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Development of in vitro enChIP and its applications to analysis of molecular mechanisms underlying genome functions

Research Project

Project/Area Number 15K06895
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeMulti-year Fund
Section一般
Research Field Genome biology
Research InstitutionOsaka University

Principal Investigator

Fujita Toshitsugu  大阪大学, 微生物病研究所, 招へい准教授 (10550030)

Project Period (FY) 2015-04-01 – 2018-03-31
Project Status Completed (Fiscal Year 2017)
Budget Amount *help
¥5,070,000 (Direct Cost: ¥3,900,000、Indirect Cost: ¥1,170,000)
Fiscal Year 2017: ¥1,950,000 (Direct Cost: ¥1,500,000、Indirect Cost: ¥450,000)
Fiscal Year 2016: ¥1,690,000 (Direct Cost: ¥1,300,000、Indirect Cost: ¥390,000)
Fiscal Year 2015: ¥1,430,000 (Direct Cost: ¥1,100,000、Indirect Cost: ¥330,000)
Keywordsin vitro enChIP / enChIP / locus-specific ChIP / ChIP / CRISPR / TAL / chromatin / chromosomal conformation
Outline of Final Research Achievements

Elucidation of molecular mechanisms underlying genome functions requires identification of molecules interacting with genomic regions of interest in vivo. In this study, we developed in vitro enChIP using purified CRISPR complexes to isolate a target genomic region while retaining molecular interactions. Combining in vitro enChIP with next-generation sequencing analysis, we succeeded in identifying genomic regions that interact with a target locus in vivo. In addition, we showed that an interacting genomic region works as an enhancer to upregulate transcription from the target locus. Thus, in vitro enChIP is a useful tool for elucidation of molecular mechanisms underlying genome functions.

Report

(4 results)
  • 2017 Annual Research Report   Final Research Report ( PDF )
  • 2016 Research-status Report
  • 2015 Research-status Report
  • Research Products

    (25 results)

All 2018 2017 2016 2015 Other

All Int'l Joint Research (1 results) Journal Article (12 results) (of which Int'l Joint Research: 1 results,  Peer Reviewed: 12 results,  Open Access: 12 results,  Acknowledgement Compliant: 6 results) Presentation (7 results) (of which Int'l Joint Research: 1 results,  Invited: 1 results) Book (3 results) Remarks (2 results)

  • [Int'l Joint Research] Lund University(Sweden)

    • Related Report
      2017 Annual Research Report
  • [Journal Article] Promoter-associated proteins of EPAS1 identified by enChIP-MS ? A putative role of HDX as a negative regulator2018

    • Author(s)
      Hamidian Arash、Vaapil Marica、von Stedingk Kristoffer、Fujita Toshitsugu、Persson Camilla U.、Eriksson Pontus、Veerla Srinivas、De Preter Katleen、Speleman Frank、Fujii Hodaka、P?hlman Sven、Mohlin Sofie
    • Journal Title

      Biochemical and Biophysical Research Communications

      Volume: 499 Issue: 2 Pages: 291-298

    • DOI

      10.1016/j.bbrc.2018.03.150

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Transgenic mouse lines expressing the 3xFLAG-dCas9 protein for enChIP analysis2018

    • Author(s)
      Fujita Toshitsugu、Kitaura Fusako、Oji Asami、Tanigawa Naoki、Yuno Miyuki、Ikawa Masahito、Taniuchi Ichiro、Fujii Hodaka
    • Journal Title

      Genes to Cells

      Volume: 23 Issue: 4 Pages: 318-325

    • DOI

      10.1111/gtc.12573

    • NAID

      120006957429

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] enChIP systems using different CRISPR orthologues and epitope tags2018

    • Author(s)
      Fujita Toshitsugu、Yuno Miyuki、Fujii Hodaka
    • Journal Title

      BMC Research Notes

      Volume: 11 Issue: 1 Pages: 154-154

    • DOI

      10.1186/s13104-018-3262-4

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Locus-specific ChIP combined with NGS analysis reveals genomic regulatory regions that physically interact with the Pax5 promoter in a chicken B cell line2017

    • Author(s)
      Fujita Toshitsugu、Kitaura Fusako、Yuno Miyuki、Suzuki Yutaka、Sugano Sumio、Fujii Hodaka
    • Journal Title

      DNA Research

      Volume: 24 Issue: 5 Pages: 537-548

    • DOI

      10.1093/dnares/dsx023

    • NAID

      120006583339

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Identification of physical interactions between genomic regions by enChIP-Seq2017

    • Author(s)
      Fujita Toshitsugu、Yuno Miyuki、Suzuki Yutaka、Sugano Sumio、Fujii Hodaka
    • Journal Title

      Genes to Cells

      Volume: 22 Issue: 6 Pages: 506-520

    • DOI

      10.1111/gtc.12492

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] in vitro engineered DNA-binding molecule-mediated chromatin immunoprecipitation (in vitro enChIP) using CRISPR ribonucleoproteins in combination with next-generation sequencing (in vitro enChIP-Seq) for the identification of chromosomal interactions2017

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

      Bio-protocol

      Volume: 7 Issue: 22 Pages: 1-12

    • DOI

      10.21769/bioprotoc.2612

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Allele-specific locus binding and genome editing by CRISPR at the p16INK4a locus2016

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

      Sci Rep

      Volume: 6 Issue: 1 Pages: 30485-30485

    • DOI

      10.1038/srep30485

    • Related Report
      2016 Research-status Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Efficient sequence-specific isolation of DNA fragments and chromatin by in vitro enChIP technology using recombinant CRISPR ribonucleoproteins.2016

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

      Genes Cells

      Volume: 21 Issue: 4 Pages: 370-377

    • DOI

      10.1111/gtc.12341

    • Related Report
      2015 Research-status Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Isolation of Specific Genomic Regions and Identification of Associated Molecules by enChIP.2016

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

      J Vis Exp

      Volume: 107 Issue: 107

    • DOI

      10.3791/53478

    • Related Report
      2015 Research-status Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Biochemical Analysis of Genome Functions Using Locus-Specific Chromatin Immunoprecipitation Technologies.2016

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

      Gene Regul Syst Bio

      Volume: 10 Pages: 1-9

    • DOI

      10.4137/grsb.s32520

    • Related Report
      2015 Research-status Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Applications of Engineered DNA-Binding Molecules Such as TAL Proteins and the CRISPR/Cas System in Biology Research.2015

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

      Int J Mol Sci

      Volume: 16 Issue: 10 Pages: 23143-23164

    • DOI

      10.3390/ijms161023143

    • Related Report
      2015 Research-status Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Isolation of Specific Genomic Regions and Identification of Their Associated Molecules by Engineered DNA-Binding Molecule-Mediated Chromatin Immunoprecipitation (enChIP) Using the CRISPR System and TAL Proteins.2015

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

      Int J Mol Sci

      Volume: 16 Issue: 9 Pages: 21802-21812

    • DOI

      10.3390/ijms160921802

    • Related Report
      2015 Research-status Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Presentation] CRISPRを利用したin vitro enChIP法の開発およびゲノム領域間相互作用の検出への応用2017

    • Author(s)
      藤田敏次、藤井穂高
    • Organizer
      2017年度生命科学系学会合同年次大会
    • Related Report
      2017 Annual Research Report
  • [Presentation] enChIP using CRISPR: a method for identification of molecules interacting with a locus of interest2017

    • Author(s)
      Fujita Toshitsugu、Fujii Hodaka
    • Organizer
      Cell Symposia, CRISPR: From Biology to Technology and Novel Therapeutics
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research
  • [Presentation] p16INK4a遺伝子座を標的としたCRISPRによるアレル特異的なゲノム結合およびゲノム編集2016

    • Author(s)
      藤田敏次、藤井穂高
    • Organizer
      第39回日本分子生物学会年会
    • Place of Presentation
      パシフィコ横浜(神奈川県・横浜市)
    • Year and Date
      2016-11-30
    • Related Report
      2016 Research-status Report
  • [Presentation] Development of enChIP and its applications to locus-specific biochemical analysis of genome functions.2016

    • Author(s)
      Fujita T, Fujii H
    • Organizer
      12th EMBL Conference Transcription and Chromatin
    • Place of Presentation
      EMBL (Heidelberg, Germany)
    • Year and Date
      2016-08-28
    • Related Report
      2016 Research-status Report
  • [Presentation] エピジェネティック制御機構の生化学的解析に向けたin vitro enChIP法の開発2016

    • Author(s)
      藤田敏次、藤井穂高
    • Organizer
      第10回日本エピジェネティクス研究会年会
    • Place of Presentation
      千里ライフサイエンスセンター(大阪府・豊中市)
    • Year and Date
      2016-05-02
    • Related Report
      2016 Research-status Report
  • [Presentation] 遺伝子座特異的クロマチン免疫沈降法の開発およびエピジェネティック研究への応用2016

    • Author(s)
      藤田敏次
    • Organizer
      第10回日本エピジェネティクス研究会年会
    • Place of Presentation
      千里ライフサイエンスセンター(大阪府・豊中市)
    • Year and Date
      2016-05-02
    • Related Report
      2016 Research-status Report
    • Invited
  • [Presentation] Locus-specific biochemical analysis of genome functions using the locus-specific chromatin immunoprecipitaion technologies iChIP/enChIP2015

    • Author(s)
      Fujita T, Fujii H.
    • Organizer
      第38回日本分子生物学会年会
    • Place of Presentation
      神戸商工会議所:3階 神商ホールB(第27会場)
    • Year and Date
      2015-12-03
    • Related Report
      2015 Research-status Report
  • [Book] Handbook of epigenetics : the new molecular and medical genetics2017

    • Author(s)
      Fujita Toshitsugu、Fujii Hodaka
    • Total Pages
      18
    • Publisher
      Academic Press, an imprint of Elsevier
    • ISBN
      9780128053881
    • Related Report
      2017 Annual Research Report
  • [Book] 生体の科学2017

    • Author(s)
      藤田敏次、藤井穂高
    • Total Pages
      5
    • Publisher
      医学書院
    • Related Report
      2017 Annual Research Report
  • [Book] 進化するゲノム編集技術2015

    • Author(s)
      真下知士、山本卓、佐久間哲史、坂本尚昭、石野良純、中川一路、濡木理、香月康宏、押村光雄、斉藤慎太、黒沢綾、足立典隆、藤田敏次、藤井穂高、中村崇裕、吉見一人、等合計58名
    • Total Pages
      386
    • Publisher
      株式会社エヌ・ティー・エス
    • Related Report
      2015 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/top/index.html

    • Related Report
      2016 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
      2015 Research-status Report

URL: 

Published: 2015-04-16   Modified: 2019-03-29  

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