Comprehensive and functional analysis of Medaka small RNAs using next generation sequencer

2011 Fiscal Year Final Research Report

• Project/Area Number: 21310125
• 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: ASAKAWA Shuichi 東京大学, 大学院・農学生命科学研究科, 教授 (30231872)
• Co-Investigator(Kenkyū-buntansha): FUJIMORI Kazuhiro (独)産業技術総合研究所, 研究員 (60273025) ; SHIMIZU Atsushi 慶應義塾大学, 医学部, 助教 (30327655)
• Co-Investigator(Renkei-kenkyūsha): SAKAI Kosuke 慶應義塾大学, 医学部, 助教 (70245463) ; MITSUYAMA Susumu 慶應義塾大学, 医学部, 助教 (30296727) ; KOJIMA SABINE Kazuko 慶應義塾大学, 医学部, 研究員 (10445439)
• Project Period (FY): 2009 – 2011
• Keywords: 動物ゲノム / メダカ / トラフグ / 次世代シーケンサー / 小分子RNA / マイクロRNA / piRNA / トランスクリプトーム

Research Abstract

In this study, we analyzed the sequences of small RNAs(miRNA, piRNA, siRNA) extracted form tissues(Fast muscle, slow muscle, intestine, eye, brain, liver, ovary, testis, and embryos) of medaka(Oryzias latipes) and torafugu(Takifugu rubripes), and showed the expression profiles of the RNAs. In the tissues except for ovary and testis, the major species of expression were miRNAs, whereas in the ovary and testis, those were assumed to be piRNAs. There were found many unknown RNA species that were commonly expressed in medaka and torafugu

Research Products

• [Presentation] Comprehensive analysis of small RNA in Takifugu rubripes and Oryzias latipes (2012)
  • Author(s): C. Wongwarangkana, M. Akiba, R. Terai, K. Negoro, K. E. Fujimori, S. Kinoshita, A. Shimizu, K. Sakai, S. K. Kojima, S. Mitsuyama, I. Kikuzato, M. Teruya, M. Nezuo, S. Yano, Y. Miwa, Y. Imada, Y. Sato, T. Masatoshi, J. Kudoh, T. Hirano N. Shimizu, S. Watab
  • Organizer: Seventeenth Annual Meeting of the RNA Society
  • Place of Presentation: Michigan, USA
  • Year and Date: 20120600
• [Presentation] Function of intronic miRNA of myosin heavy chain gene, MYH14, in fish muscle formation (2012)
  • Author(s): Bhuyian, S. S., Kinoshita, S., Ceyhun, S., Asaduzzaman, Md., Asakawa, S., Watabe, S.
  • Organizer: 平成24年度日本水産学会春季大会
  • Place of Presentation: 東京
  • Year and Date: 20120326-30
• [Presentation] Comprehensive analysis of small RNAs in Oryzias latipes and Takifugu rubripes (2012)
  • Author(s): C. Wongwarangkana, M. Akiba, R. Terai, K. Negoro, K. E. Fujimori, S. Kinoshita, A. Shimizu, K. Sakai, S. K. Kojima, S. Mitsuyama, I. Kikuzato, M. Teruya, M. Nezuo, S. Yano, Y. Miwa, Y. Imada, Y. Sato, T. Masatoshi, J. Kudoh, T. Hirano N. Shimizu, S. Watab
  • Organizer: The Japanese Society of Fisheries Science Spring meeting 2012
  • Place of Presentation: Tokyo University of Marine Sciences and Technology
  • Year and Date: 20120300
• [Presentation] Regulation of myosin heavy chain gene expression and muscle development in teleosts (2011)
  • Author(s): Kinoshita, S., Bhuyian, S. S., Ceyhun, S. B., Asaduzzaman, Md., Asakawa, S., Watabe, S.
  • Organizer: The International Symposium on Muscle Biochemistry
  • Place of Presentation: Tokyo
  • Year and Date: 20111027-29
• [Presentation] Different expression patterns of the myosin heavy chain gene, MYH14, including its intronic miRNA among a few model fish species (2011)
  • Author(s): Bhuyian, S. S., Kinoshita, S., Ceyhun, S., Asaduzzaman, Md., Asakawa, S., Watabe, S.
  • Organizer: The International Symposium on Muscle Biochemistry
  • Place of Presentation: Tokyo
  • Year and Date: 20111027-29
• [Presentation] Sequencing and Function Analysis of Takifugu rubripes Small RNA (2011)
  • Author(s): C. Wongwarangkana, M. Akiba, R. Terai, K. Negoro, K. E. Fujimori, S. Kinoshita, A. Shimizu, K. Sakai, S. K. Kojima, S. Mitsuyama, I. Kikuzato, M. Teruya, M. Nezuo, S. Yano, Y. Miwa, Y. Imada, Y. Sato, T. Masatoshi, J. Kudoh, T. Hirano N. Shimizu, S. Watab
  • Organizer: The international symposium of muscle biochemistry
  • Place of Presentation: The University of Tokyo
  • Year and Date: 20111000
• [Presentation] Differential expression of the myosin heavy chain gene, MYH14, and its intronic miRNA among fish species (2011)
  • Author(s): Bhuyian, S. S., Kinoshita, S., Ceyhun, S., Asaduzzaman, Md., Asakawa, S., Watabe, S.
  • Organizer: 平成23年度日本水産学会秋季大会
  • Place of Presentation: 長崎
  • Year and Date: 20110928-1002
• [Presentation] Comprehensive analysis of small RNA in Takifugu rubripes (2011)
  • Author(s): C. Wongwarangkana, M. Akiba, R. Terai, K. Negoro, K. E. Fujimori, S. Kinoshita, A. Shimizu, K. Sakai, S. K. Kojima, S. Mitsuyama, I. Kikuzato, M. Teruya, M. Nezuo, S. Yano, Y. Miwa, Y. Imada, Y. Sato, T. Masatoshi, J. Kudoh, T. Hirano N. Shimizu, S. Watabe, S. Asakawa
  • Organizer: Sixteenth Annual Meeting of the RNA Society
  • Place of Presentation: Kyoto, Japan
  • Year and Date: 20110600
• [Presentation] Expression Profile of micro RNAs in Takifugu rubripes (2011)
  • Author(s): チャニンヤーウォンワランカナ・寺井良太・根来庫介・秋葉正毅・小野陽介、藤森一浩、木下滋晴、清水厚志・堺弘介・小島サビヌ和子・満山進、喜久里育也・佐藤友紀、照屋盛実、鼠尾まい子・矢野修一・三輪友希乃・今田有美・塚原正俊、工藤純、平野隆、清水信義、渡部終五、浅川修一
  • Organizer: The Japanese Society of Fisheries Science Spring meeting 2011
  • Place of Presentation: Tokyo University of Marine Sciences and Technology
  • Year and Date: 20110300
• [Presentation] Comprehensive analysis of small RNAs in Takifugu rubripes (2011)
  • Author(s): 浅川修一・チャニンヤーウォンワランカナ・寺井良太・根来庫介・秋葉正毅・小野陽介、藤森一浩、木下滋晴、清水厚志・堺弘介・小島サビヌ和子・満山進、喜久里育也・佐藤友紀、照屋盛実、鼠尾まい子・矢野修一・三輪友希乃・今田有美・塚原正俊、工藤純、平野隆、清水信義、渡部終五
  • Organizer: The Japanese Society of Fisheries Science Spring meeting 2011
  • Place of Presentation: Tokyo University of Marine Sciences and Technology
  • Year and Date: 20110300
• [Presentation] Sequencing and functional analysis of Takifugu rubripes and Oryzias latipes small RNA (2010)
  • Author(s): C. Wongwarangkana, M. Akiba, R. Terai, K. Negoro, K. E. Fujimori, S. Kinoshita, A. Shimizu, K. Sakai, S. K. Kojima, S. Mitsuyama, I. Kikuzato, M. Teruya, M. Nezuo, S. Yano, Y. Miwa, Y. Imada, Y. Sato, T. Masatoshi, J. Kudoh, T. Hirano, N. Shimizu, S. Watabe, S. Asakawa
  • Organizer: The 4th Asian Young Researchers Conference on Computational and Omics Biology, Matrix Biopolis
  • Place of Presentation: Singapore
  • Year and Date: 20101200
• [Presentation] 次世代シーケンサーを用いたメダカ・トラフグ小分子RNAのシーケンシング (2010)
  • Author(s): 浅川修一・チャニンヤーウォンワランカナ・寺井良太・根来庫介・秋葉正毅・小野陽介、藤森一浩、木下滋晴、清水厚志・堺弘介・小島サビヌ和子・満山進、喜久里育也・佐藤友紀、照屋盛実、鼠尾まい子・矢野修一・三輪友希乃・今田有美・塚原正俊、工藤純、平野隆、清水信義、渡部終五
  • Organizer: The Japanese Society of Fisheries Science Autumn meeting 2010
  • Place of Presentation: Kyoto University
  • Year and Date: 20100900
• [Presentation] Sequencing and functional analysis of Takifugu rubripes and Oryzias latipes small RNA (2010)
  • Author(s): C. Wongwarangkana, M. Akiba, K. E. Fujimori, S. Kinoshita, A. Shimizu, K. Sakai, S. K. Kojima, S. Mitsuyama, I. Kikuzato, Y. Sato, K. Teruya, A. Shiroma, M. Teruya, M. Nezuo, S. Yano, Y. Miwa, Y. Imada, M. Tsukahara, J. Kudoh, T. Hirano, N. Shimizu, S. Watabe, S. Asakawa
  • Organizer: International Symposium on Biodiversity Sciences
  • Place of Presentation: Nagoya, Japan
  • Year and Date: 20100700
• [Presentation] Deep sequencing and profiling of micro RNAs in torafugu and medaka, The Japanese Society of Fisheries Science Spring meeting 2010 (2010)
  • Author(s): チャニンヤーウォンワランカナ・秋葉正毅、藤森一浩、木下滋晴、清水厚志・堺弘介・小島サビヌ和子・満山進、喜久里育也・佐藤友紀、照屋盛実、鼠尾まい子・矢野修一・三輪友希乃・今田有美・塚原正俊、工藤純、平野隆、清水信義、渡部終五・浅川修一
  • Organizer: College of Bioresource Sciences
  • Place of Presentation: Nihon University
  • Year and Date: 20100300
• [Presentation] メダカ・トラフグ小分子RNAの解析, The Japanese Society of Fisheries Science Spring meeting 2010 (2010)
  • Author(s): 浅川修一・チャニンヤーウォンワランカナ・秋葉正毅、藤森一浩、木下滋晴、清水厚志・堺弘介・小島サビヌ和子・満山進、喜久里育也・佐藤友紀、照屋盛実、鼠尾まい子・矢野修一・三輪友希乃・今田有美・塚原正俊、工藤純、平野隆、清水信義、渡部終五・浅川修一
  • Organizer: College of Bioresource Sciences
  • Place of Presentation: Nihon University
  • Year and Date: 20100300
• [Remarks]
  • URL: http://133.11.222.76/
• [Remarks] データーサーバー
  • URL: http://133.11.222.76/blast/blast.html