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Designing promoter sequences

Research Project

Project/Area Number 22240032
Research Category

Grant-in-Aid for Scientific Research (A)

Allocation TypeSingle-year Grants
Section一般
Research Field Bioinformatics/Life informatics
Research InstitutionKyoto University

Principal Investigator

YADA Tetsushi  京都大学, 大学院・情報学研究科, 准教授 (10322728)

Co-Investigator(Kenkyū-buntansha) SUZUKI Yutaka  京都大学, 大学院・新領域創成科学研究科, 准教授 (40323646)
Project Period (FY) 2010 – 2012
Project Status Completed (Fiscal Year 2012)
Budget Amount *help
¥50,050,000 (Direct Cost: ¥38,500,000、Indirect Cost: ¥11,550,000)
Fiscal Year 2012: ¥15,860,000 (Direct Cost: ¥12,200,000、Indirect Cost: ¥3,660,000)
Fiscal Year 2011: ¥15,860,000 (Direct Cost: ¥12,200,000、Indirect Cost: ¥3,660,000)
Fiscal Year 2010: ¥18,330,000 (Direct Cost: ¥14,100,000、Indirect Cost: ¥4,230,000)
Keywordsプロモーター / 転写制御 / バイオインフォマティクス / ゲノム生物学 / 合成生物学 / 生体生命情報学 / ゲノム / 発現制御 / モデル化
Research Abstract

We have developed a computational method of designing DNA base sequences of promoters whose transcriptional activities satisfies a given condition (transcriptional strength in a given cell line). The method has introduced two base substitutions into human CRE promoter, then we have verified that these substitutions successfully increased its transcriptional strength in HEK293T cell line ~2.5 times as high as that of the original promoter. On the other hand, it has become clear that designing promoter sequences is interestingly difficult in the case of existing overlapping TFBSs (transcriptional factor binding sites) such as human IFNB promoter.

Report

(4 results)
  • 2012 Annual Research Report   Final Research Report ( PDF )
  • 2011 Annual Research Report
  • 2010 Annual Research Report
  • Research Products

    (23 results)

All 2013 2012 2011 2010 Other

All Journal Article (7 results) (of which Peer Reviewed: 6 results) Presentation (15 results) Remarks (1 results)

  • [Journal Article] miRNA-target prediction based on transcriptional regulation2013

    • Author(s)
      Fujiwara,T., Yada,T.
    • Journal Title

      BMC Genomics

      Volume: 14(Suppl.2) Issue: S2

    • DOI

      10.1186/1471-2164-14-s2-s3

    • Related Report
      2012 Annual Research Report 2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] Large-scale motif discovery using DNA Gray code and equiprobable oligomers2012

    • Author(s)
      Ichinose,N., Yada,T.,Gotoh,O.
    • Journal Title

      Bioinform

      Volume: 28 Issue: 1 Pages: 25-31

    • DOI

      10.1093/bioinformatics/btr606

    • NAID

      120004873969

    • Related Report
      2012 Final Research Report 2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Predicting promoter activities of primary human DNA sequences2011

    • Author(s)
      Irie,T., Park,S.-J., Yamashita,R., Seki,M., Yada,T., Sugano,S., Nakai,K., Suzuki,Y.
    • Journal Title

      Nucl. Acids Res.

      Volume: 39 Issue: 11 Pages: e75-e75

    • DOI

      10.1093/nar/gkr173

    • Related Report
      2012 Final Research Report 2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Linear regression models predicting strength of transcriptional activity of promoters2011

    • Author(s)
      Yada,T., Yoshida,K., Morita,M., Taniguchi,T., Irie,T., Suzuki,Y.
    • Journal Title

      Genome Inform

      Volume: 25 Pages: 53-60

    • NAID

      130004567843

    • URL

      https://www.jstage.jst.go.jp/article/gi/25/1/25_1_53/_pdf

    • Related Report
      2012 Final Research Report 2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] DNA配列から転写因子結合部位を予測・検索するWEBツール2011

    • Author(s)
      入江拓磨,鈴木穰
    • Journal Title

      実験医学

      Volume: 29 Pages: 625-629

    • Related Report
      2012 Final Research Report 2010 Annual Research Report
  • [Journal Article] Linear regression models predicting strength of transcriptional activity of promoters2011

    • Author(s)
      Yada, T., et al.
    • Journal Title

      Genome Informatics

      Volume: In press

    • NAID

      130004567843

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Predicting promoter activities of primary human DNA sequences2011

    • Author(s)
      Irie, T., et al.
    • Journal Title

      Nucleic Acids Research

      Volume: In press

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Presentation] A statistical model for predicting transcription activities based on linear regression2012

    • Author(s)
      Liu,Y., Ichinose,N., Yada,T
    • Organizer
      日本バイオインフォマティクス学会年会
    • Place of Presentation
      東京
    • Related Report
      2012 Final Research Report
  • [Presentation] プロモタ配列の設計2012

    • Author(s)
      矢田哲士
    • Organizer
      第35回日本分子生物学会年会
    • Place of Presentation
      福岡
    • Related Report
      2012 Final Research Report
  • [Presentation] 超並列シクエンサを用いたヒト変異プロモーターのハイスループット解析2012

    • Author(s)
      入江拓磨,関真秀,菅野純夫,矢田哲士,鈴木穰
    • Organizer
      第35回日本分子生物学会年会
    • Place of Presentation
      福岡
    • Related Report
      2012 Final Research Report
  • [Presentation] miRNA-target prediction based on transcriptional regulation2012

    • Author(s)
      Fujiwara,T., Yada,T
    • Organizer
      ISCB-Asia/SCCG
    • Place of Presentation
      Shenzhen, China
    • Related Report
      2012 Final Research Report
  • [Presentation] プロモーター配列の設計2012

    • Author(s)
      矢田哲士
    • Organizer
      第35回日本分子生物学会年会
    • Place of Presentation
      福岡国際会議場・マリンメッセ福岡(福岡県)
    • Related Report
      2012 Annual Research Report
  • [Presentation] 超並列シークエンサーを用いたヒト変異プロモーターのハイスループット解析2012

    • Author(s)
      入江拓磨
    • Organizer
      第35回日本分子生物学会年会
    • Place of Presentation
      福岡国際会議場・マリンメッセ福岡(福岡県)
    • Related Report
      2012 Annual Research Report
  • [Presentation] A statistical model for predicting transcription activities based on linear regression2012

    • Author(s)
      Y. Liu
    • Organizer
      日本バイオインフォマティクス学会年会
    • Place of Presentation
      タワーホール船堀(東京都)
    • Related Report
      2012 Annual Research Report
  • [Presentation] miRNA-target prediction based on transcriptional regulation2012

    • Author(s)
      T.Fujiwara
    • Organizer
      ISCB-Asia/SCCG
    • Place of Presentation
      Dameisha Beach(Shenzhen, China)
    • Related Report
      2012 Annual Research Report
  • [Presentation] Transcriptome analysis of human genes, Multilevel Systems Biology2011

    • Author(s)
      Suzuki,Y
    • Organizer
      Genome, Structure, and Networks
    • Place of Presentation
      Osaka, Japan
    • Related Report
      2012 Final Research Report
  • [Presentation] Predicting promoter activities of primary human DNA sequences2011

    • Author(s)
      Irie,T., Park,S.-J., Yamashita,R., Seki,M., Yada,T., Sugano,S., Nakai,K., Suzuki,Y.
    • Organizer
      第34回日本分子生物学会年会
    • Place of Presentation
      横浜
    • Related Report
      2012 Final Research Report 2011 Annual Research Report
  • [Presentation] Transcriptome analysis of human genes2011

    • Author(s)
      Y.Suzuki
    • Organizer
      Multilevel Systems Biology : Genomes, Structures, and Networks
    • Place of Presentation
      Osaka, Japan
    • Related Report
      2011 Annual Research Report
  • [Presentation] Predicting promoter activities of primary human DNA sequences2010

    • Author(s)
      Irie, T., et al.
    • Organizer
      Biochemistry and Molecular Biology BMB2010
    • Place of Presentation
      Kobe
    • Year and Date
      2010-12-09
    • Related Report
      2010 Annual Research Report
  • [Presentation] Linear regression models predicting strength of transcriptional activity of promoters2010

    • Author(s)
      Yada,T., Yoshida,K., Morita,M., Taniguchi,T., Irie,T., Suzuki,Y.
    • Organizer
      日本バイオインフォマティクス学会年会
    • Place of Presentation
      福岡
    • Related Report
      2012 Final Research Report
  • [Presentation] Predicting promoter activities of primary human DNA sequences2010

    • Author(s)
      Irie,T., Park,S.-J., Yamashita,R., Seki,M., Yada,T., Sugano,S., Nakai,K., Suzuki,Y.
    • Organizer
      Biochemistry and Molecular Biology BMB2010
    • Place of Presentation
      Kobe,Japan
    • Related Report
      2012 Final Research Report
  • [Presentation] Linear regression models which predict transcriptional activities from promoter sequences2010

    • Author(s)
      Yada, T., et al.
    • Organizer
      Annual Conference of JSBi (Japanese Society for Bioinformatics)
    • Place of Presentation
      Fukuoka
    • Related Report
      2010 Annual Research Report
  • [Remarks]

    • URL

      http://www.genome.ist.i.kyoto-u.ac.jp/~ichinose/hegma/

    • Related Report
      2012 Final Research Report

URL: 

Published: 2010-11-30   Modified: 2019-07-29  

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