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Structural basis of LLPS of RNA repeats related to neurodegenerative diseases

Research Project

Project/Area Number 20H03192
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypeSingle-year Grants
Section一般
Review Section Basic Section 43020:Structural biochemistry-related
Research InstitutionKyoto University

Principal Investigator

Katahira Masato  京都大学, エネルギー理工学研究所, 教授 (70211844)

Project Period (FY) 2020-04-01 – 2023-03-31
Project Status Completed (Fiscal Year 2023)
Budget Amount *help
¥17,810,000 (Direct Cost: ¥13,700,000、Indirect Cost: ¥4,110,000)
Fiscal Year 2022: ¥4,290,000 (Direct Cost: ¥3,300,000、Indirect Cost: ¥990,000)
Fiscal Year 2021: ¥5,460,000 (Direct Cost: ¥4,200,000、Indirect Cost: ¥1,260,000)
Fiscal Year 2020: ¥8,060,000 (Direct Cost: ¥6,200,000、Indirect Cost: ¥1,860,000)
Keywords液液相分離 / コンデンセート / 拡散係数 / 並進運動 / 横緩和時間 / 回転運動 / 核酸 / 並進拡散 / 横緩和 / 核酸構造 / NMR / 反復配列 / ダイナミクス / 反復配列RNA / 構造 / RNA / 神経変性疾患
Outline of Research at the Start

最近、RNA分子のみでも液液相分離(LLPS)が起こる事が報告された。当該RNAは反復配列からなるが(ポリRNA)、反復回数が閾値を超えると相転移して、LLPS状態ないしはゲル化状態となる事が報告された。本研究ではこのポリRNAに関し、塩基対の形成様式(2次構造)とその強さ、及び3次元フォールドの概略を、NMR法によってin vitro及びヒト生細胞中においても決定する。得られた構造に基づいて、何故反復回数が閾値を超えた場合にのみ相転移が生じるのかを解明する。また、LLPS等の人為的な操作にも挑戦する。

Outline of Final Research Achievements

Regarding the liquid-liquid phase separation (Sato et al., Science Advances, 2020) that occurs with Y-shaped DNA (Y-DNA) discovered by Takinoue et al., the behavior of molecules in the condensate layer was analyzed by determining the diffusion coefficient reflecting the speed of translational motion and the transverse relaxation time reflecting the speed of rotational motion by NMR method. In the case of Y-DNA in condensate, both translational and rotational were suppressed. When other molecules are involved in this condensate, it was found that the translation and rotation may or may not be suppressed, depending on the size and charge of the molecules. The findings obtained in this study are significant in understanding and utilizing the droplets generated by liquid-liquid phase separation as reaction fields.

Academic Significance and Societal Importance of the Research Achievements

タンパク質あるいはタンパク質と核酸の複合体が液液相分離を生じる事が見いだされ、生命現象を理解する鍵となる事象として大きな注目を集めている。また液液相分離で生じる液滴は、反応場として活用できる可能性もある。その後、核酸のみで生じる液液相分離も見出されたが、知見は未だ限られている。今回核酸のみからなるコンデンセート中の分子の挙動に関する定量的な情報が得られた事により、同液滴に関する理解とその応用が格段に進むと考えられる。

Report

(4 results)
  • 2023 Final Research Report ( PDF )
  • 2022 Annual Research Report
  • 2021 Annual Research Report
  • 2020 Annual Research Report
  • Research Products

    (15 results)

All 2023 2022 2021 Other

All Journal Article (5 results) (of which Int'l Joint Research: 3 results,  Peer Reviewed: 5 results,  Open Access: 2 results) Presentation (8 results) (of which Int'l Joint Research: 5 results,  Invited: 3 results) Remarks (2 results)

  • [Journal Article] Complex Formation of an RNA Aptamer with a Part of HIV-1 Tat through Induction of Base Triples in Living Human Cells Proven by In-Cell NMR2023

    • Author(s)
      Eladl Omar、Yamaoki Yudai、Kondo Keiko、Nagata Takashi、Katahira Masato
    • Journal Title

      International Journal of Molecular Sciences

      Volume: 24 Issue: 10 Pages: 9069-9069

    • DOI

      10.3390/ijms24109069

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Detection of interaction between an RNA aptamer and its target compound in living human cells using 2D in-cell NMR2023

    • Author(s)
      Eladl Omar、Yamaoki Yudai、Kondo Keiko、Nagata Takashi、Katahira Masato
    • Journal Title

      Chemical Communications

      Volume: 59 Issue: 1 Pages: 102-105

    • DOI

      10.1039/d2cc05576g

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Shedding light on the base-pair opening dynamics of nucleic acids in living human cells2022

    • Author(s)
      Yamaoki Yudai、Nagata Takashi、Kondo Keiko、Sakamoto Tomoki、Takami Shohei、Katahira Masato
    • Journal Title

      Nature Communications

      Volume: 13 Issue: 1 Pages: 7143-7143

    • DOI

      10.1038/s41467-022-34822-4

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Non-coding RNA suppresses FUS aggregation caused by mechanistic shear stress on pipetting in a sequence-dependent manner2021

    • Author(s)
      Hamad Nesreen、Yoneda Ryoma、So Masatomo、Kurokawa Riki、Nagata Takashi、Katahira Masato
    • Journal Title

      Scientific Reports

      Volume: 11 Issue: 1 Pages: 9523-9523

    • DOI

      10.1038/s41598-021-89075-w

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Detection of parallel and antiparallel DNA triplex structures in living human cells using in-cell NMR2021

    • Author(s)
      Sakamoto Tomoki、Yamaoki Yudai、Nagata Takashi、Katahira Masato
    • Journal Title

      Chemical Communications

      Volume: 57 Issue: 52 Pages: 5364-6367

    • DOI

      10.1039/d1cc01761f

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed
  • [Presentation] Structure, dynamics and interaction of nucleic acids in living human cells as revealed by in-cell NMR2023

    • Author(s)
      Masato Katahira
    • Organizer
      The 10th Asia-Pacific NMR
    • Related Report
      2022 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Base pair opening dynamics of G4 and aptamer-ligand interaction in living human cells as revealed by in-cell NMR2023

    • Author(s)
      Masato Katahira
    • Organizer
      Nucleic Acids Secondary Structures: G4s and Beyond
    • Related Report
      2022 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Difference in the base-pair opening dynamics of nucleic acids between in vitro and in-cell conditions2023

    • Author(s)
      Masato Katahira
    • Organizer
      International Society of Magnetic Resonance 2023
    • Related Report
      2022 Annual Research Report
    • Int'l Joint Research
  • [Presentation] 核酸から成る液滴のNMR法を用いた物理化学的解析2022

    • Author(s)
      川上愛加, 山置佑大, 近藤敬子, 阪本知樹, 永田崇, 片平正人
    • Organizer
      第45回日本分子生物学会
    • Related Report
      2021 Annual Research Report
  • [Presentation] NMR法による核酸のコンデンセートおよびヒト生細胞内における核酸の塩基対開閉ダイナミクスの解析2022

    • Author(s)
      山置佑大, 永田崇, 川上愛加, 阪本知樹, Eladl Omar, 近藤敬子, 片平正人
    • Organizer
      第45回日本分子生物学会
    • Related Report
      2021 Annual Research Report
  • [Presentation] Non-coding RNA suppresses FUS aggregation caused by mechanistic shear stress on pipetting in a sequence-dependent manner2021

    • Author(s)
      Katahira, M.
    • Organizer
      The 44th Annual Meeting of the Molecular Biology Society of Japan
    • Related Report
      2020 Annual Research Report
    • Invited
  • [Presentation] Analysis of fused in sarcoma aggregation caused by shear stress and suppression of aggregation by non-coding RNA2021

    • Author(s)
      Kurokawa, R., Hamad, N., Yoneda, R., So, M., Kondo, K., Yamaoki, Y., Nagata, T. and Katahira, M.
    • Organizer
      The 12th International Symposium of Advanced Energy Science
    • Related Report
      2020 Annual Research Report
    • Int'l Joint Research
  • [Presentation] n-cell NMR analysis of the structure and dynamics of hairpin and G-quadruplex structures in the living human cells2021

    • Author(s)
      Yamaoki, Y., Nagata, T., Kondo, K., Sakamoto, T., Takami, S., and Katahira, M.
    • Organizer
      22nd International Society of Magnetic Resonance Conference
    • Related Report
      2020 Annual Research Report
    • Int'l Joint Research
  • [Remarks] 片平研究室

    • URL

      https://www.iae.kyoto-u.ac.jp/bio/

    • Related Report
      2022 Annual Research Report
  • [Remarks] 片平研究室

    • URL

      http://www.iae.kyoto-u.ac.jp/bio/

    • Related Report
      2021 Annual Research Report 2020 Annual Research Report

URL: 

Published: 2020-04-28   Modified: 2025-01-30  

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