Comprehensive finding of small RNAs encoded in a Ciona genome

2010 Fiscal Year Final Research Report

• Project/Area Number: 20310115
• Research Category: Grant-in-Aid for Scientific Research (B)
• Allocation Type: Single-year Grants
• Section: 一般
• Research Field: 基礎ゲノム科学
• Research Institution: The University of Tokyo
• Principal Investigator: NAKAI Kenta The University of Tokyo, 医科学研究所, 教授 (60217643)
• Co-Investigator(Kenkyū-buntansha): KUSAKABE Takehiro 甲南大学, 理工学部, 教授 (40280862) ; INOUE Kunio 神戸大学, 大学院・理学研究科, 教授 (40252415)
• Co-Investigator(Renkei-kenkyūsha): SUZUKI Yutaka 東京大学, 大学院・新領域創成科学研究科, 准教授 (40323646) ; 岡村 浩司 お茶の水女子大学, 生命報学教育研究センター, 特任講師 (80456194)
• Project Period (FY): 2008 – 2010
• Keywords: ゲノム解析 / 組織特異的発現 / カタユウレイボヤ / メダカ / miRNA / Piwi / 進化的保存

Research Abstract

In recent years, it has been clarified that small RNAs, like miRNAs, play important roles in a wide range of cellular activities. In this study, taking the advantage of our collaborative experience in the analysis of transcriptional regulation in Ciona intestinalis, a model organism of vertebrates, we predicted a comprehensive set of miRNAs encoded in the Ciona genome. Then, a list of novel candidate genes were obtained with a reliability measure. For some genes showing interesting expression pattern, their evolutionary divergence/conservation was clarified through more detailed characterization.

Research Products

• [Journal Article] Ependymal cells of chordate larvae arestem-like cells that form the adultnervous system. (2011)
  • Author(s): Takeo Horie, Ryoko Shinki, YosukeOgura, Takehiro G.Kusakabe, NoriSatoh, Yasunori Sasakura
  • Journal Title: Nature 469(7331) Pages: 525-528
• [Journal Article] Cross-validated methods forpromoter/transcription start sitemapping in SL trans-spliced genes,established using the Ciona intestinalistroponin I gene (2011)
  • Author(s): P.Khare, S.I.Mortimer, C.L.Cleto, K.Okamura, Y.Suzuki, T.Kusakabe, K.Nakai, T.H.Meedel, K.E.M.Hastings
  • Journal Title: Nucleic Acids Res 39(7) Pages: 2638-2648
• [Journal Article] Genomic organization and embryonicexpression of miR-430 in medaka(Oryzias latipes): insights into thepost-transcriptional gene regulation in early development. (2010)
  • Author(s): Tani, S., Kusakabe, R., Naruse, K., Sakamoto, H., Inoue, K.
  • Journal Title: Gene 449 Pages: 41-49
• [Journal Article] The ANISEED database : Digitalrepresentation, formalization, and elucidation of a chordate developmentalprogram (2010)
  • Author(s): Olivier Tassy, Delphine Dauga, FabriceDaian, Daniel Sobral, Francois Robin, Pierre Khoueiry, David Salgado, Vanessa Fox, Daniele Caillol, RenaudSchiappa, Baptiste Laporte, Anne Rios, Guillaume Luxardi, Takehiro Kusakabe, Jean-Stephane Joly, Sebastien Darras, Lionel Christiaen, Magali Contensin, Helene Auger, Clement Lamy, ClareHudson, Ute Rothbacher, Michael J.Gilchrist, Kazuhiro W.Makabe, KohjiHotta, Shigeki Fujiwara, Nori Satoh, Yutaka Satou, Patrick Lemaire
  • Journal Title: Genome Res. 20(10) Pages: 1459-1468
• [Journal Article] Gradual transitionfrom mosaic to global DNA methylationpatterns during deuterostome evolution (2010)
  • Author(s): Kohji Okamura, Kazuaki A.Matsumoto, Kenta Nakai
  • Journal Title: BMC Bioinformatics 11(Suppl7) Pages: S2
• [Journal Article] DAZL relievesmiRNA-mediated repression ofgermline mRNAs by controlling poly(A)tail length in zebrafish. (2009)
  • Author(s): Takeda, Y., Mishima, Y., Fujiwara, T.,Sakamoto, H., Inoue,K.
  • Journal Title: PLoS ONE 4 e7513(7)
• [Journal Article] A useful approachto total analysis of RISC-associatedRNA. (2009)
  • Author(s): Hayashida, Y., Nishibu, T., Inoue, K., Kurokawa, T.
  • Journal Title: BMC Research Notes 2 Pages: 169
• [Presentation] Sequence analyses ofgenetic and epigenetic information fortranscriptional regulation (2011)
  • Author(s): 中井謙太
  • Organizer: The 9th AsiaPacific Bioinformatics Conference(APBC2011)
  • Place of Presentation: 仁川、韓国(keynote speech)
  • Year and Date: 20110111-20110114
• [Presentation] Gene expression and possible rolesof protein families involved inbiogenesis and functions of small RNAsin the nervous system of the ascidianCiona intestinalis(SW2-04; P-094) (2010)
  • Author(s): 一瀬葵、宮本由紀、寺嶋泰子、島井光太郎、西辻光希、白江-倉林麻貴、中村輝、日下部りえ、中井謙太、井上邦夫、日下部岳広
  • Organizer: 日本発生生物学会第43回大会
  • Place of Presentation: 国立京都国際会館(ポスター)、芝蘭会館(サテライトワークショップ)
  • Year and Date: 20100620-20100623
• [Presentation] Gene expression patterns andpossible developmental roles of proteinfamilies involved in biogenesis and functions of small noncoding RNAs inCiona intestinalis (2010)
  • Author(s): T.Kusakabe, A.Ichinose, Y.Miyamoto, Y.Terashima, K.Shimai, K.Nishitsuji, M.Shiraekurabayashi, A.Nakamura, R.Kusakabe, K.Nakai, K.Inoue
  • Organizer: 2nd Joint Meeting OfThe SFBD and JSDB 2010-From Cellsto Organs
  • Place of Presentation: InstitutPasteur-Paris (France)
  • Year and Date: 20100526-20100528
• [Presentation] メダカ錐体オプシン遺伝子と転写調節領域を共有するmiRNA遺伝子(1E1345) (2010)
  • Author(s): 大道裕, 日下部岳広
  • Organizer: 日本動物学会第81回東京大会
  • Place of Presentation: 東京大学教養学部(駒場キャンパス)(口演発表)
  • Year and Date: 2010-09-23
• [Presentation] カタユウレイボヤ脳胞におけるpiwiの新奇機能の解析(1H1700) (2010)
  • Author(s): 島井光太郎, 一瀬葵, 宮本由紀, 寺島泰子, 西辻光希, 白江-倉林麻貴, 中村輝, 日下部りえ, 中井謙太, 井上邦夫, 日下部岳広
  • Organizer: 日本動物学会第81回東京大会
  • Place of Presentation: 東京大学教養学部(駒場キャンパス)(口演発表)
  • Year and Date: 2010-09-23
• [Presentation] Control ofgermline/somatic cell distinction bymiRNA function in zebrafish (2010)
  • Author(s): 井上邦夫
  • Organizer: A satellitesymposium on Germ Cells in SDB-JSDB Joint Meeting 2010
  • Place of Presentation: New Mexico,USA
  • Year and Date: 2010-08-05