Exploring RNA modifications using enzymatic probe and its applications

• Project/Area Number: 26560442
• Research Category: Grant-in-Aid for Challenging Exploratory Research
• Allocation Type: Multi-year Fund
• Research Field: Chemical biology
• Research Institution: The University of Tokyo
• Principal Investigator: Suzuki Takeo 東京大学, 工学(系)研究科(研究院), 講師 (90533125)
• Project Period (FY): 2014-04-01 – 2016-03-31
• Project Status: Completed (Fiscal Year 2015)
• Budget Amount: ¥3,510,000 (Direct Cost: ¥2,700,000、Indirect Cost: ¥810,000); Fiscal Year 2015: ¥1,690,000 (Direct Cost: ¥1,300,000、Indirect Cost: ¥390,000); Fiscal Year 2014: ¥1,820,000 (Direct Cost: ¥1,400,000、Indirect Cost: ¥420,000)
• Keywords: RNA修飾 / 修飾酵素 / 特異的標識 / 網羅的探索 / RNA / 化学標識 / 化学修飾

Outline of Final Research Achievements

We aimed to explore transcriptome-wide RNA modifications with new techniques using covalent complexes between RNA modification and RNA modifying enzyme. We transiently expressed a modifying enzyme of interest in HeLa cells that were cultured under supplying a nucleic acid analogue molecule and could collect bound RNA from immune-precipitated RNA-enzyme complex in the analogue molecule dependent manner. Moreover, we examined a novel RNA modification labeling method based on enzymatic conversion of specific RNA modifications followed by nucleophilic substitution reaction. The method may provide a new solution to detect those specific modifications.

Research Products

• [Journal Article] A single methylation of 23S rRNA triggers late steps of 50S ribosomal subunit assembly (2015)
  • Author(s): Arai, T., Ishiguro, K., Kimura, S., Sakaguchi, Y., Suzuki, T. and Suzuki, T.
  • Journal Title: Proc. Natl. Acad. Sci. USA. Volume: 112 Issue: 34
  • DOI: 10.1073/pnas.1506749112
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] Cdk5rap1-mediated 2-methylthio modification of mitochondrial tRNAs governs protein translation and contributes to myopathy in mice and humans. (2015)
  • Author(s): Wei FY, Zhou B, Suzuki T, Miyata K, Ujihara Y, Horiguchi H, Takahashi N, Xie P, Michiue H, Fujimura A, Kaitsuka T, Matsui H, Koga Y, Mohri S, Suzuki T, Oike Y, Tomizawa K.
  • Journal Title: Cell Metab Volume: 21 Issue: 3 Pages: 413-6
  • DOI: 10.1016/j.cmet.2015.01.019
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] RNAの修飾欠損と疾患 (2015)
  • Author(s): 鈴木 勉、浅野 奏、鈴木 健夫
  • Journal Title: ファルマシア Volume: 51 Pages: 32-36
  • NAID: 130007447866
• [Journal Article] Human NAT10 is an ATP-dependent RNA acetyltransferase responsible for N4-acetylcytidine formation in 18S rRNA (2014)
  • Author(s): Satoshi Ito, Sayuri Horikawa, Tateki Suzuki, Hiroki Kawauchi, Yoshikazu Tanaka, Takeo Suzuki, and Tsutomu Suzuki
  • Journal Title: The Journal of Biological Chemistry Volume: 289 Issue: 52 Pages: 35724-35730
  • DOI: 10.1074/jbc.c114.602698
  • Peer Reviewed / Open Access
• [Journal Article] A single acetylation of 18S rRNA is essential for biogenesis of the small ribosomal subunit in Saccharomyces cerevisiae (2014)
  • Author(s): Ito, S., Akamatsu, Y., Noma, A., Kimura, S., Miyauchi, K., Ikeuchi, Y., Suzuki, T. and Suzuki, T
  • Journal Title: J. Biol. Chem. Volume: 289 Issue: 38 Pages: 26201-26212
  • DOI: 10.1074/jbc.m114.593996
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] 5-Hydroxymethylcytosine plays a critical role in glioblastomagenesis by recruiting the CHTOP-Methylosome complex (2014)
  • Author(s): Hiroki Takai, Tetsu Akiyama et al.
  • Journal Title: Cell Reports Volume: 9 Issue: 1 Pages: 48
  • DOI: 10.1016/j.celrep.2014.08.071
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] A complete landscape of post-transcriptional modifications in mammalian mitochondrial tRNAs (2014)
  • Author(s): Suzuki T. and Suzuki T.
  • Journal Title: Nucleic Acids Research Volume: (in press) Issue: 11 Pages: 7346-7357
  • DOI: 10.1093/nar/gku390
  • Peer Reviewed / Open Access
• [Presentation] U snRNAにおけるN6-メチルアデノシン修飾の生合成と機能解析 (2015)
  • Author(s): 石神 宥真、大平 高之、穐近 慎一郎、鈴木 健夫、鈴木 勉
  • Organizer: BMB2015
  • Place of Presentation: 神戸ポートアイランド, 神戸市, 兵庫県
  • Year and Date: 2015-12-01
• [Presentation] Exploration and functional analysis of queuosine- glycosyltransferases in mammals (2015)
  • Author(s): Xuewei Zhao, Takeo Suzuki, Tsutomu Suzuki
  • Organizer: 第17回日本RNA学会年会
  • Place of Presentation: ホテルライフォート札幌, 札幌市, 北海道
  • Year and Date: 2015-07-15
• [Presentation] Deficiency of tRNA modification causes the development of X-linked mental retardation (2015)
  • Author(s): Fan-Yan Wei, Yu Nagayoshi, Shoji Hirata, Takeo Suzuki, Tsutomu Suzuki, Kazuhito Tomizawa
  • Organizer: 第17回日本RNA学会年会
  • Place of Presentation: ホテルライフォート札幌, 札幌市, 北海道
  • Year and Date: 2015-07-15
• [Presentation] Biogenesis of 5-taurinomethyluridine in human mitochondrial tRNAs; implication for molecular pathogenesis of mitochondrial diseases (2015)
  • Author(s): Kana Asano, Takeo Suzuki, Fan-Yan Wei, Yoshiho Ikeuchi, Yuka Yashiro, Christin Tischner, Annette Hofer, Yoshihito Kishita, Yasushi Okazaki, Tina Wenz, Kazuhito Tomizawa, Tsutomu Suzuki
  • Organizer: 第17回日本RNA学会年会
  • Place of Presentation: ホテルライフォート札幌, 札幌市, 北海道
  • Year and Date: 2015-07-15
• [Presentation] ミトコンドリアtRNAタウリン修飾の生合成と機能 (2014)
  • Author(s): 鈴木 健夫、浅野 奏、魏 范研、富澤 一仁、池内 与志穂、鈴木 勉
  • Organizer: 第14回日本ミトコンドリア学会年会
  • Place of Presentation: 九大医 百年講堂、福岡市、福岡県
  • Year and Date: 2014-12-03 – 2014-12-05
• [Presentation] 哺乳類ミトコンドリアにおけるtRNA48位の5-メチルシチジン修飾酵素の同定 (2014)
  • Author(s): 中野 紗緒里、鈴木 健夫、荒木 喜美、荒木 正健、鈴木 勉
  • Organizer: 第14回日本ミトコンドリア学会年会
  • Place of Presentation: 九大医 百年講堂、福岡市、福岡県
  • Year and Date: 2014-12-03 – 2014-12-05
• [Presentation] A complete landscape of post-transcriptional modifications in mammalian mitochondrial tRNAs (2014)
  • Author(s): Suzuki, T. and Suzuki, T.
  • Organizer: The 25th tRNA conference
  • Place of Presentation: Kyllini, Greece
  • Year and Date: 2014-09-21 – 2014-09-25
• [Presentation] Mitochondrial disease as the first instance of RNA modopathy (2014)
  • Author(s): Takeo Suzuki, Kana Asano, Fan-Yan Wei, Kazuhito Tomizawa, Tsutomu Suzuki
  • Organizer: 第16回日本RNA学会年会
  • Place of Presentation: ウインクあいち、名古屋市、愛知県
  • Year and Date: 2014-07-23 – 2014-07-25
  • Invited
• [Presentation] Analysis of the functional role of FTSJ1 related to non-syndromic X-linked intellectual disability (2014)
  • Author(s): Shoji Hirata, Takeshi Chujo, Takeo Suzuki, Kenjyo Miyauchi, Yuichi Goto, Tsutomu Suzuki
  • Organizer: 第16回日本RNA学会年会
  • Place of Presentation: ウインクあいち、名古屋市、愛知県
  • Year and Date: 2014-07-23 – 2014-07-25