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Monitoring the molecular dynamics in the assembly of ncRNA machinery

Planned Research

Project AreaNeo-taxonomy of noncoding RNAs
Project/Area Number 26113007
Research Category

Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)

Allocation TypeSingle-year Grants
Review Section Biological Sciences
Research InstitutionThe University of Tokyo

Principal Investigator

Tomari Yukihide  東京大学, 定量生命科学研究所, 教授 (90447368)

Co-Investigator(Kenkyū-buntansha) 多田隈 尚史  大阪大学, 蛋白質研究所, 助教 (10339707)
Research Collaborator SASAKI Hiroshi  
YAO Chunyan  
TSUBOYAMA Kotaro  
MASUBUCHI Takeya  
Project Period (FY) 2014-07-10 – 2019-03-31
Project Status Completed (Fiscal Year 2018)
Budget Amount *help
¥172,900,000 (Direct Cost: ¥133,000,000、Indirect Cost: ¥39,900,000)
Fiscal Year 2018: ¥34,060,000 (Direct Cost: ¥26,200,000、Indirect Cost: ¥7,860,000)
Fiscal Year 2017: ¥34,060,000 (Direct Cost: ¥26,200,000、Indirect Cost: ¥7,860,000)
Fiscal Year 2016: ¥34,060,000 (Direct Cost: ¥26,200,000、Indirect Cost: ¥7,860,000)
Fiscal Year 2015: ¥33,930,000 (Direct Cost: ¥26,100,000、Indirect Cost: ¥7,830,000)
Fiscal Year 2014: ¥36,790,000 (Direct Cost: ¥28,300,000、Indirect Cost: ¥8,490,000)
Keywords一分子イメージング / RNA干渉 / Argonaute / RISC / 生化学 / 生物物理学 / RNA / タンパク質 / small RNA / 一分子観察 / siRNA
Outline of Final Research Achievements

Using the effector complex of RNA interference, called "RISC," as a model system, we developed new techniques that can monitor the molecular dynamics of ncRNA machinery in a real-time and quantitative manner at the single-molecule level. We used these techniques to study the dynamic structural changes of Argonaute proteins, the core of RISC. We found that the structure of Argonaute, which is closed in the empty state, is first opened by helper factors. After incorporating the small RNAs, Argonaute takes a fixed, semi-open structure. Moreover, our data provided molecular insights into how RISC can recognize and cleave their targets so quickly and accurately. In conclusion, single-molecule imaging allowed us to uncover these detailed molecular mechanisms, which were not readily approachable by conventional biochemistry.

Academic Significance and Societal Importance of the Research Achievements

RNA干渉は、任意の遺伝子の発現を簡便にシャットダウンできるため、基礎生物学だけではなく、医薬への応用も進められているが、その分子レベルでの詳細なメカニズムはまだ完全に理解されているとは言えない。本研究によって、RISC形成や標的切断における律速段階を高い精度で同定し、それを突破するような配列デザインや化学修飾を行うことができれば、より高い効率で作用する小分子RNAの合理的設計が可能になることが期待される。

Report

(6 results)
  • 2018 Annual Research Report   Final Research Report ( PDF )
  • 2017 Annual Research Report
  • 2016 Annual Research Report
  • 2015 Annual Research Report
  • 2014 Annual Research Report
  • Research Products

    (34 results)

All 2019 2018 2017 2016 2015 2014 Other

All Int'l Joint Research (3 results) Journal Article (18 results) (of which Int'l Joint Research: 2 results,  Peer Reviewed: 18 results,  Open Access: 2 results,  Acknowledgement Compliant: 6 results) Presentation (13 results) (of which Int'l Joint Research: 8 results,  Invited: 11 results)

  • [Int'l Joint Research] University of Toronto(カナダ)

    • Related Report
      2017 Annual Research Report
  • [Int'l Joint Research] Michigan State University(米国)

    • Related Report
      2017 Annual Research Report
  • [Int'l Joint Research] マサチューセッツ州立大学(米国)

    • Related Report
      2014 Annual Research Report
  • [Journal Article] Iruka Eliminates Dysfunctional Argonaute by Selective Ubiquitination of Its Empty State2019

    • Author(s)
      Kobayashi Hotaka, Shoji Keisuke, Kiyokawa Kaori, Negishi Lumi, Tomari Yukihide
    • Journal Title

      Molecular Cell

      Volume: 73 Issue: 1 Pages: 119-129

    • DOI

      10.1016/j.molcel.2018.10.033

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Conformational Activation of Argonaute by Distinct yet Coordinated Actions of the Hsp70 and Hsp90 Chaperone Systems2018

    • Author(s)
      Tsuboyama K, Tadakuma H, Tomari Y
    • Journal Title

      Molecular Cell

      Volume: 70 Issue: 4 Pages: 722-729

    • DOI

      10.1016/j.molcel.2018.04.010

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Pervasive yet nonuniform contributions of Dcp2 and Cnot7 to maternal mRNA clearance in zebrafish2017

    • Author(s)
      Mishima Yuichiro、Tomari Yukihide
    • Journal Title

      Genes to Cells

      Volume: 22 Issue: 7 Pages: 670-678

    • DOI

      10.1111/gtc.12504

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] ilencing messages in a unique way2017

    • Author(s)
      Hiro-oki Iwakawa and Yukihide Tomari,
    • Journal Title

      Nature Plants,

      Volume: 3 Issue: 10 Pages: 769-770

    • DOI

      10.1038/s41477-017-0028-2

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Biochemical and single-molecule analyses of the RNA silencing suppressing activity of CrPV-1A.2017

    • Author(s)
      Watanabe M, Iwakawa HO, Tadakuma H, Tomari Y.
    • Journal Title

      Nucleic Acids Res.

      Volume: 45(18) Issue: 18 Pages: 10837-10844

    • DOI

      10.1093/nar/gkx748

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Structural basis for arginine methylation-independent recognition of PIWIL1 by TDRD2.2017

    • Author(s)
      Zhang H, Liu K, Izumi N, Huang H, Ding D, Ni Z, Sidhu SS, Chen C, Tomari Y, Min J.
    • Journal Title

      Proc Natl Acad Sci U S A

      Volume: 114 Issue: 47 Pages: 12483-12488

    • DOI

      10.1073/pnas.1711486114

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Reconstitution of RNA Interference Machinery2017

    • 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
    • Related Report
      2017 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Single-Molecule Analysis for RISC Assembly and Target Cleavage2017

    • Author(s)
      Sasaki Hiroshi M., Tadakuma Hisashi, Tomari Yukihide
    • Journal Title

      Methods Mol Biol

      Volume: 1680 Pages: 145-164

    • DOI

      10.1007/978-1-4939-7339-2_10

    • ISBN
      9781493973385, 9781493973392
    • Related Report
      2017 Annual Research Report
    • Peer Reviewed
  • [Journal Article] In vitro reconstitution of chaperone-mediated human RISC assembly2017

    • 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

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed
  • [Journal Article] The poly(A) tail blocks RDR6 from converting self mRNAs into substrates for gene silencing.2017

    • Author(s)
      Baeg K, *Iwakawa HO, *Tomari Y.
    • Journal Title

      Nature Plants

      Volume: 3 Issue: 4 Pages: 17036-17036

    • DOI

      10.1038/nplants.2017.36

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Codon Usage and 3' UTR Length Determine Maternal mRNA Stability in Zebrafish2016

    • Author(s)
      Yuichiro Mishima, Yukihide Tomari
    • Journal Title

      Molecular Cell

      Volume: 61(6) Issue: 6 Pages: 874-85

    • DOI

      10.1016/j.molcel.2016.02.027

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Identification and functional analysis of the pre-piRNA 3′ Trimmer in silkworms.2016

    • Author(s)
      Izumi N, Shoji K, Sakaguchi Y, Honda S, Kirino Y, Suzuki T, Katsuma S, Tomari Y
    • Journal Title

      Cell

      Volume: 164 Issue: 5 Pages: 962-973

    • DOI

      10.1016/j.cell.2016.01.008

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Int'l Joint Research / Acknowledgement Compliant
  • [Journal Article] Defining fundamental steps in the assembly of Drosophila RNAi enzyme complex2015

    • 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

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Single-molecule analysis of the target cleavage reaction by Drosophila RNAi enzyme complex2015

    • Author(s)
      Yao C, Sasaki HM, Ueda T, *Tomari Y, *Tadakuma H
    • Journal Title

      Molecular Cell (in press)

      Volume: - Issue: 1 Pages: 125-132

    • DOI

      10.1016/j.molcel.2015.05.015

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Cryptic RNA-binding by PRC2 components EZH2 and SUZ12.2015

    • Author(s)
      Betancur JG, *Tomari Y.
    • Journal Title

      RNA Biol.

      Volume: 12 Issue: 9 Pages: 959-65

    • DOI

      10.1080/15476286.2015.1069463

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Elements and machinery of non-coding RNAs: toward their taxonomy2014

    • Author(s)
      Tetsuro Hirose, Yuichiro Mishima, Yukihide Tomari
    • Journal Title

      EMBO Reports

      Volume: 印刷中 Issue: 5 Pages: 489-507

    • DOI

      10.1002/embr.201338390

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] MicroRNAs block assembly of eIF4F translation initiation complex in Drosophila2014

    • Author(s)
      #Takashi Fukaya, #Hiro-oki Iwakawa, *Yukihide Tomari, (#同等貢献)
    • Journal Title

      Molecular Cell

      Volume: 56 Issue: 1 Pages: 67-78

    • DOI

      10.1016/j.molcel.2014.09.004

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed
  • [Journal Article] The initial uridine of primary piRNAs does not create the tenth adenine that Is the hallmark of secondary piRNAs.2014

    • Author(s)
      Wang W, Yoshikawa M, Han BW, Izumi N, Tomari Y, Weng Z, Zamore PD
    • Journal Title

      Mol Cell

      Volume: 56 Issue: 5 Pages: 708-716

    • DOI

      10.1016/j.molcel.2014.10.016

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed
  • [Presentation] Iruka ensures the quality of Argonaute by selective ubiquitination of its empty state.2018

    • Author(s)
      小林 穂高
    • Organizer
      13th Microsymposium on Small RNA Biology
    • Related Report
      2018 Annual Research Report
    • Invited
  • [Presentation] Conformational activation of Argonaute by distinct yet coordinated actions of the Hsp70 and Hsp902018

    • Author(s)
      坪山 幸太郎
    • Organizer
      The 2018 Gordon Research Conference
    • Related Report
      2018 Annual Research Report
  • [Presentation] Biochemical and biophysical dissection of RNA silencing2018

    • Author(s)
      泊 幸秀
    • Organizer
      Vienna RNA conference 2018 "RNA-REG: Tegulatory Circuits in RNA Biology"
    • Related Report
      2018 Annual Research Report
    • Invited
  • [Presentation] Iruka ensures the quality of Argonaute by selective ubiquitination of its empty state2018

    • Author(s)
      泊 幸秀
    • Organizer
      CSHA meeting on RNA Biology
    • Related Report
      2018 Annual Research Report
    • Invited
  • [Presentation] Assembly and function of the RNA silencing complex2018

    • Author(s)
      泊 幸秀
    • Organizer
      Temasek Life Sciences Laboratory Seminar Series
    • Related Report
      2018 Annual Research Report
    • Invited
  • [Presentation] Biochemical and biophysical dissection of RNA silencing pathways2017

    • Author(s)
      泊 幸秀
    • Organizer
      RNA as a guide - Barbados workshop
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Single-molecule analysis of the RNA silencing pathways2017

    • Author(s)
      泊 幸秀
    • Organizer
      RNA 2017
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Biochemical and biophysical dissection of RNA silencing pathways2017

    • Author(s)
      泊 幸秀
    • Organizer
      RNA Symposium 2017, Non-cording RNAs: Structure and Function
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Dissection of RISC assembly and function by single-molecule imaging2016

    • Author(s)
      泊 幸秀
    • Organizer
      8th International Conference on the Hsp90 Chaperone Machine
    • Place of Presentation
      Seeon Abbey, Germany
    • Year and Date
      2016-11-02
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Surveillance of aberrant mRNAs by plant RDR62016

    • Author(s)
      泊 幸秀
    • Organizer
      The Complex Life of mRNA
    • Place of Presentation
      EMBL Heidelberg, Germany
    • Year and Date
      2016-10-05
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] A clade of plant AGO proteins prefer to bind DNA (rather than RNA) targets2016

    • Author(s)
      泊 幸秀
    • Organizer
      Regulatory & Non-Cording RNAs
    • Place of Presentation
      Cold Spring Harbor Laboratory, NY, USA
    • Year and Date
      2016-08-23
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Identification of “Trimmer” the pre-piRNA trimming enzyme in silkworms2015

    • Author(s)
      泊 幸秀
    • Organizer
      Microsymposium on small RNAs
    • Place of Presentation
      IMBA, Vienna, Austria
    • Year and Date
      2015-05-04
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Defining fundamental steps in the assembly of Drosophila RNAi enzyme complex2014

    • Author(s)
      Yukihide Tomari
    • Organizer
      Joint Australia-Japan RNA Conference
    • Place of Presentation
      Sydney, Australia
    • Year and Date
      2014-11-02
    • Related Report
      2014 Annual Research Report
    • Int'l Joint Research / Invited

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Published: 2014-11-20   Modified: 2022-01-27  

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