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Elucidation of the mechanisms governing the structure, physical properties, and functions of membraneless RNP bodies

Research Project

Project/Area Number 23K23809
Project/Area Number (Other) 22H02545 (2022-2023)
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypeMulti-year Fund (2024)
Single-year Grants (2022-2023)
Section一般
Review Section Basic Section 43010:Molecular biology-related
Research InstitutionOsaka University

Principal Investigator

Yamazaki Tomohiro  大阪大学, 大学院生命機能研究科, 准教授 (90732280)

Project Period (FY) 2024-04-01 – 2025-03-31
Project Status Completed (Fiscal Year 2024)
Budget Amount *help
¥17,420,000 (Direct Cost: ¥13,400,000、Indirect Cost: ¥4,020,000)
Fiscal Year 2024: ¥5,590,000 (Direct Cost: ¥4,300,000、Indirect Cost: ¥1,290,000)
Fiscal Year 2023: ¥5,590,000 (Direct Cost: ¥4,300,000、Indirect Cost: ¥1,290,000)
Fiscal Year 2022: ¥6,240,000 (Direct Cost: ¥4,800,000、Indirect Cost: ¥1,440,000)
Keywords細胞内相分離 / 非膜性構造体 / ブロック共重合体 / ミセル化 / ソフトマター物理 / 構成的アプローチ / 天然変性タンパク質 / RNA結合タンパク質 / 非膜オルガネラ / lncRNA / MCP融合タンパク質ライブラリー / RNAウイルス / 相分離 / architectural RNA / パラスペックル / 核内ストレス体 / 非膜性オルガネラ / RNA / NEAT1 / SARS-CoV-2
Outline of Research at the Start

細胞は、生化学反応を時空間的に制御する必要がある。そのため、細胞は、相分離機構により誘導される「非膜性構造体」を利用することで、複雑な細胞内反応を支えている。申請者は、RNAが必須の骨格となる非膜性構造体を解析し、RNAがその設計図として働き、形成や機能発現を規定していることを明らかにしてきた。しかし、その理解は十分ではなく、体系的な理解には至っていない。そこで、本研究では、ソフトマター物理学や構成的アプローチなども取り入れ、RNAとそのパートナーであるRNA結合タンパク質が構築する非膜性構造体の構造・物性・機能を規定する原理を解析し、多様かつ複雑な細胞内非膜性構造体の作動原理を明らかにする。

Outline of Final Research Achievements

We aimed to elucidate the principles underlying the formation of membraneless structures mediated by RNA and their partner RNA-binding proteins. By incorporating physical theories into our analyses, we revealed that paraspeckles behave as block copolymer micelles and uncovered the role of nascent RNA in controlling the size of the internal architecture of nucleoli. We also shed light on the mechanisms that allow the coexistence of numerous membraneless structures within the cell. Furthermore, using a synthetic approach, we conducted a large-scale screen of proteins that induce membraneless structures in cells and analyzed their induction mechanisms, thereby gaining important insights into unresolved questions in the study of intracellular phase separation.

Academic Significance and Societal Importance of the Research Achievements

細胞内の多様な生命現象に相分離が関与していることが明らかになりつつあり、細胞内現象の理解においてパラダイムシフトが起こっている。本研究では、物理理論や構成的アプローチを取り入れることで、細胞内相分離の基盤となるメカニズムの解明に取り組んだ。その結果、新規の細胞内相分離現象や非膜性構造体のサイズ制御の仕組み、複数の非膜性構造体が細胞内で共存可能となる原理を明らかにした。さらに、相分離を誘導する中核的なタンパク質の大規模な同定にも成功した。これらの成果は、RNAにより誘導される多様な非膜性構造体の形成原理と機能を理解するための重要な基盤となることが期待できる。

Report

(4 results)
  • 2024 Annual Research Report   Final Research Report ( PDF )
  • 2023 Annual Research Report
  • 2022 Annual Research Report
  • Research Products

    (44 results)

All 2025 2024 2023 2022 Other

All Int'l Joint Research (2 results) Journal Article (14 results) (of which Int'l Joint Research: 2 results,  Peer Reviewed: 12 results,  Open Access: 9 results) Presentation (16 results) (of which Int'l Joint Research: 5 results,  Invited: 6 results) Book (4 results) Remarks (8 results)

  • [Int'l Joint Research] CNRS/UMS 3655, AMMICA(フランス)

    • Related Report
      2024 Annual Research Report
  • [Int'l Joint Research] CNRS/UMS 3655, AMMICA(フランス)

    • Related Report
      2023 Annual Research Report
  • [Journal Article] Biophysical Aspect of Assembly and Regulation of Nuclear Bodies Scaffolded by Architectural RNA2025

    • Author(s)
      Yamamoto Tetsuya、Yamazaki Tomohiro、Ninomiya Kensuke、Nakagawa Shinichi、Hirose Tetsuro
    • Journal Title

      Journal of Molecular Biology

      Volume: 437 Issue: 9 Pages: 169016-169016

    • DOI

      10.1016/j.jmb.2025.169016

    • Related Report
      2024 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Blocky proline/glutamine patterns in the SFPQ intrinsically disordered region dictate paraspeckle formation as a distinct membraneless organelle2025

    • Author(s)
      Takakuwa Hiro、Yoda Takao、Yamazaki Tomohiro、Hirose Tetsuro
    • Journal Title

      bioRxiv

      Volume: -

    • DOI

      10.1101/2025.02.21.639608

    • Related Report
      2024 Annual Research Report
  • [Journal Article] Huntingtin is an RNA binding protein and participates in <i>NEAT1</i> -mediated paraspeckles2024

    • Author(s)
      Yadav Manisha、Harding Rachel J.、Li Tiantian、Yamazaki Tomohiro、Hirose Tetsuro、Prinos Panagiotis、Tippett Lynette、Turner Clinton、Curtis Maurice A.、Faull Richard L.M.、Pouladi Mahmoud A.、Pearson Christopher E.、He Housheng Hansen、Arrowsmith Cheryl H.
    • Journal Title

      Science Advances

      Volume: 10 Issue: 29 Pages: 5264-5264

    • DOI

      10.1126/sciadv.ado5264

    • Related Report
      2024 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Terminal regions of UAP56 and URH49 are required for their distinct complex formation functioning to an essential role in mRNA processing and export.2024

    • Author(s)
      K-I. Fujita, T. Yamazaki, A. Mayeda, S. Masuda
    • Journal Title

      Biochemical and Biophysical Research Communications

      Volume: 703 Pages: 149682-149682

    • DOI

      10.1016/j.bbrc.2024.149682

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Structural differences between the closely related RNA helicases, UAP56 and URH49, fashion distinct functional apo-complexes.2024

    • Author(s)
      K-I. Fujita, M. Ito, M. Irie, K. Harada, N. Fujiwara, Y. Ikeda, H. Yoshioka, T. Yamazaki, M. Kojima, B. Mikami, A. Mayeda, S. Masuda
    • Journal Title

      Nature Communications

      Volume: 15 Issue: 1 Pages: 455-455

    • DOI

      10.1038/s41467-023-44217-8

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] 4.5SH RNA counteracts deleterious exonization of SINE B1 in mice2023

    • Author(s)
      Yoshimoto Rei、Nakayama Yuta、Nomura Ikuko、Yamamoto Ikuko、Nakagawa Yumeka、Tanaka Shigeyuki、Kurihara Misuzu、Suzuki Yu、Kobayashi Takehiko、Kozuka-Hata Hiroko、Oyama Masaaki、Mito Mari、Iwasaki Shintaro、Yamazaki Tomohiro、Hirose Tetsuro、Araki Kimi、Nakagawa Shinichi
    • Journal Title

      Molecular Cell

      Volume: 83 Issue: 24 Pages: 4479-4493

    • DOI

      10.1016/j.molcel.2023.11.019

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Nascent ribosomal RNA act as surfactant that suppresses growth of fibrillar centers in nucleolus2023

    • Author(s)
      Yamamoto Tetsuya、Yamazaki Tomohiro、Ninomiya Kensuke、Hirose Tetsuro
    • Journal Title

      Communications Biology

      Volume: 6 Issue: 1 Pages: 1129-1129

    • DOI

      10.1038/s42003-023-05519-1

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Shell protein composition specified by the lncRNA NEAT1 domains dictates the formation of paraspeckles as distinct membraneless organelles2023

    • Author(s)
      Takakuwa Hiro、Yamazaki Tomohiro、Souquere Sylvie、Adachi Shungo、Yoshino Hyura、Fujiwara Naoko、Yamamoto Tetsuya、Natsume Tohru、Nakagawa Shinichi、Pierron Gerard、Hirose Tetsuro
    • Journal Title

      Nature Cell Biology

      Volume: 25 Issue: 11 Pages: 1664-1675

    • DOI

      10.1038/s41556-023-01254-1

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Triblock copolymer micelle model of spherical paraspeckles2022

    • Author(s)
      Tetsuya Yamamoto, Tomohiro Yamazaki, and Tetsuro Hirose
    • Journal Title

      Front. Mol. Biosci.

      Volume: 9 Pages: 925058-925058

    • DOI

      10.3389/fmolb.2022.925058

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Micellization: A new principle in the formation of biomolecular condensates2022

    • Author(s)
      Tomohiro Yamazaki, Tetsuya Yamamoto, and Tetsuro Hirose
    • Journal Title

      Front. Mol. Biosci.

      Volume: 9 Pages: 974772-974772

    • DOI

      10.3389/fmolb.2022.974772

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Statistical Thermodynamics Approach for Intracellular Phase Separation2022

    • Author(s)
      Tomohiro Yamazaki
    • Journal Title

      Methods Mol. Biol.

      Volume: 2509 Pages: 361-393

    • DOI

      10.1007/978-1-0716-2380-0_22

    • ISBN
      9781071623794, 9781071623800
    • Related Report
      2022 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Remarkable improvement in detection of readthrough downstream-of-gene transcripts by semi-extractable RNA-sequencing2022

    • Author(s)
      Iwakiri Junichi、Tanaka Kumiko、Chujo Takeshi、Takakuwa Hiro、Yamazaki Tomohiro、Terai Goro、Asai Kiyoshi、Hirose Tetsuro
    • Journal Title

      RNA

      Volume: 29 Issue: 2 Pages: 170-177

    • DOI

      10.1261/rna.079469.122

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed
  • [Journal Article] A guide to membraneless organelles and their various roles in gene regulation2022

    • Author(s)
      Hirose Tetsuro、Ninomiya Kensuke、Nakagawa Shinichi、Yamazaki Tomohiro
    • Journal Title

      Nature Reviews Molecular Cell Biology

      Volume: 24 Issue: 4 Pages: 288-304

    • DOI

      10.1038/s41580-022-00558-8

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Editorial: The why of RNA granules: Form, function, and regulation2022

    • Author(s)
      Yamazaki Tomohiro、Audas Timothy E.、Farny Natalie G.
    • Journal Title

      Frontiers in Molecular Biosciences

      Volume: 9

    • DOI

      10.3389/fmolb.2022.1111463

    • Related Report
      2022 Annual Research Report
  • [Presentation] 細胞内非膜オルガネラの形成を誘導するタンパク質の大規模探索2024

    • Author(s)
      山崎智弘
    • Organizer
      第24回日本蛋白質科学会年会
    • Related Report
      2024 Annual Research Report
    • Invited
  • [Presentation] Micellization of block copolymers: A new principle in the formation of biomolecular condensates with RNA scaffolds2024

    • Author(s)
      Tomohiro Yamazaki, Tetsuya Yamamoto, Ichiro Taniguchi, Sota Umezaki, Hiro Takakuwa, Sylvie Souquere, Shinichi Nakagawa, Gerard Pierron, Tetsuro Hirose
    • Organizer
      International symposium on mechanical control of biological self-organization
    • Related Report
      2024 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Mapping of the NEAT1_2 lncRNA domains that define the micelle structure and morphology of paraspeckles2024

    • Author(s)
      Sota Umezaki, Tomohiro Yamazaki, Hiro Takakuwa, Tetsuro Hirose
    • Organizer
      第24回日本RNA学会年会
    • Related Report
      2024 Annual Research Report
  • [Presentation] 非膜性構造体の形成と機能に関わるlncRNAエレメントの解明2024

    • Author(s)
      山崎智弘
    • Organizer
      RNAインフォマティクス道場
    • Related Report
      2024 Annual Research Report
  • [Presentation] Large-scale identification of proteins that initiate the formation of bimolecular condensates in cells2024

    • Author(s)
      Tomohiro Yamazaki
    • Organizer
      International Symposium on Multifaceted Protein Dynamics
    • Related Report
      2024 Annual Research Report
    • Int'l Joint Research
  • [Presentation] The Formation Mechanisms and Molecular Bases:Biomolecular Condensates with RNA Scaffolds2024

    • Author(s)
      Tomohiro Yamazaki
    • Organizer
      IPR seminar, The 8th LLPS Symposium/ The Biophysical Society of Japan Joint Seminar “Toward establishing LLPS research systems”
    • Related Report
      2024 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] The Formation Mechanisms & Molecular Bases of Biomolecular Condensates with RNA Scaffolds2024

    • Author(s)
      Tomohiro Yamazaki
    • Organizer
      Paraspeckles and Condensates Symposium (2nd Internatinal Paraspeckle Focused Symposium)
    • Related Report
      2024 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Biomolecular condensates scaffolded by RNAs: Towards a theoretical and systematic understanding of their formation and function2023

    • Author(s)
      Tomohiro Yamzaki, Tetsuya Yamamoto, Hyura Yoshino, Hiro Takakuwa, Sylvie Souquere, Wakana Isshiki, Mizuki Iwata, Rie Doi, Shinichi Nakagawa, Gerard Pierron, Tetsuro Hirose
    • Organizer
      28th Annual Meeting of the RNA Society
    • Related Report
      2023 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Large-scale identification of RNA-binding proteins that initiate the formation of biomoleuclar condensates in cells2023

    • Author(s)
      Tomohiro Yamzaki, Doi Rie, Mizuki Iwata, Wakana Isshiki, Hiro Takakuwa, Tetsuro Hirose
    • Organizer
      第24回日本RNA学会年会
    • Related Report
      2023 Annual Research Report
  • [Presentation] Large-scale identification of RNA-binding proteins that initiate the formation of biomoleuclar condensates in cells2023

    • Author(s)
      山崎智弘
    • Organizer
      第1回関西RNA club
    • Related Report
      2023 Annual Research Report
    • Invited
  • [Presentation] 物理理論と構成的アプローチを用いたRNAを足場とする非膜性構造体の作動原理の理解2023

    • Author(s)
      山崎智弘、山本哲也、高桑央、吉野彪羅、Sylvie Souquere、土井理恵、岩田瑞季、一色和奏、梅崎創太、中川真一、Gerard Pierron、廣瀬哲郎
    • Organizer
      第96回日本生化学会大会
    • Related Report
      2023 Annual Research Report
    • Invited
  • [Presentation] パラスペックルのミセル構造と形態を規定するNEAT1_2 RNAドメインマッピング2023

    • Author(s)
      梅崎創太、山崎智弘、高桑央、廣瀬哲郎
    • Organizer
      第46回日本分子生物学会年会
    • Related Report
      2023 Annual Research Report
  • [Presentation] Formation mechanisms of SARS-CoV-2 viral RNPs with cellular host proteins2023

    • Author(s)
      山崎 智弘、土井 理恵、廣瀬 哲郎
    • Organizer
      大阪大学先導的学際研究機構 RNAフロンティアサイエンス部門 第一回 RNA-FSシンポジウム RNA研究が拓く生命科学
    • Related Report
      2022 Annual Research Report
  • [Presentation] Biomolecular condensates scaffolded by RNAs: towards their theoretical and systematic understandings2022

    • Author(s)
      Tomohiro Yamazaki, Tetsuya Yamamoto, Hyura Yoshino, Hiro Takakuwa, Sylvie Souquere, Wakana Isshiki, Mizuki Iwata, Rie Doi, Shinichi Nakagawa, Gerard Pierron, Tetsuro Hirose
    • Organizer
      第23回日本RNA学会年会
    • Related Report
      2022 Annual Research Report
  • [Presentation] RNAを設計図とする非膜オルガネラの形成原理2022

    • Author(s)
      山崎 智弘、山本 哲也、吉野 彪羅、高桑 央、Sylvie Souquere、土井 理恵、岩田 瑞季、一色 和奏、中川 真一、Gerard Pierron、廣瀬 哲郎
    • Organizer
      RNAフロンティアミーティング
    • Related Report
      2022 Annual Research Report
  • [Presentation] 理論と構成的アプローチを用いたRNAを足場とする非膜オルガネラの形成原理の解析2022

    • Author(s)
      Tomohiro Yamazaki, Tetsuya Yamamoto, Hyura Yoshino, Hiro Takakuwa, Sylvie Souquere, Wakana Isshiki, Mizuki Iwata, Rie Doi, Shinichi Nakagawa, Gerard Pierron, Tetsuro Hirose
    • Organizer
      第45回日本分子生物学会年会
    • Related Report
      2022 Annual Research Report
    • Invited
  • [Book] “情報”から“マテリアル” へ ノンコーディングRNA研究(分担執筆)「非膜オルガネラの骨格として働くarcRNA」2024

    • Author(s)
      山崎智弘、廣瀬哲郎
    • Total Pages
      205
    • Publisher
      羊土社
    • Related Report
      2024 Annual Research Report
  • [Book] 「非ドメイン型arcRAによる非膜オルガネラ形成」Medical Science Digest2023

    • Author(s)
      山崎智弘、廣瀬哲郎
    • Total Pages
      66
    • Publisher
      ニューサイエンス社
    • Related Report
      2023 Annual Research Report
  • [Book] フロントランナー直伝 相分離解析プロトコール2022

    • Author(s)
      山崎智弘、廣瀬哲郎(担当、分担執筆、範囲:レビュー編4:細胞内相分離におけるRNAの役割)
    • Total Pages
      247
    • Publisher
      羊土社
    • ISBN
      9784758122597
    • Related Report
      2022 Annual Research Report
  • [Book] セントラルドグマの新常識2022

    • Author(s)
      山崎智弘、山本哲也、廣瀬哲郎(担当、分担執筆、範囲:RNAの新常識6:細胞内構造体の骨格として働くRNA)
    • Total Pages
      264
    • Publisher
      羊土社
    • ISBN
      9784758104043
    • Related Report
      2022 Annual Research Report
  • [Remarks] Hirose Lab

    • URL

      https://hirose-lab.com/

    • Related Report
      2024 Annual Research Report 2023 Annual Research Report
  • [Remarks] RNA生体機能研究室

    • Related Report
      2024 Annual Research Report
  • [Remarks] 生成中のRNAは核小体の内部構造を制御する「界面活性剤」として働く

    • URL

      https://www.fbs.osaka-u.ac.jp/ja/research_results/papers/detail/1076

    • Related Report
      2023 Annual Research Report
  • [Remarks] 膜を持たないオルガネラが混じり合わずに存在できるしくみを解明

    • URL

      https://www.fbs.osaka-u.ac.jp/ja/research_results/papers/detail/1074

    • Related Report
      2023 Annual Research Report
  • [Remarks] ヒトゲノムの繰り返し配列から作られるRNAとその反復のなせる技

    • URL

      https://www.fbs.osaka-u.ac.jp/ja/research_results/papers/detail/1068

    • Related Report
      2023 Annual Research Report
  • [Remarks] RNA生体機能研究室

    • URL

      https://www.fbs.osaka-u.ac.jp/ja/research_group/detail/7

    • Related Report
      2023 Annual Research Report
  • [Remarks] Hirose Lab (RNA生体機能研究室)

    • URL

      http://hirose-lab.com/

    • Related Report
      2022 Annual Research Report
  • [Remarks] 大阪大学大学院生命機能研究科 細胞ネットワーク講座 RNA生体機能研究室

    • URL

      https://www.fbs.osaka-u.ac.jp/ja/research_group/detail/7

    • Related Report
      2022 Annual Research Report

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Published: 2022-04-19   Modified: 2026-01-16  

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