Epitranscriptome analysis of sporulating budding yeast

• Project/Area Number: 25620125
• Research Category: Grant-in-Aid for Challenging Exploratory Research
• Allocation Type: Multi-year Fund
• Research Field: Bio-related chemistry
• Research Institution: The University of Tokyo
• Principal Investigator: SUZUKI Tsutomu 東京大学, 工学(系)研究科(研究院), 教授 (20292782)
• Project Period (FY): 2013-04-01 – 2015-03-31
• Project Status: Completed (Fiscal Year 2014)
• Budget Amount: ¥4,030,000 (Direct Cost: ¥3,100,000、Indirect Cost: ¥930,000); Fiscal Year 2014: ¥780,000 (Direct Cost: ¥600,000、Indirect Cost: ¥180,000); Fiscal Year 2013: ¥3,250,000 (Direct Cost: ¥2,500,000、Indirect Cost: ¥750,000)
• Keywords: RNA修飾 / N6メチルアデノシン / m6A / 胞子形成 / ＲＮＡエピジェネティクス

Outline of Final Research Achievements

Eukaryotic mRNAs and non-coding RNAs contain various post-transcriptional modifications including 5’ cap structure, inosine (I), 5-methylcytidine (m5C), and N6-methyladenosine (m6A). To investigate functional roles of m6A, we screened m6A sites on mRNAs in sporulating budding yeast. More than 8,000 candidate regions were mapped in about 3,000 genes in Saccharomyces cerevisiae by m6A-seq which is a biochemical method to identify m6A regions by immunoprecipitation of m6A-containing RNA fragment by anti-m6A antibody combined with deep sequencing. In addition, we identified a single m6A site in IME1 mRNA by RNA mass spectrometric analysis. However, this m6A site was not confirmed by m6A-seq, exposing a problem of anti-m6A antibody with poor specificity.

Research Products

• [Journal Article] Iron-sulfur proteins responsible for RNA modifications (2015)
  • Author(s): Kimura S., Suzuki T.
  • Journal Title: Biochimica et Biophysica Acta Volume: 1853 Issue: 6 Pages: 1272-1283
  • DOI: 10.1016/j.bbamcr.2014.12.010
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Rectifier of aberrant mRNA splicing recovers tRNA modification in familial dysautonomia. (2015)
  • Author(s): Yoshida M, Kataoka N, Miyauchi K, Ohe K, Iida K, Yoshida S, Nojima T, Okuno Y, Onogi H, Usui T, Takeuchi A, Hosoya T, Suzuki T, Hagiwara M.
  • Journal Title: Proc Natl Acad Sci U S A. Volume: 112（9） Issue: 9 Pages: 2764-2769
  • DOI: 10.1073/pnas.1415525112
  • Peer Reviewed / Open Access / 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] Defining fundamental steps in the assembly of Drosophila RNAi enzyme complex (2015)
  • Author(s): Shintaro Iwasaki, Hiroshi M. Sasaki, Yuriko Sakaguchi, Tsutomu Suzuki, Hisashi Tadakuma, & Yukihide Tomari
  • Journal Title: Nature Volume: NA Issue: 7553 Pages: 0-0
  • DOI: 10.1038/nature14254
  • Peer Reviewed / 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
• [Journal Article] Discovery of the b-barrel-type RNA methyltransferase responsible for N6-methylation of N6-threonylcarbamoyladenosine in tRNAs (2014)
  • Author(s): Kimura S., Miyauchi K., Ikeuchi Y., Thiaville PC., Crecy-Lagard Vd., Suzuki T.
  • Journal Title: Nucleic Acids Research Volume: 42 Issue: 14 Pages: 9350-9365
  • DOI: 10.1093/nar/gku618
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [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] 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] 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: 48-60
  • DOI: 10.1016/j.celrep.2014.08.071
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Convergent evolution of AUA decoding in bacteria and archaea (2014)
  • Author(s): Tsutomu Suzuki and Tomoyuki Numata
  • Journal Title: RNA Biology Volume: 11 Issue: 12 Pages: 1586-1596
  • DOI: 10.4161/15476286.2014.992281
  • Peer Reviewed / 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 Res. Volume: in press
  • Peer Reviewed
• [Journal Article] Structural Dynamics of a Mitochondrial tRNA Possessing Weak Thermo dynamic Stability (2014)
  • Author(s): Hari Bhaskaran, Takaaki Taniguchi, Takeo Suzuki, Tsutomu Suzuki, and John J. Perona
  • Journal Title: Biochemistry Volume: 53(a) Issue: 9 Pages: 1456-1465
  • DOI: 10.1021/bi401449z
  • Peer Reviewed / Open Access
• [Journal Article] A biochemical landscape of A-to-I RNA editing in the human brain transcriptome (2014)
  • Author(s): Sakurai, M., Ueda, H., Yano, T., Okada, S., Terajima, H., Mitsuyama, T., Toyoda, A., Fujiyama, A., Kawabata, H. and Suzuki, T.
  • Journal Title: Genome Res Volume: 24 Issue: 3 Pages: 522-534
  • DOI: 10.1101/gr.162537.113
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Biochemical and mass spectrometric analysis of 3'-end methylation of piRNAs (2014)
  • Author(s): Suzuki T, Miyauchi K, Sakaguchi Y, Suzuki T
  • Journal Title: Methods Mol. Biol Volume: 1093 Pages: 59-72
  • DOI: 10.1007/978-1-62703-694-8_6
  • ISBN: 9781627036931, 9781627036948
  • Peer Reviewed
• [Journal Article] Poly (A)-specific ribonuclease mediates 3'-end trimming of Argonaute2-cleaved precursor microRNAs (2013)
  • Author(s): Yoda M, Cifuentes D, Izumi N, Sakaguchi Y. Suzuki T. Giraldez AJ.
  • Journal Title: Cell Report Volume: 5 Issue: 3 Pages: 715-726
  • DOI: 10.1016/j.celrep.2013.09.029
  • Peer Reviewed / Open Access
• [Journal Article] Distinct tRNA modifications in the thermo-acidophilic archaeon, Thermoplasma acidophilum (2013)
  • Author(s): Tomikawa, C., Ohira, T., Inoue, Y., Kawamura, T., Yamagishi, A., Suzuki, T. and Hori, H.
  • Journal Title: FEBS Lett Volume: 587 Issue: 21 Pages: 3575-3580
  • DOI: 10.1016/j.febslet.2013.09.021
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Quantitative PCR measurement of tRNA 2 methylthio modification for assessing type 2 diabetes risk. (2013)
  • Author(s): Kie, Pei-Yu, et al.
  • Journal Title: Clinical Chemistry Volume: 59 Issue: 11 Pages: 1604-1612
  • DOI: 10.1373/clinchem.2013.210401
  • Peer Reviewed / Open Access
• [Journal Article] Crystal structure of a putative methyltransferase SAV1081 from Staphylococcus aureus (2013)
  • Author(s): Kita, S., Tanaka, Y., Hirano, N., Kimura, S., Suzuki, T., Suzuki, T., Yao, M. and Tanaka, I.
  • Journal Title: Protein & Peptide Letters Volume: 20 Issue: 5 Pages: 530-537
  • DOI: 10.2174/0929866511320050006
  • Peer Reviewed / Acknowledgement Compliant
• [Presentation] Essential RNA acetyltransferase required for ribosome biogenesis and tRNA modification (2015)
  • Author(s): Tsutomu Suzuki
  • Organizer: GRC on RNA editing and modification
  • Place of Presentation: Lucca, Italy
  • Year and Date: 2015-03-09
  • Invited
• [Presentation] RNA修飾の多彩な機能と疾患 (2015)
  • Author(s): 鈴木 勉
  • Organizer: 埼玉医科大学ゲノム医学研究センター学術集会
  • Place of Presentation: 埼玉医科大学ゲノム医学研究センター、埼玉県日高市
  • Year and Date: 2015-01-27
  • Invited
• [Presentation] Mitochondrial diseases caused by deficient tRNA modifications (2014)
  • Author(s): Tsutomu Suzuki
  • Organizer: AussieMit2014
  • Place of Presentation: Perth, Australia
  • Year and Date: 2014-12-01
  • Invited
• [Presentation] A single acetylation of 18S rRNA regulates ribosome biogenesis by sensing cellular energy status (2014)
  • Author(s): Tsutomu Suzuki
  • Organizer: Joint Australia and Japan RNA meeting (JAJRNA2014)
  • Place of Presentation: Sydney, Australia
  • Year and Date: 2014-11-05
  • Invited
• [Presentation] Biogenesis and function of cyclic t6A and derivatives (2014)
  • Author(s): Tsutomu Suzuki
  • Organizer: 25th tRNA conference
  • Place of Presentation: Kyllini, Greece
  • Year and Date: 2014-09-22
  • Invited
• [Presentation] ヒトはなぜ病気になるのでしょう？～病気の原因を分子レベルで探る～ (2014)
  • Author(s): 鈴木 勉
  • Organizer: 高校生のためのオープンキャンパス2014
  • Place of Presentation: 東京大学本郷キャンパス、東京
  • Year and Date: 2014-08-06
  • Invited
• [Presentation] RNAエピジェネティクスと生命現象
  • Author(s): 鈴木 勉
  • Organizer: 第16回生命化学研究会
  • Place of Presentation: ＫＫＲホテル熱海（熱海）
  • Invited
• [Presentation] RNA modifications as naturally-selected chemical diversity involved in various biological processes
  • Author(s): Tsutomu Suzuki
  • Organizer: RIKEN symposium RNA Sciences in Cell and Developmental Biology III
  • Place of Presentation: 理化学研究所 発生・再生科学総合研究センター（神戸）
  • Invited
• [Presentation] RNA modifications as naturally-selected chemical diversity involved in various biological processes
  • Author(s): Tsutomu Suzuki
  • Organizer: Peking Unvi School of Life Sciences Lecture
  • Place of Presentation: Beijing, China
  • Invited
• [Presentation] RNA modifications as naturally-selected chemical diversity involved in various biological processes
  • Author(s): Tsutomu Suzuki
  • Organizer: Riboclub2013
  • Place of Presentation: Quebec, Canada
• [Presentation] RNAエピジェネティクスと生命現象
  • Author(s): 鈴木 勉
  • Organizer: Symposium on Frontier Science and Technology
  • Place of Presentation: 高知工科大学（高知）
  • Invited
• [Presentation] Biogenesis and function of cyclic N6-threonylcarbamoyladenosine as a widely distributed tRNA hypermodification
  • Author(s): Tsutomu Suzuki
  • Organizer: The 18th annual meeting of the RNA society
  • Place of Presentation: Davos, Switzerland
  • Invited
• [Book] RNAの修飾欠損と疾患/ファルマシア (2015)
  • Author(s): 鈴木 勉、浅野 奏、鈴木健夫
  • Total Pages: 5
  • Publisher: 公益社団法人 日本薬学会
• [Book] リボソームRNAの転写後修飾の生合成と機能 (2013)
  • Author(s): 荒井大河、伊藤理、鈴木 勉
  • Total Pages: 13
  • Publisher: 生化学