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Identification and characterization of interactions between genomic regions using the locus-specific chromatin immunoprecipitation technology

Research Project

Project/Area Number 15H04329
Research Category

Grant-in-Aid for Scientific Research (B)

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

Principal Investigator

Fujii Hodaka  大阪大学, 微生物病研究所, 招へい教授 (30302665)

Co-Investigator(Kenkyū-buntansha) 藤田 敏次  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
¥12,090,000 (Direct Cost: ¥9,300,000、Indirect Cost: ¥2,790,000)
Fiscal Year 2017: ¥3,900,000 (Direct Cost: ¥3,000,000、Indirect Cost: ¥900,000)
Fiscal Year 2016: ¥3,900,000 (Direct Cost: ¥3,000,000、Indirect Cost: ¥900,000)
Fiscal Year 2015: ¥4,290,000 (Direct Cost: ¥3,300,000、Indirect Cost: ¥990,000)
Keywordsクロマチン / エピジェネティクス / ゲノム生化学 / enChIP / iChIP / 核内三次元構造 / ゲノム領域間相互作用 / 次世代シークエンス法
Outline of Final Research Achievements

Using the locus-specific chromatin immunoprecipitation (ChIP) technology, we identified many genomic regions interacting with the β-globin gene 5'HS5 region constitutively or inducibly by induction of differentiation with sodium butyrate (NaB). Expression of a group of genes in the vicinity of the interacting sites was induced by NaB stimulation, suggesting that NaB-induced interactions between genomic regions is involved in regulation of the cooperative gene expression program. In addition, in an effort to elucidate molecular mechanisms of dynamic regulation of interferon-inducible genes, we developed enChIP systems using different dCas9 orthologues and tags. We further showed that the yields of the novel enChIP systems are sufficiently high for their practical use.

Report

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

    (40 results)

All 2018 2017 2016 2015 Other

All Int'l Joint Research (9 results) Journal Article (13 results) (of which Int'l Joint Research: 1 results,  Peer Reviewed: 13 results,  Open Access: 13 results,  Acknowledgement Compliant: 8 results) Presentation (10 results) (of which Int'l Joint Research: 5 results,  Invited: 3 results) Book (3 results) Remarks (3 results) Patent(Industrial Property Rights) (2 results) (of which Overseas: 1 results)

  • [Int'l Joint Research] Shaare Zedek Medical Center(イスラエル)

    • Related Report
      2017 Annual Research Report
  • [Int'l Joint Research] Postech(韓国)

    • Related Report
      2017 Annual Research Report
  • [Int'l Joint Research] Lund University(スウェーデン)

    • Related Report
      2017 Annual Research Report
  • [Int'l Joint Research] Lund University(スウェーデン)

    • Related Report
      2016 Annual Research Report
  • [Int'l Joint Research] University of Alabama at Birmingham/University of California San Diego(米国)

    • Related Report
      2016 Annual Research Report
  • [Int'l Joint Research] Shaare Zedek Medical Center/Technion, Israel Institute of Technology(イスラエル)

    • Related Report
      2016 Annual Research Report
  • [Int'l Joint Research] l'institut du thorax/Lab Genome et Developpement des Plantes(フランス)

    • Related Report
      2016 Annual Research Report
  • [Int'l Joint Research] Institute for Basic Science(韓国)

    • Related Report
      2016 Annual Research Report
  • [Int'l Joint Research]

    • Related Report
      2016 Annual Research Report
  • [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] 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] 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] 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] Identification of physical interactions between genomic regions by enChIP-Seq2017

    • Author(s)
      Fujita T, Yuno M, Suzuki Y, Sugano S, Fujii H
    • Journal Title

      Genes Cells

      Volume: in press

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [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 Annual Research 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 Annual Research 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 Annual Research 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 Annual Research Report
    • Peer Reviewed / Open Access / 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
      2015 Annual Research 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 Annual Research 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 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Presentation] Biochemical analysis of 4D-Nucleome using locus-specific chromatin immunoprecipitation (locus-specific ChIP)2017

    • Author(s)
      Hodaka Fujii
    • Organizer
      第40回日本分子生物学会年会/2017年度生命科学系学会合同年次大会(ConBio2017)
    • Related Report
      2017 Annual Research Report
    • Invited
  • [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
    • Year and Date
      2016-11-30
    • Related Report
      2016 Annual Research Report
  • [Presentation] Development of enChIP and its applications to locus-specific biochemical analysis of genome functions2016

    • Author(s)
      Fujita T, Fujii H
    • Organizer
      12th EMBL Conference Transcription and Chromatin
    • Place of Presentation
      EMBL Advanced Training Centre, Heidelberg, Germany
    • Year and Date
      2016-08-27
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research
  • [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
    • Year and Date
      2016-05-19
    • Related Report
      2016 Annual Research Report
  • [Presentation] 遺伝子座特異的クロマチン免疫沈降法によるゲノム機能発現機構の解析:核内三次元構造解析への応用を中心として2016

    • Author(s)
      藤田 敏次、藤井 穂高
    • Organizer
      第33回染色体ワークショップ・第14回核ダイナミクス研究会
    • Place of Presentation
      松島一の坊
    • Year and Date
      2016-01-12
    • Related Report
      2015 Annual Research Report
  • [Presentation] Biochemical analysis of genome functions using locus-specific chromatin immunoprecipitation technologies: iChIP and enChIP2016

    • Author(s)
      Fujii H
    • Organizer
      The International Conference on Transcription Cycle International 2016
    • Place of Presentation
      東京大学理学部小柴ホール、東京都
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] 組換え蛋白質を利用したin vitro遺伝子座特異的クロマチン免疫沈降法による転写・エピジェネティック制御機構の解析2015

    • Author(s)
      藤井 穂高
    • Organizer
      BMB2015(第38回日本分子生物学会年会・第88回日本生化学会 合同大会)
    • Place of Presentation
      神戸ポートアイランド
    • Year and Date
      2015-12-01
    • Related Report
      2015 Annual Research Report
    • Invited
  • [Presentation] Locus-specific biochemical analysis of genome functions using enChIP: an application of CRISPR/Cas and TAL to purification of specific genomic regions2015

    • Author(s)
      Fujii H
    • Organizer
      TGE2015 Conference on Transposition and Genome Engineering 2015
    • Place of Presentation
      奈良春日野国際フォーラム
    • Year and Date
      2015-11-17
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Locus-specific biochemical analysis of genome functions using enChIP: an application of CRISPR/Cas to purification of specific genomic regions2015

    • Author(s)
      Fujita T, and Fujii H
    • Organizer
      Cold Spring Harbor meeting: Genome Engineering: The CRISPR/Cas Revolution
    • Place of Presentation
      Cold Spring Harbor Laboratory, Cold Spring Harbor, USA
    • Year and Date
      2015-09-24
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Locus-specific biochemical analysis of genome functions using enChIP: an application of CRISPR/Cas and TAL to purification of specific genomic regions2015

    • Author(s)
      Fujita T, and Fujii H
    • Organizer
      FASEB Science Research Conference "Transcription, Chromatin, and Epigenetics"
    • Place of Presentation
      West Palm Beach Marriott, Palm Beach, USA
    • Year and Date
      2015-06-28
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research
  • [Book] Handbook of epigenetics : the new molecular and medical genetics2017

    • Author(s)
      Tollefsbol, Trygve O.
    • Total Pages
      668
    • Publisher
      Academic Press, an imprint of Elsevier
    • ISBN
      9780128053881
    • Related Report
      2017 Annual Research Report
  • [Book] Handbook of Epigenetics 2nd edition2017

    • Author(s)
      Fujita T, Fujii H
    • Publisher
      Elsevier
    • Related Report
      2016 Annual Research Report
  • [Book] Chromatin Protocols2015

    • Author(s)
      Fujita T, Fujii H
    • Total Pages
      492
    • Publisher
      Springer
    • Related Report
      2015 Annual Research Report
  • [Remarks] 弘前大学大学院医学研究科/医学部医学科 ゲノム生化学講座 web ページ

    • URL

      http://www.med.hirosaki-u.ac.jp/~bgb/

    • Related Report
      2017 Annual Research Report
  • [Remarks] 藤井研究室ホームページ(大阪大学)

    • URL

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

    • Related Report
      2016 Annual Research Report
  • [Remarks] 藤井研究室ホームページ

    • URL

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

    • Related Report
      2015 Annual Research Report
  • [Patent(Industrial Property Rights)] DNA間相互作用の解析方法2016

    • 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
      2016-11-18
    • Related Report
      2016 Annual Research Report
    • Overseas
  • [Patent(Industrial Property Rights)] DNA間相互作用の解析方法2015

    • 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
    • Industrial Property Number
      2015-231329
    • Filing Date
      2015-11-27
    • Related Report
      2015 Annual Research Report

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

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