Identification of non-coding conserved motifs and their relationships with polymorphism

• Project/Area Number: 21510215
• Research Category: Grant-in-Aid for Scientific Research (C)
• Allocation Type: Single-year Grants
• Section: 一般
• Research Field: ゲノム情報科学
• Research Institution: Kyoto University
• Principal Investigator: SUYAMA Mikita 京都大学, 医学研究科, 准教授 (70452365)
• Project Period (FY): 2009 – 2011
• Project Status: Completed (Fiscal Year 2011)
• Budget Amount: ¥4,550,000 (Direct Cost: ¥3,500,000、Indirect Cost: ¥1,050,000); Fiscal Year 2011: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000); Fiscal Year 2010: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000); Fiscal Year 2009: ¥1,950,000 (Direct Cost: ¥1,500,000、Indirect Cost: ¥450,000)
• Keywords: ゲノム / バイオインフォマティクス / 多型解析

Research Abstract

By using genome sequence alignments, We have identified many non-coding motifs that are conserved among mammalian species. For these motifs, we mainly focused on the cis-regulatory elements that regulate splicing. As the results, we revealed the existence of a network of cis-regulatory elements to achieve complicated regulations of alternative splicing. Extending this methodology to the identification of transcription factor binding sites, and to analyze the relationships between these motifs and single nucleotide polymorphisms(SNPs) are still under way. The computational environments and programs developed in this research project should facilitate further progress of these analyses in future.

Research Products

• [Journal Article] A polymorphism of the POLG2 gene is genetically associated with the invasiveness of urinary bladder cancer in Japanese males (2011)
  • Author(s): C. Ratanajaraya, H. Nishiyama, M. Takahashi, T. Kawaguchi, R. Saito, Y. Mikami, M. Suyama, M. Lathrop, R. Yamada, O. Ogawa, F. Matsuda.
  • Journal Title: J. Hum. Genet Volume: 56 Issue: 8 Pages: 572-576
  • DOI: 10.1038/jhg.2011.60
  • NAID: 10030660404
  • Peer Reviewed
• [Journal Article] A network of conserved co-occurring motifs for the regulation of alternative splicing (2010)
  • Author(s): Suyama M, Harrington ED, Vinokourova S, von Knebel Doeberitz M, Ohara O, Bork P.
  • Journal Title: Nucleic Acids Res Volume: 38 Issue: 22 Pages: 7916-7926
  • DOI: 10.1093/nar/gkq705
  • Peer Reviewed
• [Journal Article] A network of conserved co-occurring motifs for the regulation of alternative splicing (2010)
  • Author(s): Suyama M, Harrington ED, Vinokourova S, von Knebel Doeberitz M, Ohara O, Bork P
  • Journal Title: Nucleic Acids Research Volume: 38 Pages: 7916-7926
  • Peer Reviewed
• [Presentation] RNA-Seq解析による胎仔型および成獣型ライディッヒ細胞特異的発現マーカー遺伝子の検索 (2011)
  • Author(s): 宮林香奈子, 嶋雄一, 馬場崇, 大竹博之, 佐藤哲也, 大川恭行, 須山幹太, 諸橋憲一郎
  • Organizer: 第34回日本分子生物学会年会
  • Place of Presentation: 横浜
• [Presentation] ChIP-Seq法によるAd4BP/SF-1の標的遺伝子の同定 (2011)
  • Author(s): 馬場崇, 大竹博之, 宮林香奈子, 嶋雄一, 佐藤哲也, 木村宏, 大川恭行, 須山幹太, 諸橋憲一郎
  • Organizer: 第34回日本分子生物学会年会
  • Place of Presentation: 横浜
• [Presentation] ChIP-Seqデータを用いた核内受容体共役因子の探索 (2011)
  • Author(s): 佐藤哲也, 須山幹太
  • Organizer: 第34回日本分子生物学会年会
  • Place of Presentation: 横浜
• [Presentation] RNA-Seq解析による胎仔型および成獣型ライディッヒ細胞特異的発現マーカー遺伝子の検索 (2011)
  • Author(s): 宮林香奈子, 嶋雄一, 馬場崇, 大竹博之, 佐藤哲也, 大川恭行, 須山幹太, 諸橋憲一郎
  • Organizer: 第34回日本分子生物学会年会
  • Place of Presentation: パシフィコ横浜
• [Presentation] ChIP-Seq法によるAd4BP/SF-1の標的遺伝子の同定 (2011)
  • Author(s): 馬場崇, 大竹博之, 宮林香奈子, 嶋雄一, 佐藤哲也, 木村宏, 大川恭行, 須山幹太, 諸橋憲一郎
  • Organizer: 第34回日本分子生物学会年会
  • Place of Presentation: パシフィコ横浜
• [Presentation] ChIP-Seqデータを用いた核内受容体共役因子の探索 (2011)
  • Author(s): 佐藤哲也, 須山幹太
  • Organizer: 第34回日本分子生物学会年会
  • Place of Presentation: パシフィコ横浜
• [Presentation] Identification of cis-regulatory elements by using genome alignment and high-throughput data (2009)
  • Author(s): Mikita Suyama
  • Organizer: The 4th Global COE International Symposium 2009 joint with the 19th Hot Spring Harbor Symposium "Molecular Evolution and Bioinformatics"
  • Place of Presentation: 九州大学、福岡
  • Year and Date: 2009-11-02