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Linking novel bioactive compounds to their targets and pathways using chemical genomics and morphological profiling

Research Project

Project/Area Number 15H04483
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypeSingle-year Grants
Section一般
Research Field Applied microbiology
Research InstitutionInstitute of Physical and Chemical Research

Principal Investigator

Boone Charles  国立研究開発法人理化学研究所, 環境資源科学研究センター, チームリーダー (70601342)

Co-Investigator(Kenkyū-buntansha) 大矢 禎一  東京大学, 大学院新領域創成科学研究科, 教授 (20183767)
Project Period (FY) 2015-04-01 – 2018-03-31
Project Status Completed (Fiscal Year 2017)
Budget Amount *help
¥17,160,000 (Direct Cost: ¥13,200,000、Indirect Cost: ¥3,960,000)
Fiscal Year 2017: ¥2,990,000 (Direct Cost: ¥2,300,000、Indirect Cost: ¥690,000)
Fiscal Year 2016: ¥5,330,000 (Direct Cost: ¥4,100,000、Indirect Cost: ¥1,230,000)
Fiscal Year 2015: ¥8,840,000 (Direct Cost: ¥6,800,000、Indirect Cost: ¥2,040,000)
Keywordschemical genomics / morphological profiling / yeast / target identification
Outline of Final Research Achievements

Combining chemical genomics profiling based on genetic interactions and morphological profiling using a sophisticated image-processing program, CalMorph, we developed a multi-dimensional strategy for linking novel bioactive compounds to their targets and pathways. We established a high-throughput chemical-genetic screening platform to functionally annotate large compound collections in a rapid and systematic manner using next generation sequencing. Furthermore, we assembled a computational platform for functionally annotating compounds to specific biological processes and pathways. Finally, we applied our chemical-genomic/morphological profiling pipeline to annotate 13,524 compounds in total by screening seven diverse compound collections including the RIKEN NPDepo library.

Report

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

    (49 results)

All 2018 2017 2016 2015 Other

All Int'l Joint Research (6 results) Journal Article (18 results) (of which Int'l Joint Research: 15 results,  Peer Reviewed: 17 results,  Open Access: 11 results,  Acknowledgement Compliant: 4 results) Presentation (22 results) (of which Int'l Joint Research: 14 results,  Invited: 16 results) Book (1 results) Remarks (2 results)

  • [Int'l Joint Research] トロント大学(カナダ)

    • Related Report
      2017 Annual Research Report
  • [Int'l Joint Research] ミネソタ大学(米国)

    • Related Report
      2017 Annual Research Report
  • [Int'l Joint Research] ミネソタ大学(米国)

    • Related Report
      2016 Annual Research Report
  • [Int'l Joint Research] トロント大学(カナダ)

    • Related Report
      2016 Annual Research Report
  • [Int'l Joint Research] ストラスブール大学/リヨン大学(フランス)

    • Related Report
      2016 Annual Research Report
  • [Int'l Joint Research] University of Minnesota(米国)

    • Related Report
      2015 Annual Research Report
  • [Journal Article] MOSAIC: a chemical-genetic interaction data repository and web resource for exploring chemical modes of action2018

    • Author(s)
      Nelson J, Simpkins SW, Safizadeh H, Li SC, Piotrowski JS, Hirano H, Yashiroda Y, Osada H, Yoshida M, Boone C, Myers CL.
    • Journal Title

      Bioinformatics

      Volume: 34 Issue: 7 Pages: 1251-1252

    • DOI

      10.1093/bioinformatics/btx732

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Global study of holistic morphological effectors in the budding yeast Saccharomyces cerevisiae2018

    • Author(s)
      Suzuki G, Wang Y, Kubo K, Hirata E, Ohnuki S, Ohya Y
    • Journal Title

      BMC Genomics

      Volume: 19 Issue: 1 Pages: 149-149

    • DOI

      10.1186/s12864-018-4526-z

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Testing the neutral hypothesis of phenotypic evolution2018

    • Author(s)
      Ho WC, Ohya Y, Zhang J
    • Journal Title

      Proc Natl Acad Sci U S A

      Volume: 114 Issue: 46 Pages: 12219-12224

    • DOI

      10.1073/pnas.1710351114

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Functional annotation of chemical libraries across diverse biological processes.2017

    • Author(s)
      Piotrowski JS, Li SC, Deshpande R.......Shirahige K,......Boone C.
    • Journal Title

      Nat Chem Biol.

      Volume: 13 Issue: 9 Pages: 982-993

    • DOI

      10.1038/nchembio.2436

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Phenotypic diagnosis of lineage and differentiation during sake yeast breeding2017

    • Author(s)
      Shinsuke Ohnuki, Hiroki Okada, Anne Friedrich, Yoichiro Kanno, Tetsuya Goshima, Hirokazu Hasuda, Masaaki Inahashi, Naoto Okazaki, Hiroyasu Tamura, Ryo Nakamura, Dai Hirata, Hisashi Fukuda, Hitoshi Shimoi, Katsuhiko Kitamoto, Daisuke Watanabe, Joseph Schacherer, Takeshi Akao, Yoshikazu Ohya
    • Journal Title

      G3 (Bethesda)

      Volume: 7 Issue: 8 Pages: 2807-2820

    • DOI

      10.1534/g3.117.044099

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Systematic analysis of Ca2+ homoeostasis in Saccharomyces cerevisiae based on chemical-genetic interaction profiles2017

    • Author(s)
      Farzan Ghanegolmohammadi, Mitsunori Yoshida, Shinsuke Ohnuki, Yuko Sukegawa, Hiroki Okada, Keisuke Obara, Akio Kihara, Kuninori Suzuki, Tetsuya Kojima, Nozomu Yachie, Dai Hirata, Yoshikazu Ohya
    • Journal Title

      Mol. Biol. Cell

      Volume: 28 Issue: 23 Pages: 3415-3427

    • DOI

      10.1091/mbc.e17-04-0216

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] The Dual Activity Responsible for the Elongation and Branching of β-(1,3)-Glucan in the Fungal Cell Wall.2017

    • Author(s)
      Aimanianda V, Simenel C, Garnaud C, Clavaud C, Tada R, Barbin L, Mouyna I, Heddergott C, Popolo L, Ohya Y, Delepierre M, Latge JP
    • Journal Title

      MBio

      Volume: 8 Issue: 3

    • DOI

      10.1128/mbio.00619-17

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Exploring genetic suppression interactions on a global scale2016

    • Author(s)
      van Leeuwen J, Pons C, Mellor JC, Yamaguchi TN, Friesen H, ..., and Boone C.
    • Journal Title

      Science

      Volume: 354 Issue: 6312

    • DOI

      10.1126/science.aag0839

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] A global genetic interaction network maps a wiring diagram of cellular function2016

    • Author(s)
      Costanzo M, VanderSluis B, Koch EN, Baryshnikova A, Pons C, ..., and Boone C.
    • Journal Title

      Science

      Volume: 353 Issue: 6306

    • DOI

      10.1126/science.aaf1420

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Examination and Disruption of the Yeast Cell Wall2016

    • Author(s)
      Okada H, Kono K, Neiman AM, Ohya Y
    • Journal Title

      Cold Spring Harb Protoc.

      Volume: 2016 Issue: 8 Pages: 078659-078659

    • DOI

      10.1101/pdb.top078659

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Fluorescent Labeling of Yeast Cell Wall Components.2016

    • Author(s)
      Okada H, Ohya Y
    • Journal Title

      Cold Spring Harb Protoc.

      Volume: 2016 Issue: 8 Pages: 085241-085241

    • DOI

      10.1101/pdb.prot085241

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Exploiting Single-Cell Quantitative Data to Map Genetic Variants Having Probabilistic Effects.2016

    • Author(s)
      Chuffart F, Richard M, Jost D, Burny C, Duplus-Bottin H, Ohya Y, Yvert G.
    • Journal Title

      PLOS Genetics

      Volume: 12 Issue: 8 Pages: e1006213-e1006213

    • DOI

      10.1371/journal.pgen.1006213

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
  • [Journal Article] Identification of a mutation causing a defective spindle assembly checkpoint in high ethyl caproate-producing sake yeast strain K1801.2016

    • Author(s)
      Goshima T, Nakamura R, Kume K, Okada H, Ichikawa E, Tamura H, Hasuda H, Inahashi M, Okazaki N, Akao T, Shimoi H, Mizunuma M, Ohya Y, Hirata D.
    • Journal Title

      Biosci Biotechnol Biochem.

      Volume: 80 Issue: 8 Pages: 1657-62

    • DOI

      10.1080/09168451.2016.1184963

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Large-Scale Survey of Intraspecific Fitness and Cell Morphology Variation in a Protoploid Yeast Species.2016

    • Author(s)
      Jung PP, Sigwalt A, Ohnuki S, de Montigny J, Ohya Y, Schacherer J.
    • Journal Title

      G3

      Volume: 6 Issue: 4 Pages: 1063-71

    • DOI

      10.1534/g3.115.026682

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
  • [Journal Article] Plant-derived antifungal agent poacic acid targets β-1,3-glucan2015

    • Author(s)
      Piotrowski JS, Okada H, Lu F, Li SC, Hinchman L, Ranjan A, Smith DL, Higbee AJ, Ulbrich A, Coon JJ, Deshpande R, Bukhman YV, McIlwain S, Ong IM, Myers CL, Boone C, Landick R, Ralph J, Kabbage M, Ohya Y
    • Journal Title

      Proc Natl Acad Sci U S A

      Volume: 112 Issue: 12

    • DOI

      10.1073/pnas.1410400112

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Chemical genomic profiling via barcode sequencing to predict compound mode of action.2015

    • Author(s)
      Piotrowski JS, Simpkins SW, Li SC, Deshpande R, McIlwain SJ, Ong IM, Myers CL, Boone C, Andersen RJ.
    • Journal Title

      Methods Mol Biol

      Volume: 1263 Pages: 299-318

    • DOI

      10.1007/978-1-4939-2269-7_23

    • ISBN
      9781493922680, 9781493922697
    • Related Report
      2015 Annual Research Report
    • Open Access / Int'l Joint Research
  • [Journal Article] Controlling microbial contamination during hydrolysis of AFEX-pretreated corn stover and switchgrass: effects on hydrolysate composition, microbial response and fermentation.2015

    • Author(s)
      Serate J, Xie D, Pohlmann E, Donald C Jr, Shabani M, Hinchman L, Higbee A, Mcgee M, La Reau A, Klinger GE, Li S, Myers CL, Boone C, Bates DM, Cavalier D, Eilert D, Oates LG, Sanford G, Sato TK, Dale B, Landick R, Piotrowski J, Ong RG, Zhang Y.
    • Journal Title

      Biotechnol Biofuels

      Volume: 8 Issue: 1 Pages: 180-180

    • DOI

      10.1186/s13068-015-0356-2

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Profiling of the effects of antifungal agents on yeast cells based on morphometric analysis.2015

    • Author(s)
      Gebre AA, Okada H, Kim C, Kubo K, Ohnuki S, Ohya Y.
    • Journal Title

      FEMS Yeast Res.

      Volume: 15 Issue: 5 Pages: fov040-fov040

    • DOI

      10.1093/femsyr/fov040

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Presentation] Mapping Chemical-Genetic Interactions to Link Bioactive Compounds to Cellular Targets2018

    • Author(s)
      Charles Boone
    • Organizer
      新学術領域研究「化学コミュニケーションのフロンティア」第2回公開シンポジウム
    • Related Report
      2017 Annual Research Report
    • Invited
  • [Presentation] A global genetic interaction network maps a wiring diagram of cellular function2017

    • Author(s)
      Charles Boone
    • Organizer
      Opportunities and Challenges of Exploiting Synthetic Lethality in Cancer
    • Place of Presentation
      米国 サンディエゴ
    • Year and Date
      2017-01-04
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Target Identification Using an Integrated Chemical Genetic Approach2017

    • Author(s)
      Sheena Li, Charles Boone
    • Organizer
      CIFAR meeting
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Mapping Genetic Networks on a Global Scale2017

    • Author(s)
      Charles Boone
    • Organizer
      From Genetic Networks to a Cellular Wiring Diagram
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] High-dimensional and single-cell phenotyping in Saccharomyces cerevisiae: Rational selection of the morphological parameters2017

    • Author(s)
      Yoshikazu Ohya
    • Organizer
      CIFAR Meeting
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] The book of yeast morphology is written in the language of mathematics2017

    • Author(s)
      Yoshikazu Ohya
    • Organizer
      Gene, genom and beyond
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] 酵母の細胞壁研究の魅力2017

    • Author(s)
      大矢禎一
    • Organizer
      日本植物学会シンポジウム
    • Related Report
      2017 Annual Research Report
    • Invited
  • [Presentation] 出芽酵母の形態表現型に強い影響を与える遺伝子変異株の網羅的解析2017

    • Author(s)
      鈴木吾大、王洋、大貫慎輔、大矢禎一
    • Organizer
      第50回酵母遺伝学フォーラム
    • Related Report
      2017 Annual Research Report
  • [Presentation] 高次元形態表現型に基づく遺伝子機能特異的表現型自動抽出法の開発2017

    • Author(s)
      大貫慎輔、徐聴涛、大矢禎一
    • Organizer
      第40回日本分子生物学会年会
    • Related Report
      2017 Annual Research Report
  • [Presentation] A global genetic interaction network maps a wiring diagram of cellular function2017

    • Author(s)
      Charles Boone
    • Organizer
      9th HiHA International Workshop; Toward a comprehensive understanding of a global genetic network within a cell
    • Place of Presentation
      広島大学(広島県東広島市)
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] High-dimensional and -single cell phenotyping in Saccharomyces cerevisiae2017

    • Author(s)
      Yoshikazu Ohya
    • Organizer
      9th HiHA International Workshop; Toward a comprehensive understanding of a global genetic network within a cell
    • Place of Presentation
      広島大学(広島県東広島市)
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Global Analysis of Genetic Interaction Networks in Yeast2016

    • Author(s)
      Charles Boone
    • Organizer
      Human and Mammalian Genetics and Genomics: The 57th McKusick Short Course
    • Place of Presentation
      米国 バーハーバー
    • Year and Date
      2016-07-17
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Single Cell Phenotyping of Sake Yeast2016

    • Author(s)
      大矢禎一
    • Organizer
      バイオイメージ・インフォマティクスワークショップ 2016
    • Place of Presentation
      大阪大学(大阪府吹田市)
    • Year and Date
      2016-06-22
    • Related Report
      2016 Annual Research Report
  • [Presentation] Exploring Functional Genetic Suppression Interactions on a Global Scale2016

    • Author(s)
      Charles Boone
    • Organizer
      CIFAR meeting
    • Place of Presentation
      カナダ トロント
    • Year and Date
      2016-04-15
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Application of Single Cell Phenomics in Chemical Genomics2016

    • Author(s)
      Yoshikazu Ohya
    • Organizer
      CIFAR meeting
    • Place of Presentation
      カナダ トロント
    • Year and Date
      2016-04-15
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] 清酒酵母の単細胞フェノタイピング2016

    • Author(s)
      大矢禎一
    • Organizer
      酵母細胞研究会
    • Place of Presentation
      東京大学(東京都文京区)
    • Related Report
      2016 Annual Research Report
    • Invited
  • [Presentation] A cell cycle checkpoint to insure the integrity of the cell wall synthesis2016

    • Author(s)
      Yoshikazu Ohya
    • Organizer
      LIISAIB
    • Place of Presentation
      アルゼンチン コルドバ
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] 清酒酵母今昔2016

    • Author(s)
      大矢禎一
    • Organizer
      日本酒史学会
    • Place of Presentation
      東京大学(千葉県柏市)
    • Related Report
      2016 Annual Research Report
    • Invited
  • [Presentation] New antifungal agents that inhibit cell wall synthesis2015

    • Author(s)
      Yoshikazu Ohya
    • Organizer
      Fungal Cell Wall 2015
    • Place of Presentation
      Paris, France
    • Year and Date
      2015-10-26
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Functional annotation of biological processes targeted by chemical libraries2015

    • Author(s)
      Sheena Li, Charlie Boone
    • Organizer
      27° International conference on yeast genetics and molecular biology
    • Place of Presentation
      Levico Terme, Italy
    • Year and Date
      2015-09-10
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research
  • [Presentation] 化学遺伝学と形態学のプロファイリング解析による細胞壁合成経路を標的にする抗真菌剤の探索2015

    • Author(s)
      久保 佳蓮,岡田 啓希,Abraham Abrera,Sheena Li,Jeff Piotrowski,Chad Myers,八代田 陽子,Charlie Boone, 吉田 稔,長田 裕之,斎藤 臣雄,大矢 禎一
    • Organizer
      第67回日本細胞生物学会大会
    • Place of Presentation
      タワーホール船堀(東京都江戸川区)
    • Year and Date
      2015-07-02
    • Related Report
      2015 Annual Research Report
  • [Presentation] High-dimensional morphological phenotyping in Saccharomyces cerevisiae2015

    • Author(s)
      Yoshikazu Ohya
    • Organizer
      Annual Meeting of Microbiology in Korea
    • Place of Presentation
      Changwon, Korea
    • Year and Date
      2015-04-15
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research / Invited
  • [Book] 第9章 新しい創薬ツールとしての出芽酵母(「酵母菌・麹菌・乳酸菌の産業応用展開」)2018

    • Author(s)
      久保佳蓮、大矢禎一(五味勝也、阿部敬悦・監修)
    • Total Pages
      264
    • Publisher
      シーエムシー出版
    • ISBN
      9784781313177
    • Related Report
      2017 Annual Research Report
  • [Remarks] 化合物の標的機能を決定するツールを開発-酵母の化学遺伝学アプローチで化合物の標的予測/同定が迅速に-

    • URL

      http://www.riken.jp/pr/press/2017/20170725_1/

    • Related Report
      2017 Annual Research Report
  • [Remarks] 植物由来の次世代型農薬へ

    • URL

      http://www.k.u-tokyo.ac.jp/info/entry/22_entry383/

    • Related Report
      2015 Annual Research Report

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Published: 2015-04-16   Modified: 2022-10-07  

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