., Makino K., and Ide H.
    • Journal Title

      J. Biol. Chem.

      Volume: 287 Issue: 9 Pages: 6562-6572

    • DOI

      10.1074/jbc.m111.318410

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Repair and biochemical effects of DNA. protein crosslinks2011

    • Author(s)
      Ide H., Shoulkamy M. I., Nakano T., Miyamoto-Matsubara M, and Salem A.
    • Journal Title

      Mutat. Res.

      Volume: 771 Issue: 1-2 Pages: 113-122

    • DOI

      10.1016/j.mrfmmm.2010.12.007

    • Related Report
      2011 Annual Research Report 2010 Annual Research Report
    • Peer Reviewed
  • [Presentation] 低酸素性細胞における放射線誘発DNA損傷の解析2014

    • Author(s)
      井出博,中野敏彰,瀬畑敬文,久保山政弥,杉本龍也,平山亮一,鵜澤玲子,古澤佳也
    • Organizer
      第37回日本分子生物学会
    • Place of Presentation
      横浜市
    • Year and Date
      2014-11-25 – 2014-11-27
    • Related Report
      2014 Annual Research Report
  • [Presentation] Detection of DNA-protein cross-link damage by fluorescence labeling2014

    • Author(s)
      Salem A., Nakano T., Hattori S., Hirayama R., Uzawa R., Furusawa Y., and Ide H.
    • Organizer
      日本放射線影響学会第57回大会
    • Place of Presentation
      鹿児島市
    • Year and Date
      2014-10-01 – 2014-10-03
    • Related Report
      2014 Annual Research Report
  • [Presentation] Analysis of DNA damage induced by aldehyde compounds2014

    • Author(s)
      Xie M., Shoulkamy M., Ohba S., Nakano T., and Ide H.
    • Organizer
      日本放射線影響学会第57回大会
    • Place of Presentation
      鹿児島市
    • Year and Date
      2014-10-01 – 2014-10-03
    • Related Report
      2014 Annual Research Report
  • [Presentation] Formation and repair of DNA-protein cross-link damage2014

    • Author(s)
      Ide H.
    • Organizer
      13th International Workshop on Radiation Damage to DNA
    • Place of Presentation
      Cambridge, MA, USA
    • Year and Date
      2014-06-14 – 2014-06-18
    • Related Report
      2014 Annual Research Report
    • Invited
  • [Presentation] DNA-タンパク質クロスリンクとクロマチンリモデリング2014

    • Author(s)
      井出博
    • Organizer
      新学術領域研究 ゲノム普遍的制御 第5回領域会議
    • Place of Presentation
      鳴門市
    • Year and Date
      2014-05-07 – 2014-05-09
    • Related Report
      2014 Annual Research Report
  • [Presentation] Induction and repair of DNA-protein cross-links2014

    • Author(s)
      Hiroshi Ide
    • Organizer
      International Conference on Coupling of Replication, Repair and Transcription, and Their Common Mechanism of Chromatin Remodeling
    • Place of Presentation
      Kyoto
    • Related Report
      2013 Annual Research Report
    • Invited
  • [Presentation] DNA-タンパク質クロスリンクとクロマチンリモデリング2013

    • Author(s)
      井出 博
    • Organizer
      新学術領域研究ゲノム普遍的制御 第4回領域会議
    • Place of Presentation
      鳴門市
    • Related Report
      2013 Annual Research Report
  • [Presentation] RUVBL1およびRUVBL2ノックダウン細胞のDNA損傷誘発剤感受性2013

    • Author(s)
      小野晃司
    • Organizer
      第36回日本分子生物学会年会
    • Place of Presentation
      神戸
    • Related Report
      2013 Annual Research Report
  • [Presentation] Induction and repair of DNA-protein cross-link damage2012

    • Author(s)
      Hiroshi Ide
    • Organizer
      28th RBC-NIRS International Symposium: Radiation-associated Repair Proteins and DNA Repair Network
    • Place of Presentation
      Kyoto (Japan)
    • Year and Date
      2012-11-29
    • Related Report
      2012 Annual Research Report
    • Invited
  • [Presentation] Detection and biological consequences of DNA-protein crosslink damage2012

    • Author(s)
      Hiroshi Ide
    • Organizer
      12th International Workshop on Radiation Damage to DNA
    • Place of Presentation
      Prague (Czech Republic)
    • Year and Date
      2012-06-02
    • Related Report
      2012 Annual Research Report
    • Invited
  • [Presentation] Unique properties of DNA-protein cross-links as a barrier to transcription and replication2012

    • Author(s)
      Hiroshi Ide
    • Organizer
      4th US-Japan DNA Repair Meeting
    • Place of Presentation
      Leesburg (USA)
    • Year and Date
      2012-04-11
    • Related Report
      2012 Annual Research Report
    • Invited
  • [Presentation] Error prone transcription induced by DNA-protein crosslink damage2011

    • Author(s)
      井出博
    • Organizer
      第34回日本分子生物学会
    • Place of Presentation
      横浜市
    • Year and Date
      2011-12-15
    • Related Report
      2011 Annual Research Report
  • [Presentation] DNA-タンパク質クロスリンク損傷の生成と生物影響2011

    • Author(s)
      井出博
    • Organizer
      日本放射線影響学会54回大会
    • Place of Presentation
      神戸市
    • Year and Date
      2011-11-18
    • Related Report
      2011 Annual Research Report
  • [Presentation] DNA-タンパク質クロスリンク損傷の複製,転写,修復への影響2010

    • Author(s)
      井出博
    • Organizer
      第33回日本分子生物学会年会
    • Place of Presentation
      神戸市
    • Year and Date
      2010-12-07
    • Related Report
      2010 Annual Research Report
  • [Presentation] DNA-タンパク質クロスリンクの修復および損傷許容機構2010

    • Author(s)
      井出博
    • Organizer
      日本遺伝学会第82回大会
    • Place of Presentation
      札幌市(招待講演)
    • Year and Date
      2010-09-20
    • Related Report
      2010 Annual Research Report
  • [Book] DNA Repair2015

    • Author(s)
      Ide H., Nakano T., Shoulkamy M., and Salem A.
    • Total Pages
      38
    • Publisher
      Formation, repair, and biological effects of DNA-protein cross-link damage
    • Related Report
      2014 Annual Research Report

URL: 

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

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