• Search Research Projects
  • Search Researchers
  • How to Use
  1. Back to previous page

Biochemical approaches to understanding the reaction platforms of the piRNA pathway

Research Project

Project/Area Number 18H05271
Research Category

Grant-in-Aid for Scientific Research (S)

Allocation TypeSingle-year Grants
Review Section Broad Section G
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) 中川 真一  北海道大学, 薬学研究院, 教授 (50324679)
Project Period (FY) 2018-06-11 – 2023-03-31
Project Status Completed (Fiscal Year 2022)
Budget Amount *help
¥193,570,000 (Direct Cost: ¥148,900,000、Indirect Cost: ¥44,670,000)
Fiscal Year 2022: ¥32,370,000 (Direct Cost: ¥24,900,000、Indirect Cost: ¥7,470,000)
Fiscal Year 2021: ¥32,370,000 (Direct Cost: ¥24,900,000、Indirect Cost: ¥7,470,000)
Fiscal Year 2020: ¥32,370,000 (Direct Cost: ¥24,900,000、Indirect Cost: ¥7,470,000)
Fiscal Year 2019: ¥51,350,000 (Direct Cost: ¥39,500,000、Indirect Cost: ¥11,850,000)
Fiscal Year 2018: ¥45,110,000 (Direct Cost: ¥34,700,000、Indirect Cost: ¥10,410,000)
KeywordspiRNA / PIWI-interacting RNA / 反応場 / RNAサイレンシング / PIWI / 小分子RNA / GTSF1 / 細胞内構造体 / nuage / P-body / ミトコンドリア / Zucchini / Trimmer
Outline of Final Research Achievements

We have developed unique biochemical systems that take out the entire "reaction platforms" for piRNAs from cells into test tubes with retaining their proper functions. We have also developed bioinformatic frameworks that can extract the "rules" behind those biochemical reactions. By combining these two approaches, we uncovered how piRNA precursors are processed into mature piRNAs on the outer membrane of mitochondria. Moreover, we discovered a new reaction platform for piRNAs in silkworms and proposed its biological significance. We have also identified novel accessory factors that highly accelerate the piRNA biogenesis reaction. Finally, we carefully characterized a representative "piRNA cluster," the genomic region from which piRNAs are produced.

Academic Significance and Societal Importance of the Research Achievements

piRNAが機能する「反応場」を、正しく活性のある形で試験管内に取り出し、piRNAがはたらくまさにその「現場」を丁寧に素過程に分けて生化学的に解析するとともに、その結果を生物情報学的に検証しさらに発展させることによって、これまでにモデルに過ぎなかったpiRNAの成熟過程の分子メカニズムを正確に明らかにすることに成功した。また、これまでは、基本的には触媒作用を持つ酵素によってのみ再構成され理解されてきた生化学系に、「反応場」という観点を取り入れたことは、piRNA経路だけにとどまらず、細胞内の反応場に依存する他の様々な経路に広く適応可能であり、大きな波及効果を生み出すと考えられる。

Assessment Rating
Ex-post Assessment Comments (Rating)

A+: In light of the aim of introducing the research area into the research categories, more research outcomes have been produced than expected.

Assessment Rating
Interim Assessment Comments (Rating)

A: In light of the aim of introducing the research area into the research categories, the expected progress has been made in research.

Report

(11 results)
  • 2023 Ex-post Assessment (Comments) ( PDF )
  • 2022 Annual Research Report   Final Research Report ( PDF )
  • 2021 Annual Research Report
  • 2020 Abstract (Interim Assessment) ( PDF )   Annual Research Report   Interim Assessment (Comments) ( PDF )
  • 2019 Annual Research Report
  • 2018 Abstract ( PDF )   Comments on the Screening Results ( PDF )   Annual Research Report
  • Research Products

    (44 results)

All 2023 2022 2021 2020 2019 2018 Other

All Int'l Joint Research (8 results) Journal Article (20 results) (of which Int'l Joint Research: 4 results,  Peer Reviewed: 20 results,  Open Access: 12 results) Presentation (14 results) (of which Int'l Joint Research: 13 results,  Invited: 14 results) Patent(Industrial Property Rights) (2 results) (of which Overseas: 1 results)

  • [Int'l Joint Research] University of Massachusetts/Thomas Jefferson University/Scripps Research(米国)

    • Related Report
      2022 Annual Research Report
  • [Int'l Joint Research] 上海科技大学(中国)

    • Related Report
      2022 Annual Research Report
  • [Int'l Joint Research] University of Massachusetts/Thomas Jefferson University(米国)

    • Related Report
      2021 Annual Research Report
  • [Int'l Joint Research] 上海科技大学(中国)

    • Related Report
      2021 Annual Research Report
  • [Int'l Joint Research] University of Massachusetts/Thomas Jefferson University(米国)

    • Related Report
      2020 Annual Research Report
  • [Int'l Joint Research] 上海科技大学(中国)

    • Related Report
      2020 Annual Research Report
  • [Int'l Joint Research] Thomas Jefferson University(米国)

    • Related Report
      2019 Annual Research Report
  • [Int'l Joint Research] Chinese Academy of Sciences(中国)

    • Related Report
      2019 Annual Research Report
  • [Journal Article] The piRNA cluster torimochi is an expanding transposon in cultured silkworm cells2023

    • Author(s)
      Shoji Keisuke、Umemura Yusuke、Katsuma Susumu、Tomari Yukihide
    • Journal Title

      PLOS Genetics

      Volume: 19 Issue: 2 Pages: e1010632-e1010632

    • DOI

      10.1371/journal.pgen.1010632

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Functional specialization of monocot DCL3 and DCL5 proteins through the evolution of the PAZ domain2022

    • Author(s)
      Chen Shirui、Liu Wei、Naganuma Masahiro、Tomari Yukihide、Iwakawa Hiro-oki
    • Journal Title

      Nucleic Acids Research

      Volume: 50 Issue: 8 Pages: 4669-4684

    • DOI

      10.1093/nar/gkac223

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Structure of the Dicer-2-R2D2 heterodimer bound to a small RNA duplex2022

    • Author(s)
      Yamaguchi Sonomi、Naganuma Masahiro、Nishizawa Tomohiro、Kusakizako Tsukasa、Tomari Yukihide、Nishimasu Hiroshi、Nureki Osamu
    • Journal Title

      Nature

      Volume: 607 Issue: 7918 Pages: 393-398

    • DOI

      10.1038/s41586-022-04790-2

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] GTSF1 accelerates target RNA cleavage by PIWI-clade Argonaute proteins2022

    • Author(s)
      Arif Amena、Bailey Shannon、Izumi Natsuko、Anzelon Todd A.、Ozata Deniz M.、Andersson Cecilia、Gainetdinov Ildar、MacRae Ian J.、Tomari Yukihide、Zamore Phillip D.
    • Journal Title

      Nature

      Volume: 608 Issue: 7923 Pages: 618-625

    • DOI

      10.1038/s41586-022-05009-0

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Revisiting the Glass Treatment for Single-Molecule Analysis of ncRNA Function2022

    • Author(s)
      Shen Shuting、Naganuma Masahiro、Tomari Yukihide、Tadakuma Hisashi
    • Journal Title

      Methods Mol Biol

      Volume: 2022;2509 Pages: 209-231

    • DOI

      10.1007/978-1-0716-2380-0_13

    • ISBN
      9781071623794, 9781071623800
    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] The two Gtsf paralogs in silkworms orthogonally activate their partner PIWI proteins for target cleavage2022

    • Author(s)
      Izumi Natsuko、Shoji Keisuke、Kiuchi Takashi、Katsuma Susumu、Tomari Yukihide
    • Journal Title

      RNA

      Volume: 29 Issue: 1 Pages: 18-29

    • DOI

      10.1261/rna.079380.122

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] The mechanisms of siRNA selection by plant Argonaute proteins triggering DNA methylation2022

    • Author(s)
      Liu Wei、Shoji Keisuke、Naganuma Masahiro、Tomari Yukihide、Iwakawa Hiro-oki
    • Journal Title

      Nucleic Acids Research

      Volume: 50 Issue: 22 Pages: 12997-13010

    • DOI

      10.1093/nar/gkac1135

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Life of RISC: Formation, action, and degradation of RNA-induced silencing complex2022

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

      Molecular Cell

      Volume: 82 Issue: 1 Pages: 30-43

    • DOI

      10.1016/j.molcel.2021.11.026

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Ribosome stalling caused by the Argonaute-microRNA-SGS3 complex regulates the production of secondary siRNAs in plants2021

    • Author(s)
      Iwakawa Hiro-oki、Lam Andy Y.W.、Mine Akira、Fujita Tomoya、Kiyokawa Kaori、Yoshikawa Manabu、Takeda Atsushi、Iwasaki Shintaro、Tomari Yukihide
    • Journal Title

      Cell Reports

      Volume: 35 Issue: 13 Pages: 109300-109300

    • DOI

      10.1016/j.celrep.2021.109300

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Single-molecule analysis of processive double-stranded RNA cleavage by Drosophila Dicer-22021

    • Author(s)
      Naganuma Masahiro、Tadakuma Hisashi、Tomari Yukihide
    • Journal Title

      Nature Communications

      Volume: 12 Issue: 1 Pages: 4268-4268

    • DOI

      10.1038/s41467-021-24555-1

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] RNase κ promotes robust piRNA production by generating 2',3'-cyclic phosphate-containing precursors.2021

    • Author(s)
      Shigematsu M, Kawamura T, Morichika K, Izumi N, Kiuchi T, Honda S, Pliatsika V, Matsubara R, Rigoutsos I, Katsuma S, Tomari Y, Kirino Y.
    • Journal Title

      Nat Commun.

      Volume: 12 Issue: 1 Pages: 4498-4498

    • DOI

      10.1038/s41467-021-24681-w

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Cell-free reconstitution reveals the molecular mechanisms for the initiation of secondary siRNA biogenesis in plants2021

    • Author(s)
      Sakurai Yuriki、Baeg Kyungmin、Lam Andy Y. W.、Shoji Keisuke、Tomari Yukihide、Iwakawa Hiro-oki
    • Journal Title

      Proceedings of the National Academy of Sciences

      Volume: 118 Issue: 31

    • DOI

      10.1073/pnas.2102889118

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Mechanistic analysis of the enhanced RNAi activity by 6-mCEPh-purine at the 5′ end of the siRNA guide strand2020

    • Author(s)
      Brechin Vincent、Shinohara Fumikazu、Saito Jun-ichi、Seitz Herv?、Tomari Yukihide
    • Journal Title

      RNA

      Volume: 27 Issue: 2 Pages: 151-162

    • DOI

      10.1261/rna.073775.119

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed
  • [Journal Article] siRNA potency enhancement via chemical modifications of nucleotide bases at the 5′-end of the siRNA guide strand2020

    • Author(s)
      Shinohara Fumikazu、Oashi Taiji、Harumoto Toshimasa、Nishikawa Tomoyuki、Takayama Yuki、Miyagi Hikaru、Takahashi Yuichi、Nakajima Takahiro、Sawada Takashi、Koda Yasuo、Makino Asana、Sato Atsuko、Hamaguchi Kaori、Suzuki Michihiko、Yamamoto Junichiro、Tomari Yukihide、Saito Jun-Ichi
    • Journal Title

      RNA

      Volume: 27 Issue: 2 Pages: 163-173

    • DOI

      10.1261/rna.073783.119

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Zucchini consensus motifs determine the mechanism of pre-piRNA production2020

    • Author(s)
      Izumi Natsuko、Shoji Keisuke、Suzuki Yutaka、Katsuma Susumu、Tomari Yukihide
    • Journal Title

      Nature

      Volume: 578 Issue: 7794 Pages: 311-316

    • DOI

      10.1038/s41586-020-1966-9

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed
  • [Journal Article] A Widespread Family of Heat-Resistant Obscure (Hero) Proteins Protect Against Protein Instability and Aggregation2020

    • Author(s)
      Tsuboyama K, Osaki T, Matsuura-Suzuki E, Kozuka-Hata H, Okada Y, Oyama M, Ikeuchi Y, Iwasaki S, Tomari Y
    • Journal Title

      PLOS Biology

      Volume: 18 Issue: 3 Pages: 3000632-3000632

    • DOI

      10.1371/journal.pbio.3000632

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] VCP Machinery Mediates Autophagic Degradation of Empty Argonaute2019

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

      Cell Reports

      Volume: 28 Issue: 5 Pages: 1144-1153

    • DOI

      10.1016/j.celrep.2019.07.003

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Identification of an AGO (Argonaute) protein as a prey of TER94/VCP2019

    • Author(s)
      Kobayashi Hotaka、Tomari Yukihide
    • Journal Title

      Autophagy

      Volume: 16 Issue: 1 Pages: 190-192

    • DOI

      10.1080/15548627.2019.1691351

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed
  • [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
  • [Presentation] Small RNAs2022

    • Author(s)
      泊 幸秀
    • Organizer
      RNA2022, Colorado, USA
    • Related Report
      2022 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] The two Gtsf paralogs in silkworms orthogonally activate their partner PIWI proteins for target cleavage2022

    • Author(s)
      泊 幸秀
    • Organizer
      The ”Argonautes” conference, Regensburg, Germany
    • Related Report
      2022 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] A canonical chaperone and a heat-resistant obscure (Hero) protein mediate similar aggregation suppression and conformational extension of TDP-432022

    • Author(s)
      泊 幸秀
    • Organizer
      Cold Spring Harbor Asia, RNA Biology, AWAJI, Japan
    • Related Report
      2022 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Assembly of the RNA Silencing Complex (and Beyond)2021

    • Author(s)
      泊 幸秀
    • Organizer
      2021 RNA Biology Symposium
    • Related Report
      2021 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] RNAサイレンシング複合体の形成と機能2021

    • Author(s)
      泊 幸秀
    • Organizer
      日本エピジェネティクス研究会
    • Related Report
      2020 Annual Research Report
    • Invited
  • [Presentation] Hero proteins: widespread protectors against protein instability2020

    • Author(s)
      泊 幸秀
    • Organizer
      MBSJ 2020 Workshop
    • Related Report
      2020 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] The mechanism of pre-piRNA production2020

    • Author(s)
      泊 幸秀
    • Organizer
      UTRs in Development and Disease
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Assembly of the RNA-induced silencing complex and beyond2019

    • Author(s)
      泊 幸秀
    • Organizer
      RiboClub the 20th Anniversary
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Assembly and function of the RNA silencing complex2019

    • Author(s)
      泊 幸秀
    • Organizer
      FASEB SRC The RNA Localization and Local Translation Conference
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] 3′-end maturation of silkworm piRNAs2019

    • Author(s)
      泊 幸秀
    • Organizer
      Keystone Symposia Small Regulatory RNAs
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] A conserved step-wise maturation mechanism of piRNAs2018

    • Author(s)
      泊 幸秀
    • Organizer
      EMBO Workshop: piRNAs and PIWI proteins
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Biochemical and biophysical dissection of RNA silencing2018

    • Author(s)
      泊 幸秀
    • Organizer
      RNA-REG: Regulatory Circuits in RNA Biology
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Iruka ensures the quality of Argonaute by selective ubiquitination of its empty state2018

    • Author(s)
      泊 幸秀
    • Organizer
      CSH Asia Meeting on RNA Biology
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Iruka ensures the quality of Argonaute by selective ubiquitination of its empty state2018

    • Author(s)
      泊 幸秀
    • Organizer
      Joint Australia-Japan RNA Meeting 2018
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research / Invited
  • [Patent(Industrial Property Rights)] クライアントタンパク質を保護するタンパク質のスクリーニング方法並びに生理活性タンパク質安定化タンパク質および該タンパク質を含む医薬組成物2019

    • Inventor(s)
      泊 幸秀、岩崎 信太郎、坪山 幸太郎、他4名
    • Industrial Property Rights Holder
      東京大学
    • Industrial Property Rights Type
      特許
    • Filing Date
      2019
    • Related Report
      2019 Annual Research Report
  • [Patent(Industrial Property Rights)] Protein stabilization by fully unstructured proteins2018

    • Inventor(s)
      坪山 幸太郎, 岩崎 信太郎, 泊 幸秀
    • Industrial Property Rights Holder
      東京大学
    • Industrial Property Rights Type
      特許
    • Filing Date
      2018
    • Related Report
      2018 Annual Research Report
    • Overseas

URL: 

Published: 2018-06-12   Modified: 2024-03-28  

Information User Guide FAQ News Terms of Use Attribution of KAKENHI

Powered by NII kakenhi