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Disome-Seq: a genome-wide survey for parametric ribosome collisions

Planned Research

Project AreaParametric biology based on translation rate regulatory mechanism
Project/Area Number 20H05784
Research Category

Grant-in-Aid for Transformative Research Areas (B)

Allocation TypeSingle-year Grants
Review Section Transformative Research Areas, Section (III)
Research InstitutionInstitute of Physical and Chemical Research

Principal Investigator

Iwasaki Shintaro  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) 2020-10-02 – 2023-03-31
Project Status Completed (Fiscal Year 2023)
Budget Amount *help
¥38,220,000 (Direct Cost: ¥29,400,000、Indirect Cost: ¥8,820,000)
Fiscal Year 2022: ¥11,310,000 (Direct Cost: ¥8,700,000、Indirect Cost: ¥2,610,000)
Fiscal Year 2021: ¥12,350,000 (Direct Cost: ¥9,500,000、Indirect Cost: ¥2,850,000)
Fiscal Year 2020: ¥14,560,000 (Direct Cost: ¥11,200,000、Indirect Cost: ¥3,360,000)
Keywords翻訳 / RNA / Ribosome profiling / Disome / Cas13 / Ribosome / Disome-Seq
Outline of Research at the Start

リボソームがコドンを読み取る速度は一定ではなく、むしろパラメトリックに進行し、一時停止および渋滞をする例があることが報告されている。しかしながらその全容や速度制限にかかわる共通の原理・ルールは全く明らかにされていない。これはリボソーム一時停止を網羅的に、かつ高感度に探索する技術がこれまで皆無であったことによる。本研究ではこの問題を解決する『Disome-Seq法』と呼ばれる新規技術を確立し、リボソーム一時停止を探索するとともに、班員が得意とする物理化学的な影響 (原田・岡部)あるいは高次生命現象 (土居、池内)でどのように制御されるかを理解することを目指す。

Outline of Final Research Achievements

In this research project, we developed a new method (termed Disome-Seq), which can comprehensively survey ribosome collision sites across transcriptome (Han et al. Cell Rep 2020). We applied this method to humans, zebrafish (Han et al. Cell Rep 2020), and bacteria (Fujita et al. RNA 2022). To engineer the parametric nature of translation artificially, we also developed CRISPRδ, which is based on dCas13 (Apostolopoulos et al. Nat Commun 2024).

Academic Significance and Societal Importance of the Research Achievements

Disome-Seq法は翻訳そのものに関する基礎研究はもとより、リボソーム渋滞が原因で発症する疾患(神経変性疾患など)の理解に貢献すると期待できる。CRISPRδ(クリスパー・デルタ)法は、非常に特異的であるため遺伝子の機能を理解するという基礎生物学的応用ができる。また、ウイルス特異的な翻訳様式や神経変性疾患の原因となり得る特殊な翻訳様式も抑制できることから、さまざまな応用につながることが期待される。

Report

(2 results)
  • 2023 Final Research Report ( PDF )
  • 2020 Annual Research Report
  • Research Products

    (13 results)

All 2021 2020 Other

All Int'l Joint Research (1 results) Journal Article (9 results) (of which Int'l Joint Research: 5 results,  Peer Reviewed: 9 results,  Open Access: 6 results) Presentation (1 results) (of which Invited: 1 results) Remarks (2 results)

  • [Int'l Joint Research] University of California, Berkeley/University of California, San Francisco(米国)

    • Related Report
      2020 Annual Research Report
  • [Journal Article] The Pentatricopeptide Repeat Protein PGR3 Is Required for the Translation of petL and ndhG by Binding Their 5′ UTRs2021

    • Author(s)
      Higashi Haruka、Kato Yoshinobu、Fujita Tomoya、Iwasaki Shintaro、Nakamura Masayuki、Nishimura Yoshiki、Takenaka Mizuki、Shikanai Toshiharu
    • Journal Title

      Plant and Cell Physiology

      Volume: - Issue: 7 Pages: 1-10

    • DOI

      10.1093/pcp/pcaa180

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Spliceostatin A interaction with SF3B1 limits U1 snRNP availability and causes premature cleavage and polyadenylation.2021

    • Author(s)
      Yoshimoto, R., Chhipi-Shrestha, J.K., Schneider-Poetsch, T., Furuno, M., Burroughs, A.M., Noma, S., Suzuki, H., Hayashizaki, Y., Mayeda, A., Nakagawa, S., Kaida, D., Iwasaki, S., Yoshida, M.
    • Journal Title

      Cell Chem. Biol.

      Volume: - Issue: 9 Pages: 1356-1365

    • DOI

      10.1016/j.chembiol.2021.03.002

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Dual targeting of DDX3 and eIF4A by the translation inhibitor rocaglamide A2021

    • Author(s)
      Chen Mingming、Asanuma Miwako、Takahashi Mari、Shichino Yuichi、Mito Mari、Fujiwara Koichi、Saito Hironori、Floor Stephen N.、Ingolia Nicholas T.、Sodeoka Mikiko、Dodo Kosuke、Ito Takuhiro、Iwasaki Shintaro
    • Journal Title

      Cell Chemical Biology

      Volume: 28 Issue: 4 Pages: 475-486

    • DOI

      10.1016/j.chembiol.2020.11.008

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Genome-wide survey of ribosome collision.2020

    • Author(s)
      Han, P., Shichino, Y., Schneider-Poetsch, T., Mito, M., Hashimoto, S., Udagawa, T., Kohno, K., Yoshida, M., Mishima, Y., Inada, T., Iwasaki, S.
    • Journal Title

      Cell Rep.

      Volume: 31(5) Issue: 5 Pages: 107610-107610

    • DOI

      10.1016/j.celrep.2020.107610

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] N-terminal deletion of Swi3 created by the deletion of a dubious ORF YJL175W mitigates protein burden effect in S. cerevisiae2020

    • Author(s)
      Saeki Nozomu、Eguchi Yuichi、Kintaka Reiko、Makanae Koji、Shichino Yuichi、Iwasaki Shintaro、Kanno Manabu、Kimura Nobutada、Moriya Hisao
    • Journal Title

      Scientific Reports

      Volume: 10 Issue: 1 Pages: 9500-9500

    • DOI

      10.1038/s41598-020-66307-z

    • NAID

      120006883501

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Implications of RNG140 (caprin2)-mediated translational regulation in eye lens differentiation2020

    • Author(s)
      Kaori Nakazawa, Yuichi Shichino,Shintaro Iwasaki, and Nobuyuki Shiina
    • Journal Title

      Journal of Biological Chemistry

      Volume: 295 Issue: 44 Pages: 15029-15044

    • DOI

      10.1074/jbc.ra120.012715

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Complete chemical structures of human mitochondrial tRNAs2020

    • Author(s)
      Suzuki Takeo、Yashiro Yuka、Kikuchi Ittoku、Ishigami Yuma、Saito Hironori、Matsuzawa Ikuya、Okada Shunpei、Mito Mari、Iwasaki Shintaro、Ma Ding、Zhao Xuewei、Asano Kana、Lin Huan、Kirino Yohei、Sakaguchi Yuriko、Suzuki Tsutomu
    • Journal Title

      Nature Communications

      Volume: 11 Issue: 1 Pages: 1-15

    • DOI

      10.1038/s41467-020-18068-6

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Ribosomal protein S7 ubiquitination during ER stress in yeast is associated with selective mRNA translation and stress outcome2020

    • Author(s)
      Matsuki Yasuko、Matsuo Yoshitaka、Nakano Yu、Iwasaki Shintaro、Yoko Hideyuki、Udagawa Tsuyoshi、Li Sihan、Saeki Yasushi、Yoshihisa Tohru、Tanaka Keiji、Ingolia Nicholas T.、Inada Toshifumi
    • Journal Title

      Scientific Reports

      Volume: 10 Issue: 1 Pages: 19669-19669

    • DOI

      10.1038/s41598-020-76239-3

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Protocol for disome profiling to survey ribosome collision in humans and zebrafish.2020

    • Author(s)
      Mito M, Mishima Y, and Iwasaki S
    • Journal Title

      STAR Protoc.

      Volume: 1 Issue: 3 Pages: 100168-100168

    • DOI

      10.1016/j.xpro.2020.100168

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access
  • [Presentation] 抗がん作用をもつ小分子Rocaglamide AによるDDX3とeIF4Aを介した二重翻訳阻害2020

    • Author(s)
      岩崎信太郎
    • Organizer
      第93回日本生化学大会
    • Related Report
      2020 Annual Research Report
    • Invited
  • [Remarks]

    • URL

      http://iwasakirna.com/publications.php

    • Related Report
      2020 Annual Research Report
  • [Remarks]

    • URL

      https://www.riken.jp/research/labs/chief/rna_sys_biochem/index.html

    • Related Report
      2020 Annual Research Report

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Published: 2020-10-30   Modified: 2025-01-30  

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