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

• Project/Area Number: 21200039
• Research Category: Grant-in-Aid for Scientific Research on Innovative Areas (Research a proposed research project)
• Allocation Type: Single-year Grants
• Research Field: Molecular biology; ゲノム情報科学
• Research Institution: University 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
• Project Status: Completed (Fiscal Year 2011)
• Budget Amount: ¥30,940,000 (Direct Cost: ¥23,800,000、Indirect Cost: ¥7,140,000); Fiscal Year 2011: ¥10,010,000 (Direct Cost: ¥7,700,000、Indirect Cost: ¥2,310,000); Fiscal Year 2010: ¥10,010,000 (Direct Cost: ¥7,700,000、Indirect Cost: ¥2,310,000); Fiscal Year 2009: ¥10,920,000 (Direct Cost: ¥8,400,000、Indirect Cost: ¥2,520,000)
• Keywords: RNA / アンチセンスRNA / 低分子RNA / non-coding RNA / NMR / 立体構造 / センス-アンチセンス転写産物 / SAT(センス-アンチセンス転写産物) / non-codin RNA

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

• [Journal Article] An ES cell-differentiation system recapitulates a developmentally regulated neuron-specific parent-of-origin expressivity (2012)
  • 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] Genome-wide impact of endogenous antisense transcripts in eukaryotes (2012)
  • Author(s): Numata K, Kiyosawa H
  • Journal Title: Frontiers in Bioscience Volume: 17 Pages: 300-315
  • Peer Reviewed
• [Journal Article] An ES cell-differentiation system recapitulates a developmentally regulated neuron-specific parent-of-origin expressivity (2012)
  • Author(s): Kohama C, et al
  • Journal Title: Human Molecular Genetics Volume: 21 Pages: 1391-1401
  • Peer Reviewed
• [Journal Article] A new entropy model for RNA : part III, Is the folding free energy landscape of RNA funnel shaped? (2012)
  • Author(s): Dawson W, Takai T, Ito I, Shimizu K, Kawai G
  • Journal Title: Journal of Nucleic Acids Investigation 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 (2012)
  • Author(s): Dawson W, Yamamoto K, Shimizu K, Kawai G
  • Journal Title: Journal of Nucleic Acids Investigation 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 (2012)
  • Author(s): Dawson W, Yamamoto K, Kawai G
  • Journal Title: Journal of Nucleic Acids Investigation Volume: (in press)
  • Peer Reviewed
• [Journal Article] Comprehensive expressional analyses of antisense transcripts in colon cancer tissues using artificial antisense probes (2011)
  • 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: 42-42
  • Peer Reviewed
• [Journal Article] Highly parallel SNP genotyping reveals high-resolution landscape of mono-allelic Ube3a expression associated with locus-wide antisense transcription. (2011)
  • Author(s): Numata K, et al.
  • Journal Title: Nucleic Acids Research Volume: 39 Pages: 2649-2657
  • Peer Reviewed
• [Journal Article] A small nucleolar RNA functions in rRNA processing in C. elegans (2010)
  • 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] 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: 日本生化学会
  • Place of Presentation: 国立京都国際会館(京都府)
  • Year and Date: 2011-09-24
• [Presentation] マウスSAT領域から転写される50-100 nt長のncRNA候補について (2011)
  • Author(s): 牛田千里、河合剛太、清澤秀孔
  • Organizer: 第10回新しいncRNA/RNPを見つける会
  • Place of Presentation: 沖縄
  • Year and Date: 2011-09-16
• [Presentation] Analysis of Small RNAs, with 50-100 nt Length, from the Loci of the Sense-Antisense Transcription in Mouse Genome (2011)
  • 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 loci (2011)
  • 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] Clustering and Structural Analysis of Small RNAs, with 50-100 nt Length, from the Loci of the Sense-Antisense Transcription in Mouse Genome (2011)
  • Author(s): Kawai G, Ushida C, Kiyosawa H
  • Organizer: RNA2011(国際RNA学会)
  • Place of Presentation: 国立京都国際会館(京都府)
• [Presentation] Expression of Small RNAs, with 50-100 nt Length, from the Loci of the Sense-Antisense Transcription in Mouse Genome (2011)
  • Author(s): Ushida C, Ono T, Saito R, Osanai Y, Shindo Y, Kaneko N, Kawai G, Kiyosawa H
  • Organizer: RNA2011(国際RNA学会)
  • Place of Presentation: 国立京都国際会館(京都府)
• [Presentation] NMR試料管内転写によるRNAのNMRスペクトルの測定 (2010)
  • Author(s): 斉藤裕之, その他
  • Organizer: 日本核磁気共鳴学会年会
  • Place of Presentation: 東京
  • Year and Date: 2010-11-17
• [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
  • Publisher: Caister Academic Press
• [Book] Genome-wide analysis of sense-antisense transcripts, in "Non-coding RNAs and Epigenetic Regulation of Gene Expression : Drivers of Natural Selection," (2012)
  • Author(s): Kohama C, Kiyosawa H
  • Publisher: Caister Academic Press, Norwich, U.K.
• [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
  • 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
  • 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
  • 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
  • Publisher: CRC press
• [Remarks]
  • URL: http://www.le.it-chiba.ac.jp/kawai/mouserna/index.html
• [Remarks]
  • URL: http://www.le.it-chiba.ac.jp/kawai/mouserna/index.html
• [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
  • Acquisition Date: 2010-10-08