Designing promoter sequences

• Project/Area Number: 22240032
• Research Category: Grant-in-Aid for Scientific Research (A)
• Allocation Type: Single-year Grants
• Section: 一般
• Research Field: Bioinformatics/Life informatics
• Research Institution: Kyoto 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: ¥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.

Research Products

• [Journal Article] miRNA-target prediction based on transcriptional regulation (2013)
  • Author(s): Fujiwara,T., Yada,T.
  • Journal Title: BMC Genomics Volume: 14(Suppl.2) Issue: S2
  • DOI: 10.1186/1471-2164-14-s2-s3
  • Peer Reviewed
• [Journal Article] Large-scale motif discovery using DNA Gray code and equiprobable oligomers (2012)
  • 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
  • Peer Reviewed
• [Journal Article] Predicting promoter activities of primary human DNA sequences (2011)
  • 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
  • Peer Reviewed
• [Journal Article] Linear regression models predicting strength of transcriptional activity of promoters (2011)
  • 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
  • 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
• [Journal Article] Linear regression models predicting strength of transcriptional activity of promoters (2011)
  • Author(s): Yada, T., et al.
  • Journal Title: Genome Informatics Volume: In press
  • NAID: 130004567843
  • Peer Reviewed
• [Journal Article] Predicting promoter activities of primary human DNA sequences (2011)
  • Author(s): Irie, T., et al.
  • Journal Title: Nucleic Acids Research Volume: In press
  • Peer Reviewed
• [Presentation] A statistical model for predicting transcription activities based on linear regression (2012)
  • 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
• [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
• [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
• [Presentation] miRNA-target prediction based on transcriptional regulation (2012)
  • Author(s): Fujiwara,T., Yada,T
  • Organizer: ISCB-Asia/SCCG
  • Place of Presentation: Shenzhen, China
• [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)
• [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)
• [Presentation] A statistical model for predicting transcription activities based on linear regression (2012)
  • 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)
• [Presentation] miRNA-target prediction based on transcriptional regulation (2012)
  • Author(s): T.Fujiwara
  • Organizer: ISCB-Asia/SCCG
  • Place of Presentation: Dameisha Beach(Shenzhen, China)
• [Presentation] Transcriptome analysis of human genes, Multilevel Systems Biology (2011)
  • Author(s): Suzuki,Y
  • Organizer: Genome, Structure, and Networks
  • Place of Presentation: Osaka, Japan
• [Presentation] Predicting promoter activities of primary human DNA sequences (2011)
  • 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
• [Presentation] Transcriptome analysis of human genes (2011)
  • Author(s): Y.Suzuki
  • Organizer: Multilevel Systems Biology : Genomes, Structures, and Networks
  • Place of Presentation: Osaka, Japan
• [Presentation] Predicting promoter activities of primary human DNA sequences (2010)
  • Author(s): Irie, T., et al.
  • Organizer: Biochemistry and Molecular Biology BMB2010
  • Place of Presentation: Kobe
  • Year and Date: 2010-12-09
• [Presentation] Linear regression models predicting strength of transcriptional activity of promoters (2010)
  • 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
• [Presentation] Predicting promoter activities of primary human DNA sequences (2010)
  • 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
• [Presentation] Linear regression models which predict transcriptional activities from promoter sequences (2010)
  • Author(s): Yada, T., et al.
  • Organizer: Annual Conference of JSBi (Japanese Society for Bioinformatics)
  • Place of Presentation: Fukuoka
• [Remarks]
  • URL: http://www.genome.ist.i.kyoto-u.ac.jp/~ichinose/hegma/