Chasing translation along the time by novel ribosome profiling

• Project Area: Nascent-chain Biology
• Project/Area Number: 17H05679
• 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: Institute of Physical and Chemical Research
• Principal Investigator: 岩崎 信太郎 国立研究開発法人理化学研究所, 開拓研究本部, 主任研究員 (80611441)
• Project Period (FY): 2017-04-01 – 2019-03-31
• Project Status: Completed (Fiscal Year 2018)
• Budget Amount: ¥13,000,000 (Direct Cost: ¥10,000,000、Indirect Cost: ¥3,000,000); Fiscal Year 2018: ¥6,500,000 (Direct Cost: ¥5,000,000、Indirect Cost: ¥1,500,000); Fiscal Year 2017: ¥6,500,000 (Direct Cost: ¥5,000,000、Indirect Cost: ¥1,500,000)
• Keywords: 翻訳 / Ribosome / Ribosome profiling / eIF4A / リボソーム / mRNA / RNA / 発現制御 / ゲノム

Outline of Annual Research Achievements

本研究では、合成されたばかりの若いmRNAとある程度時間がたった古いmRNAの間でどのような翻訳制御の差があるかを網羅的かつ定量的に解析することを目的としている。この目的のために、1) RNAを一定時間uridineの誘導体でpulseラベルし、経時的にchaseすることで、ラベルされたRNAの挙動を時間経過とともに追うこと、 2) またラベルされたRNAを特異的回収し、ribosome profiling法を応用することで、その翻訳動態を解析することを計画してきた。この目的を達成するために、微小サンプルに対する新規ribosome profiling法の確立が急務となった。実際にcarrier oligoをサンプル中に加え、サンプルロスや反応効率の減少を防ぎつつ、最終的に酵素的にcarrier oligoを除去する方法を確立し、必要サンプル量を1/1000程度まで抑えることに成功している。
また、新学術領域内での共同研究を推進してきた。特に理研伊藤らのグループとともに抗がん作用をもつ翻訳阻害剤Rocaglamide AによるmRNA選択性の構造基盤を明らかにした。Rocaglamide AはRNA結合タンパク質である翻訳開始因子eIF4Aを標的としつつ、AやGが連続したポリプリン配列に対する特異性を与えることが生化学的に分かっていた。Rocaglamide A、eIF4A、ポリプリンRNAの共結晶の構造から
Rocaglamide Aが、eIF4AとポリプリンRNAが形成する境界面に結合する非常にユニークな阻害剤であることがわかった。また、Rocaglamide Aが直接塩基を認識し、配列特異性を生み出していることも明らかになった。

Research Progress Status

平成30年度が最終年度であるため、記入しない。

Strategy for Future Research Activity

平成30年度が最終年度であるため、記入しない。

Research Products

• [Int'l Joint Research] University of California, Berkeley(米国)
• [Journal Article] tChIP-Sea : cell-type-specific Eepigenome profiling (2019)
  • Author(s): Mito M, Kadota M., Nakagawa S. *, Iwasaki S. *
  • Journal Title: J. Vis. Exp Volume: 143 Issue: 143
  • DOI: 10.3791/58298
  • Peer Reviewed
• [Journal Article] The Translation Inhibitor Rocaglamide Targets a Bimolecular Cavity between eIF4A and Polypurine RNA (2019)
  • Author(s): Iwasaki Shintaro、Iwasaki Wakana、Takahashi Mari、Sakamoto Ayako、Watanabe Chiduru、Shichino Yuichi、Floor Stephen N.、Fujiwara Koichi、Mito Mari、Dodo Kosuke、Sodeoka Mikiko、Imataka Hiroaki、Honma Teruki、Fukuzawa Kaori、Ito Takuhiro、Ingolia Nicholas T.
  • Journal Title: Molecular Cell Volume: 73 Issue: 4 Pages: 738-748
  • DOI: 10.1016/j.molcel.2018.11.026
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] The diverse modes of eIF4A inhibition (2018)
  • Author(s): 岩崎 信太郎
  • Journal Title: 生化学 Volume: 90 Issue: 2 Pages: 211-215
  • DOI: 10.14952/SEIKAGAKU.2018.900211
  • NAID: 40021617531
  • ISSN: 0037-1017
  • Year and Date: 2018-04-25
• [Journal Article] Cap-specific terminal N6-methylation of RNA by an RNA polymerase II?associated methyltransferase (2018)
  • Author(s): Akichika Shinichiro、Hirano Seiichi、Shichino Yuichi、Suzuki Takeo、Nishimasu Hiroshi、Ishitani Ryuichiro、Sugita Ai、Hirose Yutaka、Iwasaki Shintaro、Nureki Osamu、Suzuki Tsutomu
  • Journal Title: Science Volume: 363 Issue: 363 Pages: 1-7
  • DOI: 10.1126/science.aav0080
  • Peer Reviewed / Open Access
• [Journal Article] Cell Type-Specific Survey of Epigenetic Modifications by Tandem Chromatin Immunoprecipitation Sequencing (2018)
  • Author(s): Mito Mari、Kadota Mitsutaka、Tanaka Kaori、Furuta Yasuhide、Abe Kuniya、Iwasaki Shintaro、Nakagawa Shinichi
  • Journal Title: Scientific Reports Volume: 8 Issue: 1 Pages: 1143-1143
  • DOI: 10.1038/s41598-018-19494-9
  • NAID: 120006398777
  • Peer Reviewed / Open Access
• [Journal Article] Transcripts from downstream alternative transcription start sites evade uORF-mediated inhibition of gene expression in Arabidopsis (2018)
  • Author(s): Kurihara Yukio、Makita Yuko、Kawashima Mika、Fujita Tomoya、Iwasaki Shintaro、Matsui Minami
  • Journal Title: Proceedings of the National Academy of Sciences USA Volume: 115 Issue: 30 Pages: 7831-7836
  • DOI: 10.1073/pnas.1804971115
  • Peer Reviewed / Open Access
• [Journal Article] UPA-seq: prediction of functional lncRNAs using differential sensitivity to UV crosslinking (2018)
  • Author(s): Komatsu T, Yokoi S, Fujii K, Mito M, Kimura Y, Iwasaki S, Nakagawa S.
  • Journal Title: RNA Volume: 24 Issue: 12 Pages: 1785-1802
  • DOI: 10.1261/rna.067611.118
  • NAID: 120006545959
  • Peer Reviewed / Open Access
• [Journal Article] The Growing Toolbox for Protein Synthesis Studies (2017)
  • Author(s): Iwasaki Shintaro、Ingolia Nicholas T.
  • Journal Title: Trends in Biochemical Sciences Volume: 42 Issue: 8 Pages: 612-624
  • DOI: 10.1016/j.tibs.2017.05.004
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Ubiquitination of stalled ribosome triggers ribosome-associated quality control (2017)
  • Author(s): Matsuo Y, Ikeuchi K, Saeki Y, Iwasaki S, Schmidt C, Udagawa T, Sato F, Tsuchiya H, Becker T, Tanaka K, Ingolia NT, Beckmann R, Inada T
  • Journal Title: Nature Communications Volume: 8 Issue: 1 Pages: 159-159
  • DOI: 10.1038/s41467-017-00188-1
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] In vitro reconstitution of chaperone-mediated human RISC assembly (2017)
  • Author(s): Naruse Ken、Matsuura-Suzuki Eriko、Watanabe Mariko、Iwasaki Shintaro、Tomari Yukihide
  • Journal Title: RNA Volume: 24 Issue: 1 Pages: 6-11
  • DOI: 10.1261/rna.063891.117
  • Peer Reviewed
• [Journal Article] Reconstitution of RNA Interference Machinery (2017)
  • Author(s): Iwasaki Shintaro、Tomari Yukihide
  • Journal Title: Methods Mol Biol. Volume: - Pages: 131-143
  • DOI: 10.1007/978-1-4939-7339-2_9
  • ISBN: 9781493973385, 9781493973392
  • Peer Reviewed
• [Presentation] Translational buffering upon splicing inhibition (2018)
  • Author(s): 岩崎信太郎
  • Organizer: 第41回日本分子生物学会年会
  • Int'l Joint Research / Invited
• [Presentation] Ribosome conformational dynamics surveyed by ribosome profiling (2018)
  • Author(s): 岩崎信太郎
  • Organizer: 2nd JAJ (Joint Australia-Japan/Japan-Australia Joint) RNA Meeting
  • Int'l Joint Research / Invited
• [Presentation] A translation inhibitor targets a bimolecular cavity between eIF4A and polypurine RNA (2018)
  • Author(s): 岩崎信太郎
  • Organizer: International Symposium on “Proteins; from the Cradle to the Grave” 2018年8月26日
  • Invited
• [Presentation] Structure and resistance of an mRNA-selective natural translation inhibitor from Aglaia plant (2018)
  • Author(s): 岩崎信太郎
  • Organizer: 第59回日本植物生理学会年会
  • Int'l Joint Research / Invited
• [Presentation] Translational buffering upon splicing inhibition (2018)
  • Author(s): 岩崎 信太郎
  • Organizer: 第41回日本分子生物学会年会
  • Int'l Joint Research / Invited
• [Presentation] Ribosome conformational dynamics surveyed by ribosome profiling (2018)
  • Author(s): 岩崎 信太郎
  • Organizer: 2nd JAJ (Joint Australia-Japan/Japan-Australia Joint) RNA Meeting
  • Int'l Joint Research / Invited
• [Presentation] A translation inhibitor targets a bimolecular cavity between eIF4A and polypurine RNA (2018)
  • Author(s): 岩崎 信太郎
  • Organizer: International Symposium on “Proteins; from the Cradle to the Grave” 2018年8月26日
  • Int'l Joint Research
• [Presentation] Structure and resistance of an mRNA-selective natural translation inhibitor from Aglaia plant (2018)
  • Author(s): 岩崎 信太郎
  • Organizer: 第59回日本植物生理学会年会
  • Int'l Joint Research / Invited
• [Presentation] Mechanism of self-resistance to natural translation inhibitor in Aglaia (2017)
  • Author(s): 岩崎 信太郎
  • Organizer: Consortium of Biological Sciences 2017
  • Int'l Joint Research / Invited
• [Presentation] Genomic and structural basis of self-resistance to natural translation inhibitor in Aglaia (2017)
  • Author(s): 岩崎 信太郎
  • Organizer: Cutting Edge Developments in RNA Biology for the Control of Gene Expression
  • Int'l Joint Research / Invited
• [Presentation] mRNA選択的翻訳阻害剤Rocaglamide Aの分子機構 (2017)
  • Author(s): 岩崎 信太郎
  • Organizer: 第11回 日本ゲノム微生物学会 若手の会
  • Invited
• [Presentation] Co-evolution of translation initiation factor 4A and its natural inhibitor rocaglates in Aglaia (2017)
  • Author(s): 岩崎 信太郎
  • Organizer: DFG-Forschergruppe 1805 Summer School 2017 on “Dynamics of translation”
  • Int'l Joint Research / Invited
• [Book] 実験医学 2017年7月号 「リボソームプロファイリングが切り拓く翻訳研究の未来」 (2017)
  • Author(s): 七野 悠一、岩崎信太郎
  • Total Pages: 6
  • Publisher: 羊土社
  • ISBN: 9784758101653
• [Remarks] 植物由来抗がん剤の仕組み －標的タンパク質にRNA配列特異性を与える小分子化合物－
  • URL: https://www.riken.jp/press/2018/20181228_1/
• [Remarks] メチルは端だが役に立つ？ －mRNAのキャップ構造におけるm6A修飾酵素の同定－
  • URL: https://www.riken.jp/press/2018/20181127_1/