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A technology to quantitatively measure protein interactomes

Research Project

Project/Area Number 15K18466
Research Category

Grant-in-Aid for Young Scientists (B)

Allocation TypeMulti-year Fund
Research Field System genome science
Research InstitutionThe University of Tokyo

Principal Investigator

Yachie Nozomu  東京大学, 先端科学技術研究センター, 准教授 (60636801)

Project Period (FY) 2015-04-01 – 2018-03-31
Project Status Completed (Fiscal Year 2017)
Budget Amount *help
¥4,290,000 (Direct Cost: ¥3,300,000、Indirect Cost: ¥990,000)
Fiscal Year 2017: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000)
Fiscal Year 2016: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000)
Fiscal Year 2015: ¥1,690,000 (Direct Cost: ¥1,300,000、Indirect Cost: ¥390,000)
KeywordsDNAバーコード / インタラクトーム / 超並列DNAシークエンシング / 酵母ツーハイブリッド / タンパク質間相互作用 / DNA barcode / タンパク質進化 / 次世代DNAシークエンサー
Outline of Final Research Achievements

We remain one or two orders of magnitude away from a complete interaction map for humans and other major model organisms. Completion will require screening at substantially larger scales with many complementary assays, requiring further efficiency gains in proteome-scale interaction mapping. Here, we report Barcode Fusion Genetics-Yeast Two-Hybrid (BFG-Y2H), by which a full matrix of protein pairs can be screened in a single multiplexed strain pool. BFG-Y2H uses Cre recombination to fuse DNA barcodes from distinct plasmids, generating chimeric protein-pair barcodes that can be quantified via next-generation sequencing. We applied BFG-Y2H to four different matrices ranging in scale from ~25 K to 2.5 M protein pairs. The results show that BFG-Y2H increases the efficiency of protein matrix screening, with quality that is on par with state-of-the-art Y2H methods.

Report

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

    (20 results)

All 2018 2017 2016 Other

All Int'l Joint Research (5 results) Journal Article (15 results) (of which Int'l Joint Research: 4 results,  Peer Reviewed: 6 results,  Open Access: 4 results,  Acknowledgement Compliant: 1 results)

  • [Int'l Joint Research] Laval University/University of Toronto/Mt Sinai Hospital(カナダ)

    • Related Report
      2017 Annual Research Report
  • [Int'l Joint Research] Harvard University(米国)

    • Related Report
      2017 Annual Research Report
  • [Int'l Joint Research] University of Toronto/Mt Sinai Hospital/Laval University(カナダ)

    • Related Report
      2016 Research-status Report
  • [Int'l Joint Research] Harvard Medical School(米国)

    • Related Report
      2015 Research-status Report
  • [Int'l Joint Research] University of Toronto/Mt. Sinai Hospital/Laval Univeristy(カナダ)

    • Related Report
      2015 Research-status Report
  • [Journal Article] Highly efficient CRISPR gene editing in yeast enabled by double selection2018

    • Author(s)
      Despres Philippe C、Dube Alexandre K、Nielly-Thibault Lou、Yachie Nozomu、Landry Christian R
    • Journal Title

      bioRxiv

      Volume: 262808 Pages: 262808-262808

    • DOI

      10.1101/262808

    • Related Report
      2017 Annual Research Report
  • [Journal Article] Systematic analysis of Ca2+ homoeostasis in Saccharomyces cerevisiae based on chemical-genetic interaction profiles2017

    • Author(s)
      Ghanegolmohammadia F, Yoshida M, Ohnuki S, Sukegawa Y, Okada H, Obara K, Kihara A, Suzuki K, Kojima T, Yachie N, Hirata D & Ohya Y
    • Journal Title

      Molecular Biology of the Cell

      Volume: 28 Issue: 9 Pages: 3415-3427

    • DOI

      10.1101/gr.211649.116

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Yeast genetic interaction screen of human genes associated with amyotrophic lateral sclerosis: identification of MAP2K5 kinase as a potential drug target2017

    • Author(s)
      Jo M, Chung AY, Yachie N, Seo M, Jeon H, Nam Y, Seo Y, Kim E, Zhong Q, Vidal M, Park HC, Roth FP & Suk K
    • Journal Title

      Genome Research

      Volume: 27 Pages: 1487-1500

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed
  • [Journal Article] DNAバーコードおよびゲノム編集用いた細胞系譜の一斉追跡技術2017

    • Author(s)
      石黒 宗, 森 秀人 & 谷内江 望
    • Journal Title

      生体の科学

      Volume: 68 Pages: 273-281

    • Related Report
      2017 Annual Research Report
  • [Journal Article] オミクス科学における実験数の組合せ爆発に挑むDNAバーコード技術2017

    • Author(s)
      石黒 宗, 増山 七海 & 谷内江 望
    • Journal Title

      生化学

      Volume: 89 Pages: 538-545

    • Related Report
      2017 Annual Research Report
  • [Journal Article] Siri of the Cell---生物学はiPhoneから何を学べるだろうか2017

    • Author(s)
      Anne-Ruxandra Carvunis & Trey Ideker 翻訳:森 秀人 & 谷内江 望
    • Journal Title

      実験医学別冊あなたのラボにAI×ロボットがやってくる

      Volume: NA Pages: 116-123

    • Related Report
      2017 Annual Research Report
  • [Journal Article] AI・LabDroidと交わす言葉をつくりだす2017

    • Author(s)
      山本-エヴァンス 楠, 谷内江 望
    • Journal Title

      実験医学別冊あなたのラボにAI×ロボットがやってくる

      Volume: NA Pages: 124-129

    • Related Report
      2017 Annual Research Report
  • [Journal Article] 長鎖DNA合成のオートメーション化による生命科学の未来2017

    • Author(s)
      谷内江 望
    • Journal Title

      実験医学別冊 あなたのラボにAI×ロボットがやってくる

      Volume: NA Pages: 80-91

    • Related Report
      2017 Annual Research Report
  • [Journal Article] Robotic crowd biology with Maholo LabDroids.2017

    • Author(s)
      Yachie N; Robotic Biology Consortium (inc. Masaki Matsumoto)., Natsume T.
    • Journal Title

      Nature Biotechnology

      Volume: 35 Issue: 4 Pages: 310-312

    • DOI

      10.1038/nbt.3758

    • Related Report
      2016 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] タンパク質間相互作用ネットワークの超高速マッピング2017

    • Author(s)
      増山七海, 山本-エヴァンス 楠 & 谷内江望
    • Journal Title

      バイオサイエンスとインダストリー

      Volume: 75

    • NAID

      40021066275

    • Related Report
      2016 Research-status Report
  • [Journal Article] DNAバーコードによる生命科学実験の限界突破2017

    • Author(s)
      石黒 宗, 森 秀人 & 谷内江 望
    • Journal Title

      実験医学増刊

      Volume: 35

    • Related Report
      2016 Research-status Report
  • [Journal Article] Targeted nucleotide editing using hybrid prokaryotic and vertebrate adaptive immune systems2016

    • Author(s)
      Nishida, K., Arazoe, T., Yachie, N., Banno, S., Kakimoto, M., Tabata, M., Mochizuki, M., Miyabe, A., Araki, M., Hara, K.Y., Shimatani, Z. and Kondo, A.
    • Journal Title

      Science

      Volume: 353 Issue: 6305 Pages: 6305-6305

    • DOI

      10.1126/science.aaf8729

    • Related Report
      2016 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] バーコードフージョン遺伝学2016

    • Author(s)
      山本-エヴァンス 楠, 増山 七海 & 谷内江 望
    • Journal Title

      医学のあゆみ

      Volume: 259 Pages: 832-838

    • Related Report
      2016 Research-status Report
  • [Journal Article] Pooled-matrix protein interaction screens using Barcode Fusion Genetics2016

    • Author(s)
      Yachie N, Petsalaki E, Mellor JC, Weile J, Jacob Y, Verby M, Ozturk SB, Li S, Cote AG, Mosca R, Knapp JJ, Ko M, Yu A, Gebbia M, Sahni N, Yi S, Tyagi T, Sheykhkarimli D, Roth JF, Wong C, Musa L, Snider J, Liu Y-C, Yu H, Braun P, Stagljar I, Hao T, Calderwood MA, Pelletier L, Aloy P, Hill DE, Vidal M & Roth FP
    • Journal Title

      Molecular Systems Biology

      Volume: 12 Issue: 4

    • DOI

      10.15252/msb.20156660

    • Related Report
      2015 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
  • [Journal Article] The Effects of Cis-Regulatory Mutations in the SUL1 Gene on Sulfate-Limited Fitness in Yeast2016

    • Author(s)
      Rich MS, Payen C, Rubin AF, Ong GT, Sanchez MR, Yachie N, Dunham MJ & Fields S
    • Journal Title

      Genetics

      Volume: TBA Issue: 1 Pages: 191-202

    • DOI

      10.1534/genetics.116.188037

    • Related Report
      2015 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research

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Published: 2015-04-16   Modified: 2022-06-07  

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