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Optimization of iChIP for highly sensitive identification of genome interacting molecules and application to analysis of transcriptional regulation mechanisms.

Research Project

Project/Area Number 25830131
Research Category

Grant-in-Aid for Young Scientists (B)

Allocation TypeMulti-year Fund
Research Field Genome biology
Research InstitutionOsaka University

Principal Investigator

FUJITA Toshitsugu  大阪大学, 微生物病研究所, 助教 (10550030)

Project Period (FY) 2013-04-01 – 2015-03-31
Project Status Completed (Fiscal Year 2014)
Budget Amount *help
¥4,160,000 (Direct Cost: ¥3,200,000、Indirect Cost: ¥960,000)
Fiscal Year 2014: ¥2,080,000 (Direct Cost: ¥1,600,000、Indirect Cost: ¥480,000)
Fiscal Year 2013: ¥2,080,000 (Direct Cost: ¥1,600,000、Indirect Cost: ¥480,000)
Keywordsゲノム科学 / ゲノム生物学 / 遺伝子発現調節 / 発現制御 / ゲノム機能解析 / iChIP / SILAC / Pax5 / Thy28 / RNA-Seq
Outline of Final Research Achievements

Elucidation of molecular mechanisms of genome functions requires identification of molecules interacting with genomic regions of interest in vivo. In this study, we applied iChIP, one of the locus-specific chromatin immunoprecipitation technologies, to isolate a single-copy genomic locus and comprehensively identify proteins and RNAs interacting with the locus in vivo. By combining iChIP with SILAC or RNA-sequencing, we could identify proteins or RNAs interacting with the promoter region of the endogenous single-copy chicken Pax5 gene. In addition, biochemical analysis revealed that Thy28, an identified interacting protein, is functionally required for B cell-specific transcription of the Pax5 gene via recruitment of MYH9 to the Pax5 locus in DT40 chicken B cell line. Thus, iChIP is a useful tool to elucidate molecular mechanisms of genome functions.

Report

(3 results)
  • 2014 Annual Research Report   Final Research Report ( PDF )
  • 2013 Research-status Report
  • Research Products

    (18 results)

All 2015 2014 2013 Other

All Journal Article (8 results) (of which Peer Reviewed: 7 results,  Open Access: 4 results,  Acknowledgement Compliant: 5 results) Presentation (7 results) Remarks (2 results) Patent(Industrial Property Rights) (1 results) (of which Overseas: 1 results)

  • [Journal Article] A critical role of the Thy28-MYH9 axis in B cell-specific expression of the Pax5 gene in chicken B cells2015

    • Author(s)
      Fujita T, Kitaura F, and Fujii H
    • Journal Title

      PLoS One

      Volume: 10 Issue: 1 Pages: e0116579-e0116579

    • DOI

      10.1371/journal.pone.0116579

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Isolation of Specific Genomic Regions and Identification of Associated Molecules by Engineered DNA-Binding Molecule-Mediated Chromatin Immunoprecipitation (enChIP) Using CRISPR2015

    • Author(s)
      Toshitsugu Fujita, Hodaka Fujii
    • Journal Title

      Methods in Molecular Biology

      Volume: 1288 Pages: 43-52

    • DOI

      10.1007/978-1-4939-2474-5_4

    • ISBN
      9781493924738, 9781493924745
    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Identification of Non-Coding RNAs Associated with Telomeres Using a Combination of enChIP and RNA Sequencing2015

    • Author(s)
      Toshitsugu Fujita, Miyuki Yuno, Daisuke Okuzaki, Rieko Ohki, Hodaka Fujii
    • Journal Title

      PLOS ONE

      Volume: 10 Issue: 4 Pages: e0123387-e0123387

    • DOI

      10.1371/journal.pone.0123387

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Identification of proteins associated with an IFNγ-responsive promoter by a retroviral expression system for enChIP using CRISPR2014

    • Author(s)
      Fujita T, and Fujii H
    • Journal Title

      PLoS One

      Volume: 9 Issue: 7 Pages: e103084-e103084

    • DOI

      10.1371/journal.pone.0103084

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Efficient isolation of specific genomic regions retaining molecular interactions by the iChIP system using recombinant exogenous DNA-binding proteins2014

    • Author(s)
      Fujita T, and Fujii H
    • Journal Title

      BMC Mol. Biol.

      Volume: 15 Issue: 1 Pages: 26-26

    • DOI

      10.1186/s12867-014-0026-0

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Efficient isolation of specific genomic regions and identification of associated proteins by engineered DNA-binding molecule-mediated chromatin immunoprecipitation (enChIP) using CRISPR.2013

    • Author(s)
      Fujita T, Fujii H.
    • Journal Title

      Biochem Biophys Res Commun.

      Volume: 439 Issue: 1 Pages: 132-6

    • DOI

      10.1016/j.bbrc.2013.08.013

    • Related Report
      2013 Research-status Report
    • Peer Reviewed
  • [Journal Article] Identification of telomere-associated molecules by engineered DNA-binding molecule-mediated chromatin immunoprecipitation (enChIP).2013

    • Author(s)
      Toshitsugu Fujita, Yoshinori Asano, Junko Ohtsuka, Yoko Takada, Kazunobu Saito, Rieko Ohki, Hodaka Fujii.
    • Journal Title

      Scientific Reports

      Volume: 3 Issue: 1 Pages: 3-3

    • DOI

      10.1038/srep03171

    • Related Report
      2013 Research-status Report
    • Peer Reviewed
  • [Journal Article] 挿入的クロマチン免疫沈降法(iChIP)による特定ゲノム領域結合分子の網羅的同定2013

    • Author(s)
      藤田敏次、藤井穂高
    • Journal Title

      実験医学

      Volume: 10月号 Pages: 2629-2636

    • Related Report
      2013 Research-status Report
  • [Presentation] TALやCRISPR/Casを利用したenChIP法による遺伝子座特異的生化学的ゲノム機能解析2014

    • Author(s)
      藤田敏次、藤井穂高
    • Organizer
      第37回日本分子生物学会年会
    • Place of Presentation
      パシフィコ横浜
    • Year and Date
      2014-11-25 – 2014-11-27
    • Related Report
      2014 Annual Research Report
  • [Presentation] Capturing chromatin: biochemical analysis of genome functions using the locus-specific chromatin immunoprecipitation technologies2014

    • Author(s)
      藤田敏次、藤井穂高
    • Organizer
      第37回日本分子生物学会年会
    • Place of Presentation
      パシフィコ横浜
    • Year and Date
      2014-11-25 – 2014-11-27
    • Related Report
      2014 Annual Research Report
  • [Presentation] enChIP: a method for locus-specific biochemical analysis of genome functions2014

    • Author(s)
      Toshitsugu Fujita, Hodaka Fujii
    • Organizer
      11th EMBL Conference: Transcription and Chromatin
    • Place of Presentation
      Heidelberg, Germany
    • Year and Date
      2014-08-23 – 2014-08-26
    • Related Report
      2014 Annual Research Report
  • [Presentation] enChIP法を利用したゲノム機能の生化学的解析2014

    • Author(s)
      藤田 敏次、浅野 良則、大塚 旬子、斉藤 一伸、高田 洋子、大木 理恵子、藤井 穂高
    • Organizer
      第8回日本エピジェネティクス研究年会
    • Place of Presentation
      東京大学内 伊藤国際学術研究センター
    • Year and Date
      2014-05-25 – 2014-05-27
    • Related Report
      2014 Annual Research Report
  • [Presentation] Locus-specific biochemical epigenetics / chromatin biochemistry by insertional chromatin immnoprecipitation (iChIP)2013

    • Author(s)
      藤田敏次、藤井穂高
    • Organizer
      第7回日本エピジェネティクス研究年会
    • Place of Presentation
      奈良
    • Related Report
      2013 Research-status Report
  • [Presentation] Locus-specific biochemical epigenetics / chromatin biochemistry by insertional chromatin immnoprecipitation (iChIP)2013

    • Author(s)
      藤田敏次、藤井穂高
    • Organizer
      15th International Congress of Immunology
    • Place of Presentation
      ミラノ(イタリア)
    • Related Report
      2013 Research-status Report
  • [Presentation] enChIP: a method for locus-specific biochemical analysis of genome functions2013

    • Author(s)
      藤田敏次、浅野良則、大塚旬子、斉藤一伸、高田洋子、大木理恵子、藤井穂高
    • Organizer
      第36回日本分子生物学会年会
    • Place of Presentation
      神戸
    • Related Report
      2013 Research-status Report
  • [Remarks] 大阪大学微生物病研究所 感染症学免疫学融合プログラム推進室 ゲノム生化学研究グループ

    • URL

      http://www.biken.osaka-u.ac.jp/lab/microimm/fujii/index.html

    • Related Report
      2014 Annual Research Report
  • [Remarks] 大阪大学 微生物病研究所 感染症学免疫学融合プログラム推進室 ゲノム生化学研究グループ

    • URL

      http://www.biken.osaka-u.ac.jp/lab/microimm/fujii/index.html

    • Related Report
      2013 Research-status Report
  • [Patent(Industrial Property Rights)] 内在性DNA配列特異的結合分子を用いる特定ゲノム領域の単離方法2013

    • Inventor(s)
      藤井穂高、藤田敏次
    • Industrial Property Rights Holder
      藤井穂高、藤田敏次
    • Industrial Property Rights Type
      特許
    • Filing Date
      2013-09-06
    • Related Report
      2013 Research-status Report
    • Overseas

URL: 

Published: 2014-07-25   Modified: 2019-07-29  

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