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Bioinformatics analysis reveals a putative scenario for de novo origination of genes

Research Project

Project/Area Number 25640112
Research Category

Grant-in-Aid for Challenging Exploratory Research

Allocation TypeMulti-year Fund
Research Field System genome science
Research InstitutionKyushu Institute of Technology

Principal Investigator

Yada Tetsushi  九州工業大学, 大学院情報工学研究院, 教授 (10322728)

Project Period (FY) 2013-04-01 – 2016-03-31
Project Status Completed (Fiscal Year 2015)
Budget Amount *help
¥3,900,000 (Direct Cost: ¥3,000,000、Indirect Cost: ¥900,000)
Fiscal Year 2015: ¥1,170,000 (Direct Cost: ¥900,000、Indirect Cost: ¥270,000)
Fiscal Year 2014: ¥1,170,000 (Direct Cost: ¥900,000、Indirect Cost: ¥270,000)
Fiscal Year 2013: ¥1,560,000 (Direct Cost: ¥1,200,000、Indirect Cost: ¥360,000)
Keywords遺伝子進化 / de novo誕生 / 分子進化 / 比較ゲノム / バイオインフォマティクス / 遺伝子
Outline of Final Research Achievements

Recent advances in genome research clearly show that many genes originate de novo from non-genic DNA sequences. However, little is known about scenarios of the origination. We have sketched here a putative scenario of how genes arose from non-genic sequences by applying bioinformatics analysis to Saccharomyces cerevisiae genome. That is, we have reconstructed the homologous ancestral DNA sequences before and after de novo gene origination and have observed changes between the two sequences. A putative scenario which we have successfully sketched is as follows. (1)In the beginning was GC-rich genome region. (2)Neutral mutations were accumulated in the region. (3)ORFs were extended/combined, and then (4)translation signature (Kozak sequence) was recruited.

Report

(4 results)
  • 2015 Annual Research Report   Final Research Report ( PDF )
  • 2014 Research-status Report
  • 2013 Research-status Report
  • Research Products

    (12 results)

All 2016 2015 2014 2013 Other

All Journal Article (2 results) (of which Peer Reviewed: 2 results,  Open Access: 1 results) Presentation (10 results) (of which Int'l Joint Research: 1 results,  Invited: 4 results)

  • [Journal Article] Long Noncoding RNA NEAT1-Dependent SFPQ Relocation from Promoter Region to Paraspeckle Mediates IL8 Expression upon Immune Stimuli2014

    • Author(s)
      Imamura K, Imamachi N, Akizuki G, Kumakura M, Kawaguchi A, Nagata K, Kato A, Kawaguchi Y, Sato H, Yoneda M, Kai C, Yada T, Suzuki Y, Yamada T, Ozawa T, Kaneki K, Inoue T, Kobayashi M, Kodama T, Wada Y, Sekimizu K and Akimitsu N.
    • Journal Title

      Molecular cell

      Volume: 53 Issue: 3 Pages: 393

    • DOI

      10.1016/j.molcel.2014.01.009

    • Related Report
      2013 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Tetrahedral gray code for visualization of genome information2014

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

      PLoS One

      Volume: 9(1) Issue: 1 Pages: e86133-e86133

    • DOI

      10.1371/journal.pone.0086133

    • Related Report
      2013 Research-status Report
    • Peer Reviewed
  • [Presentation] A putative scenario for de novo gene birth in Saccharomyces cerevisiae genome2016

    • Author(s)
      Tetsushi Yada
    • Organizer
      BIT2016
    • Place of Presentation
      National Yang-Ming University, Taiwan
    • Year and Date
      2016-03-03
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Observing de novo gene birth through reconstruction of ancestral DNA sequences2015

    • Author(s)
      Tetsushi Yada, Takeaki Taniguchi
    • Organizer
      生命医薬情報学連合大会2015年大会(日本バイオインフォマティクス学会2015年年会)
    • Place of Presentation
      京都大学宇治キャンパス
    • Year and Date
      2015-10-29
    • Related Report
      2015 Annual Research Report
  • [Presentation] Deciphering Regulatory Code Underlying Promoter Sequences2014

    • Author(s)
      Yada T
    • Organizer
      The 2nd BMIRC International Symposium on Advances in Bioinformatics and Medical Engineering
    • Place of Presentation
      Center of Iizuka Research and Development, Fukuoka
    • Related Report
      2013 Research-status Report
  • [Presentation] 転写因子の結合と転写の関係を明らかにする試み2014

    • Author(s)
      矢田哲士
    • Organizer
      新学術領域研究「転写サイクル」第2回トレーニングワークショップ
    • Place of Presentation
      九州工業大学, 福岡
    • Related Report
      2013 Research-status Report
    • Invited
  • [Presentation] Identifying Mutations Bringing de novo Gene Birth to Saccharomyces sensu stricto Genomes2013

    • Author(s)
      Zhang W, Ichinose N, Kumada T, Yada T
    • 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
    • Related Report
      2013 Research-status Report
  • [Presentation] Methylation Structure of Honey Bee Genome2013

    • Author(s)
      Ichinose N, Yada T, Gotoh O
    • 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
    • Related Report
      2013 Research-status Report
  • [Presentation] Motif identification based on the idea of Gibbs Sampling and Genetic Algorithm2013

    • Author(s)
      Zheng P, Ichinose N, Kumada T, Yada T
    • 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
    • Related Report
      2013 Research-status Report
  • [Presentation] Deciphering Regulatory Code from Transcription Activity Data of Mutagenesis Promoters2013

    • Author(s)
      Liu Y, Irie T, Suzuki Y, Ichinose N, Kumada T, Yada T
    • 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
    • Related Report
      2013 Research-status Report
  • [Presentation] 転写制御コードの多様性に挑む2013

    • Author(s)
      矢田哲士
    • Organizer
      ゲノム多様性のデータ利用
    • Place of Presentation
      統計数理研究所, 東京
    • Related Report
      2013 Research-status Report
    • Invited
  • [Presentation] プロモーター配列の合理的な設計に挑む

    • Author(s)
      矢田哲士
    • Organizer
      情報処理学会第37回バイオ情報学研究会
    • Place of Presentation
      九州工業大学, 福岡
    • Related Report
      2013 Research-status Report
    • Invited

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Published: 2014-07-25   Modified: 2019-07-29  

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