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2011 Fiscal Year Final Research Report

Multi-disciplinary analysis ob 50-100nt-sized,small RNAs Universally found in mouse cells

Research Project

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Project/Area Number 21200039
Research Category

Grant-in-Aid for Scientific Research on Innovative Areas (Research a proposed research project)

Allocation TypeSingle-year Grants
Research Field Molecular biology
ゲノム情報科学
Research InstitutionUniversity of Tsukuba (2011)
大学共同利用機関法人情報・システム研究機構(新領域融合研究センター、DBCLS) (2010)
The Institute of Physical and Chemical Research (2009)

Principal Investigator

KIYOSAWA Hidenori  筑波大学, 体育系, 研究員 (30295422)

Co-Investigator(Kenkyū-buntansha) KAWAI Gota  千葉工業大学, 工学部, 教授 (70211860)
USHIDA Chisato  弘前大学, 農学生命科学部, 准教授 (50250593)
Project Period (FY) 2009 – 2011
KeywordsRNA
Research Abstract

We performed genome-wide analysis of novel-sized (50-100nt) small RNAs that is originally discovered in the gene loci producing endogenous antisense RNA, based on the custom-made microarrays. The expression validation was analyzed by Northern hybridization. We developed a structural screening method by the in NMR tube transcription for the structural analysis of small RNA. We also performed a trial expression analysis of small RNAs using the next generation sequencers and structural clustering of the RNA sequences.

  • Research Products

    (20 results)

All 2012 2011 2010 2009 Other

All Journal Article (8 results) (of which Peer Reviewed: 8 results) Presentation (4 results) Book (6 results) Remarks (1 results) Patent(Industrial Property Rights) (1 results)

  • [Journal Article] An ES cell-differentiation system recapitulates a developmentally regulated neuron-specific parent-of-origin expressivity2012

    • Author(s)
      Kohama C, Kato H, Numata K, Hirose M,Og ura A, and Kiyosawa H
    • Journal Title

      Hum. Mol. Genet.

      Volume: 21 Pages: 1391-1401

    • Peer Reviewed
  • [Journal Article] Comprehensive expressional analyses of antisense transcripts in colon cancer tissues using artificial antisense probes2011

    • Author(s)
      Saito R, Kohno K, Okada Y, Osada Y, Numata K, Kohama C, Watanabe K, Nakaoka H, Yamamoto N, Kanai A, Yasue H, Murata S, Abe K, Tomita M, Ohkohchi N, and Kiyosawa H
    • Journal Title

      BMC Medical Genomics

      Volume: 4 Pages: 42

    • Peer Reviewed
  • [Journal Article] A small nucleolar RNA functions in rRNA processing in C. elegans2010

    • Author(s)
      Hokii Y, Sasano Y, Sato M, Sakamoto H, Sakata K, Shingai R, Taneda A, Oka S, Himeno H, Muto A, Fujiwara T, and Ushida C
    • Journal Title

      Nucleic Acids Res.

      Volume: 38 Pages: 5909-5918

    • Peer Reviewed
  • [Journal Article] A new entropy model for RNA : part V, Incorporating the Flory-Huggins model in structure prediction and folding

    • Author(s)
      Dawson W and Kawai G
    • Journal Title

      J. Nucleic Acids Invest.

      Volume: (in press)

    • Peer Reviewed
  • [Journal Article] new entropy model for RNA : part IV, The minimum free energy and the thermodynamically most-probable folding pathway

    • Author(s)
      Dawson W and Kawai G
    • Journal Title

      J. Nucleic Acids Invest.

      Volume: (in press)

    • Peer Reviewed
  • [Journal Article] A new entropy model for RNA : part III, Is the folding free energy landscape of RNA funnel shaped?

    • Author(s)
      Dawson W, Takai T, Ito I, Shimizu K, and Kawai G
    • Journal Title

      J. Nucleic Acids Invest.

      Volume: (in press)

    • Peer Reviewed
  • [Journal Article] A new entropy model for RNA : part II, persistence-related entropic contributions to RNA secondary structure free energy calculation

    • Author(s)
      Dawson W, Yamamot K, Shimizu K, and Kawai G
    • Journal Title

      J. Nucleic Acids Invest.

      Volume: (in press)

    • Peer Reviewed
  • [Journal Article] A new Entropy model for RNA : part I, a critique of the standard Jacobson-Stockmayer model applied to multiple cross links

    • Author(s)
      Dawson W,Yamamoto k,and Kawai G
    • Journal Title

      J.Nucleic Acids Invest.

      Volume: (in press)

    • Peer Reviewed
  • [Presentation] マウスSAT領域から発現する50-100残基RNAのクラスタリングと構造解析2011

    • Author(s)
      河合剛太、牛田千里、清澤秀孔
    • Organizer
      第84回日本生化学会大会
    • Place of Presentation
      国立京都国際会館(京都府)
    • Year and Date
      2011-09-24
  • [Presentation] Analysis of Small RNAs, with 50-100 nt Length, from the Loci of the Sense-Antisense Transcription in Mouse Genome2011

    • Author(s)
      Kawai G, Ushida C, and Kiyosawa H
    • Organizer
      The 16th Annual Meeting of The RNA Society
    • Place of Presentation
      Kyoto International Conference Center (Kyoto)
    • Year and Date
      2011-06-15
  • [Presentation] Expression of small RNAs from mouse SAT loci2011

    • Author(s)
      Ushida C, Ono T, Saito R, Osada Y, Shindo Y, Kaneko N, Kawai G, and Kiyosawa H
    • Organizer
      The 16th Annual Meeting of The RNA Society
    • Place of Presentation
      Kyoto International Conference Center (Kyoto)
    • Year and Date
      2011-06-15
  • [Presentation] NMR試験管内転写によるRNAのNMRスペクトルの測定2010

    • Author(s)
      斎藤裕之、伊谷野悠里、牛田千里、清澤秀孔、河合剛太
    • Organizer
      第49回NMR討論会
    • Place of Presentation
      タワーホール船堀(東京都)
    • Year and Date
      2010-11-15
  • [Book] Genome-wide analysis of sense-antisense transcripts, in "Non-coding RNAs and Epigenetic Regulation of Gene Expression : Drivers of Natural Selection," Morris KV (ed.),2012

    • Author(s)
      Kohama C and Kiyosawa H
    • Total Pages
      3-29
    • Publisher
      Caister Academic Press
  • [Book] 機能性RNAの分子生物学2010

    • Author(s)
      河合剛太、清澤秀孔編
    • Total Pages
      287
    • Publisher
      クバプロ
  • [Book] 機能性RNAの分子生物学」、第I章2010

    • Author(s)
      牛田千里、他
    • Total Pages
      23-24
    • Publisher
      クバプロ
  • [Book] 「機能性RNAの分子生物学」、第III章2010

    • Author(s)
      牛田千里、他
    • Total Pages
      79-109
    • Publisher
      クバプロ
  • [Book] 「機能性RNAの分子生物学」、第IV章2010

    • Author(s)
      牛田千里、他
    • Total Pages
      111-150
    • Publisher
      クバプロ
  • [Book] Isolation and characterization of small RNAs in Caenorhabditis elegans. In "Regulation of Gene Expression by Small RNAs," Rossi J and Gaur RK (ed.)2009

    • Author(s)
      Ushida C and Hokii Y
    • Total Pages
      101-121
    • Publisher
      CRC press
  • [Remarks]

    • URL

      http://www.le.it-chiba.ac.jp/kawai/mouserna/index.html

  • [Patent(Industrial Property Rights)] 低分子RNAの分析方法2010

    • Inventor(s)
      牛田千里
    • Industrial Property Rights Holder
      青森県弘前市文京町1番地国立大学法人弘前大学
    • Industrial Property Number
      特許第4599555号
    • Acquisition Date
      2010-10-08

URL: 

Published: 2013-07-31  

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