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

• 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
• Project Status: Completed (Fiscal Year 2011)
• Budget Amount: ¥16,770,000 (Direct Cost: ¥12,900,000、Indirect Cost: ¥3,870,000); Fiscal Year 2011: ¥4,290,000 (Direct Cost: ¥3,300,000、Indirect Cost: ¥990,000); Fiscal Year 2010: ¥4,290,000 (Direct Cost: ¥3,300,000、Indirect Cost: ¥990,000); Fiscal Year 2009: ¥8,190,000 (Direct Cost: ¥6,300,000、Indirect Cost: ¥1,890,000)
• 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 / miRNA / 遺伝子発現 / 魚類 / 発現フロフィール / 新規RNA

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

• [Journal Article] メダカを用いたヒト疾患モデル (2012)
  • Author(s): 清水厚志
  • Journal Title: 比較内分泌学 Volume: 36(139) Pages: 286-292
  • NAID: 10027129728
• [Journal Article] Correlation with larval body size of mRNA levels of growth hormone, growth hormone receptor I and insulin-like growth factor I in larval torafugu Takifugu rubripes (2011)
  • Author(s): Kaneko G, Furukawa S, Kurosu Y, Yamada T, Takeshima H, Nishida M, Mitsuboshi T, Otaka T, Shirasu K, Koda T, Takemasa Y, Aki S, Mochizuki T, Fukushima H, Fukuda Y, Kinoshita S, Asakawa S, Watabe S
  • Journal Title: J. Fish Biol. Volume: 79 Issue: 4 Pages: 854-874
  • DOI: 10.1111/j.1095-8649.2011.03037.x
  • Peer Reviewed
• [Journal Article] Multiple cis-elements in the 5'-flanking region of embryonic/larval fast-type of the myosin heavy chain gene of torafugu, MYH(M743-2), function in the transcriptional regulation of its expression (2011)
  • Author(s): Asaduzzaman M
  • Journal Title: Gene. Volume: 489 Pages: 41-54
  • Peer Reviewed
• [Presentation] Comprehensive analysis of small RNAs in Oryzias latipes and Takifugu rubripes (2012)
  • Author(s): チャニンヤーウォンワランカナ
  • Organizer: 平成24年度日本水産学会春季大会
  • Place of Presentation: 東京海洋大学
  • Year and Date: 2012-03-28
• [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
• [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
• [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
• [Presentation] Comprehensive analysis of small RNA in Takifugu rubripes", Sixteenth Annual Meeting of the RNA Society (2011)
  • Author(s): C.Wongwarangkana
  • Organizer: Sixteenth Annual Meeting of the RNA Society
  • Place of Presentation: Kyoto
  • Year and Date: 2011-06-17
• [Presentation] Expression profile of microRNA in Takifugu rubripes (2011)
  • Author(s): チャニンヤーウォンワランカナ
  • Organizer: 平成23年度日本水産学会春季大会
  • Place of Presentation: 東京海洋大学
  • Year and Date: 2011-03-28
• [Presentation] Comprehensive analysis of small RNAs in Takifugu rubripes (2011)
  • Organizer: 平成23年度日本水産学会春季大会
  • Place of Presentation: 東京海洋大学
  • Year and Date: 2011-03-28
• [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
• [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
• [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
• [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
• [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
• [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
• [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
• [Presentation] High throughput sequencing of the Takifugu rubripes and the Oryzias latipes small RNAs (2010)
  • Author(s): 浅川修一
  • Organizer: 第33回日本分子生物学会年会
  • Place of Presentation: 神戸国際会議場
  • Year and Date: 2010-12-09
• [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
  • Organizer: 平成22年度日本水産学会秋季大会
  • Place of Presentation: 京都大学吉田キャンパス
  • Year and Date: 2010-09-24
• [Presentation] 次世代シーケンサの種類、機能、用途 (2010)
  • Author(s): 浅川修一
  • Organizer: 第13回マリンバイオテクノロジー学会大会
  • Place of Presentation: 広島大学東広島キャンパス
  • Year and Date: 2010-05-30
• [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
  • Organizer: 日本水産学会
  • Place of Presentation: 藤沢
  • Year and Date: 2010-03-27
• [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
• [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
• [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
• [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
• [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
• [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の発現解析 (2009)
  • Author(s): 浅川修一
  • Organizer: 日本分子生物学会
  • Place of Presentation: 横浜
  • Year and Date: 2009-12-09
• [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