Deciphering Splicing Codes for Proteome Diversity.

2013 Fiscal Year Final Research Report

• Project Area: Diversity and asymmetry achieved by RNA program
• Project/Area Number: 20112004
• Research Category: Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)
• Allocation Type: Single-year Grants
• Review Section: Biological Sciences
• Research Institution: Tokyo Medical and Dental University
• Principal Investigator: KUROYANAGI Hidehito 東京医科歯科大学, 難治疾患研究所, 准教授 (30323702)
• Project Period (FY): 2008-11-13 – 2013-03-31
• Keywords: mRNA前駆体 / 選択的スプライシング / 線虫 / 蛍光レポーター / シスエレメント / 大規模シーケンシング / 組織特異性

Research Abstract

Alternative processing of precursor messenger RNAs (pre-mRNAs) is a major source of protein diversity and plays crucial roles in development, differentiation and diseases in higher eukaryotes. We have been utilizing multi-chromatic fluorescence alternative processing reporter system to visualize tissue-specific and/or developmental alternative processing patterns in living worms and isolated mutants defective in alternative processing regulation. Here we performed transcriptome analysis of the mutant worms, identified many novel target events for the regulators, analyzed their expression patterns in vivo and predicted and experimentally identified cis-elements for the regulators to reveal the "splicing code" in living organisms.

Research Products

• [Journal Article] Comprehensive analysis of mutually exclusive alternative splicing in C. elegans (2014)
  • Author(s): Kuroyanagi H, Takei S, Suzuki Y
  • Journal Title: Worm Volume: 3 Pages: e28459
  • Peer Reviewed
• [Journal Article] New Technology 選択的スプライシング可視化システム (2013)
  • Author(s): 木村まり子、黒柳秀人
  • Journal Title: Medical Science Digest Volume: 39 Pages: 502-503
• [Journal Article] Switch-like regulation of tissue-specific alternative pre-mRNA processing patterns revealed by customized fluorescence reporters (2013)
  • Author(s): Hidehito Kuroyanagi
  • Journal Title: Worm Volume: 2 Pages: e23834
  • DOI: 10.4161/worm.23834
  • Peer Reviewed
• [Journal Article] CELF family RNA-binding protein UNC-75 regulates two sets of mutually exclusive exons of the unc-32 gene in neuron-specific manners in Caenorhabditis elegans (2013)
  • Author(s): Kuroyanagi H, Watanabe Y, Hagiwara M
  • Journal Title: PLoS Genetics Volume: 9 Pages: e1003337
  • DOI: 10.1371/journal.pgen.1003337
  • Peer Reviewed
• [Journal Article] Position-dependent and neuron-specific splicing regulation by the CELF family RNA-binding protein UNC-75 in Caenorhabditis elegans (2013)
  • Author(s): Kuroyanagi H, Watanabe Y, Suzuki Y, Hagiwara M
  • Journal Title: Nucleic Acids Research Volume: 41 Pages: 4015-4025
  • DOI: 10.1093/nar/gkt097
  • Peer Reviewed
• [Journal Article] Yes-associated protein homolog, YAP-1, is involved in the thermotolerance and aging in the nematode Caenorhabditis elegans (2013)
  • Author(s): Iwasa H, Maimaiti S, Kuroyanagi H, Kawano S, Inami T, Ikeda M, Nakagawa K, Hata Y
  • Journal Title: Experimental Cell Research Volume: 319 Pages: 931-945
  • DOI: 10.1016/j.yexcr.2013.01.020
  • Peer Reviewed
• [Journal Article] Characterization of RSF-1, the Caenorhabditis elegans homolog of the Ras-association domain family protein 1 (2013)
  • Author(s): Iwasa H, Kuroyanagi H, Maimaiti S, Ikeda M, Nakagawa K, Hata Y
  • Journal Title: Experimental Cell Research Volume: 319 Pages: 1-11
  • DOI: 10.1016/j.yexcr.2012.10.008
  • Peer Reviewed
• [Journal Article] Muscle-Specific Splicing Factors ASD-2 and SUP-12 Cooperatively Switch Alternative Pre-mRNA Processing Patterns of the ADF/Cofilin Gene in Caenorhabditis elegans (2012)
  • Author(s): Ohno G, Ono K, Togo M, Watanabe Y, Ono S, Hagiwara M, Kuroyanagi H
  • Journal Title: PLoS Genetics Volume: 8 Pages: e1002991
  • DOI: 10.1371/journal.pgen.1002991
  • Peer Reviewed
• [Journal Article] Visualization and genetic analysis of alternative splicing regulation in vivo using fluorescence reporters in transgenic Caenorhabditis elegans (2010)
  • Author(s): Kuroyanagi H, Ohno G, Sakane H, Maruoka H, Hagiwara M
  • Journal Title: Nat. Protoc Volume: 5 Pages: 1495-1517
  • DOI: 10.1038/nprot.2010.107
  • Peer Reviewed
• [Journal Article] Fox-1 family of RNA-binding proteins (2009)
  • Author(s): Kuroyanagi H
  • Journal Title: Cell. Mol. Life Sci Volume: 66 Pages: 3895-3907
  • DOI: 10.1007/s00018-009-0120-5
  • Peer Reviewed
• [Presentation] 蛍光タンパク質レポーターを用いたmRNA 前駆体の転写後プロセシング制御機構の遺伝学的解析 (2013)
  • Author(s): 黒柳秀人
  • Organizer: 日本遺伝学会第85回大会
  • Place of Presentation: 慶應義塾大学 日吉キャンパス、横浜市
  • Year and Date: 20130919-21
• [Presentation] 線虫rp 遺伝子の選択的スプライシング制御機構の解析 (2013)
  • Author(s): 武井理美, 黒柳秀人
  • Organizer: 第15回日本RNA学会年会
  • Place of Presentation: 松山市
  • Year and Date: 20130724-26
• [Presentation] Ribosomal Protein L1 regulates alternative splicing of its own pre-mRNA (2013)
  • Author(s): Takei, S., & KUROYANAGI, H
  • Organizer: 19th International C. elegans Meeting
  • Place of Presentation: 米国カリフォルニア州ロサンゼルス市
  • Year and Date: 20130626-30
• [Presentation] mRNA 前駆体の選択的プロセシングパターンを可視化して解析する. (2013)
  • Author(s): 黒柳秀人
  • Organizer: 日本農芸化学会中部支部第169回例会若手シンポジウム
  • Place of Presentation: 岐阜大学 サテライトキャンパス、岐阜市
  • Year and Date: 2013-11-09
• [Presentation] 線虫rp 遺伝子の選択的スプライシング制御機構の解析 (2013)
  • Author(s): 武井理美
  • Organizer: 東京地区線虫勉強会
  • Place of Presentation: 東京大学浅野キャンパス、東京都文京区
  • Year and Date: 2013-09-28
• [Presentation] Muscle-Specific Splicing Factors ASD-2 and SUP-12 Cooperatively Switch Alternative Pre-mRNA Processing Patterns of the ADF/Cofilin Gene in C. elegans (2012)
  • Author(s): Genta Ohno, Kanako Ono, Marina Togo, Yohei Watanabe, Shoichiro Ono, Masatoshi Hagiwara, Hidehito Kuroyanagi
  • Organizer: Cold Spring Harbor Asia conferences on RNA Biology
  • Place of Presentation: 中国蘇州市
  • Year and Date: 20121008-12
• [Presentation] 普遍的に発現するRNA ポリメラーゼII会合タンパク質LST-3 はmRNA前駆体の転写と選択的スプライシングを制御する (2012)
  • Author(s): 黒柳秀人, 都甲麻理奈, 渡辺要平, 萩原正敏
  • Organizer: 第14回日本RNA学会年会
  • Place of Presentation: 東北大学
  • Year and Date: 20120718-20
• [Presentation] ASD-2 and SUP-12 cooperatively regulate muscle-specific alternative splicing of the ADF/coflin gene in C. elegans (2011)
  • Author(s): Genta Ohno, Kanako Ono, Yohei Watanabe, Marina Togo, Shoichiro Ono, Masatoshi Hagiwara, Hidehito Kuroyanagi
  • Organizer: NTU-JST Joint Meeting on RNA & Biofunctions - Asia Studies
  • Place of Presentation: 台北、台湾
  • Year and Date: 20111100
• [Presentation] FOX-1 family and UNC-75 regulate neuron-specific alternative splicing of the unc-32 gene. (2011)
  • Author(s): KUROYANAGI, H., & Hagiwara, M
  • Organizer: 18th International C. elegans Meeting
  • Place of Presentation: 米国カリフォルニア州ロサンゼルス市
  • Year and Date: 20110622-26
• [Presentation] ASD-2 and SUP-12 regulate the muscle-specific alternative splicing of actin-depolymerizing factor (ADF)/cofilin (2010)
  • Author(s): Ohno, G., Ono, S., Hagiwara, M., & KUROYANAGI, H
  • Organizer: 4th East Asia C. elegans Meeting
  • Place of Presentation: 東京都渋谷区
  • Year and Date: 20100711-14
• [Presentation] Quantitative screen for alternative splicing regulation factors in vivo (2010)
  • Author(s): Rebora, K., Zniber, I., Guignard, L., Ohno, G., KUROYANAGI, H., Fontrodona, L., Ceron, J., & Schwartz, S.J.
  • Place of Presentation: 東京都渋谷区
  • Year and Date: 20100711-14
• [Presentation] Regulation of Tissue-Specific Alternative Splicing in C. elegans (2010)
  • Author(s): 黒柳秀人
  • Organizer: The 19th CDB Meeting "RNA Sciences in Cell and Developmental Biology"
  • Place of Presentation: 理化学研究所、神戸市
  • Year and Date: 20100510-12
• [Presentation] 選択的スプライシングが線虫の筋肉異常を回復する (2009)
  • Author(s): 大野源太、斧正一郎、萩原正敏、黒柳秀人
  • Organizer: 第32回日本分子生物学会年会
  • Place of Presentation: 横浜市
  • Year and Date: 20091200
• [Presentation] 生体における選択的スプライシングの可視化と制御機構の解析 (2009)
  • Author(s): 黒柳秀人
  • Organizer: 第82回日本生化学会
  • Place of Presentation: 神戸市
  • Year and Date: 20091000
• [Presentation] Fox-1 family and CELF family RNA-binding proteins regulate neuron-specific alternative splicing in C. elegans (2009)
  • Author(s): Kuroyanagi H, Hagiwara M
  • Organizer: Cold Spring Harbor Laboratory Meeting on EUKARYOTIC mRNA PROCESSING
  • Place of Presentation: Cold Spring Harbor, NY, USA
  • Year and Date: 20090800
• [Presentation] Quantitative screen for alternative splicing regulation factors in vivo (2009)
  • Author(s): REBORA, K.G.M., ZNIBER, I., OHNO, G., KUROYANAGI, H., FONTRODONA, L., CERON, J., Jr, S.S., & DUPUY, D
  • Organizer: 17th International C. elegans Meeting
  • Place of Presentation: 米国カリフォルニア州ロサンゼルス市
  • Year and Date: 20090624-28
• [Presentation] Auto-regulation of asd-1, a Fox-1 family alternative splicing regulator (2009)
  • Author(s): KUROYANAGI, H., Kikuchi, Y., & Hagiwara, M
  • Organizer: 17th International C. elegans Meeting
  • Place of Presentation: 米国カリフォルニア州ロサンゼルス市
  • Year and Date: 20090624-28
• [Book] Chapter 28 : Single cell detection of splicing events with fluorescent splicing reporters. In Alternative pre-mRNA Splicing : Theory and Protocols (Stamm S, Smith C, and Luhrmann R, Eds.) (2012)
  • Author(s): Kuroyanagi H, Takeuchi A, Nojima T, Hagiwara M
  • Total Pages: 298-309
  • Publisher: Wiley-VCH, Weinheim, Germany
• [Book] 選択的スプライシングの分子機構と生命現象. 実験医学 増刊号 拡大・進展を続けるRNA研究の最先端 28 (2010)
  • Author(s): 大野源太, 黒柳秀人
  • Total Pages: 1591-1596
• [Book] みにれびゅー 選択的pre-mRNA スプライシング制御機構解明への新たなアプローチ. 生化学 82 (2010)
  • Author(s): 黒柳秀人
  • Total Pages: 402-411
• [Book] 選択的スプライシングの可視化と制御機構解明への応用. 蛋白質 核酸 酵素 増刊 mRNA プログラム 54 (2009)
  • Author(s): 黒柳秀人
  • Total Pages: 2044-2048
• [Remarks]
  • URL: http://www.tmd.ac.jp/end/