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Super-resolution single-molecule dynamics analysis of phase separation formation by the development of a drug-inducible system for intracellular phase separation

Research Project

Project/Area Number 20K15755
Research Category

Grant-in-Aid for Early-Career Scientists

Allocation TypeMulti-year Fund
Review Section Basic Section 43040:Biophysics-related
Research InstitutionTokyo Institute of Technology

Principal Investigator

Ito Yuma  東京工業大学, 生命理工学院, 助教 (70803245)

Project Period (FY) 2020-04-01 – 2022-03-31
Project Status Completed (Fiscal Year 2021)
Budget Amount *help
¥4,160,000 (Direct Cost: ¥3,200,000、Indirect Cost: ¥960,000)
Fiscal Year 2021: ¥2,080,000 (Direct Cost: ¥1,600,000、Indirect Cost: ¥480,000)
Fiscal Year 2020: ¥2,080,000 (Direct Cost: ¥1,600,000、Indirect Cost: ¥480,000)
Keywords1分子計測 / 生細胞イメージング / 相分離 / 生細胞1分子イメージング
Outline of Research at the Start

本研究は、細胞内のタンパク質が水と油のような異なる液滴に分かれる、相分離の性質に注目し、相分離形成の人工的な制御と、1分子可視化技術の組み合わせで、その形成過程の解明を目指す。特に相分離を担うタンパク質を薬剤添加で集合させ、独自に開発した生細胞1分子イメージング法を用いて観察し、相分離に伴う分子動態の変化をミリ秒かつナノメートルスケールで高精細に解析する。これにより、これまで観察自体が困難であった細胞内の相分離過程の詳細な知見が得られる。

Outline of Final Research Achievements

We have established an artificial system to induce intracellular droplet formation by adding drugs to investigate the phase separation mechanism essential for biological functions. This method enables us to measure molecular dynamics in droplets using single-molecule imaging in living cells. We obtained the characteristic dynamics in droplet formation as precise quantitative information at the single-molecule level for the intrinsically disordered regions of various phase-separated proteins. This method quantified the effect of the intracellular environment, molecular diffusion and exchange inside and outside the droplet, and the amino acid composition that contributes to phase separation. This study provides a tool to investigate the physical and biological properties of phase separation, which could contribute widely to life science research.

Academic Significance and Societal Importance of the Research Achievements

細胞内の相分離は遺伝子発現やタンパク質分解などの広範な生体機能を制御しており、がんや神経変性疾患などにも関与している。本研究で開発した相分離誘導系は、液滴形成における特徴的な動態を顕在化し、その基盤となる物理的な性質や分子生物学的な機構を定量的かつ高精細に計測できるものである。さらに生化学等の研究手法にも広く適用できると考えられ、相分離が関与する広範な生命科学研究へ貢献すると期待できる。

Report

(3 results)
  • 2021 Annual Research Report   Final Research Report ( PDF )
  • 2020 Research-status Report
  • Research Products

    (16 results)

All 2022 2021 2020

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

  • [Journal Article] Live imaging of transcription sites using an elongating RNA polymerase II-specific probe.2022

    • Author(s)
      Uchino S, Ito Y, Sato Y, Handa T, Ohkawa Y, Tokunaga M, Kimura H.
    • Journal Title

      J Cell Biol.

      Volume: 221 Issue: 2 Pages: 1-23

    • DOI

      10.1083/jcb.202104134

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Ribosomal protein L5 facilitates rDNA-bundled condensate and nucleolar assembly2022

    • Author(s)
      Matsumori Haruka、Watanabe Kenji、Tachiwana Hiroaki、Fujita Tomoko、Ito Yuma、Tokunaga Makio、Sakata-Sogawa Kumiko、Osakada Hiroko、Haraguchi Tokuko、Awazu Akinori、Ochiai Hiroshi、Sakata Yuka、Ochiai Koji、Toki Tsutomu、Ito Etsuro、Goldberg Ilya G、Tokunaga Kazuaki、Nakao Mitsuyoshi、Saitoh Noriko
    • Journal Title

      Life Science Alliance

      Volume: 5 Issue: 7 Pages: 1-18

    • DOI

      10.26508/lsa.202101045

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Visualizing looping of two endogenous genomic loci using synthetic zinc‐finger proteins with anti‐FLAG and anti‐HA frankenbodies in living cells2021

    • Author(s)
      Liu Yang、Zhao Ning、Kanemaki Masato T.、Yamamoto Yotaro、Sadamura Yoshifusa、Ito Yuma、Tokunaga Makio、Stasevich Timothy J.、Kimura Hiroshi
    • Journal Title

      Genes to Cells

      Volume: 26 Issue: 11 Pages: 905-926

    • DOI

      10.1111/gtc.12893

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Presentation] Live-cell single-molecule imaging of the dynamic interaction between RNA polymerase II and chromatin nanostructures2022

    • Author(s)
      Yuma Ito
    • Organizer
      The 30th Hot Spring Harbor International Symposium
    • Related Report
      2021 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Simultaneous single molecule imaging of RNA polymerase II dynamics and chromatin nanostructures in living cells2022

    • Author(s)
      Yuma Ito, Makio Tokunaga
    • Organizer
      66th Biophysical Society Annual Meeting
    • Related Report
      2021 Annual Research Report
  • [Presentation] A simulation study to evaluate improvement of three-dimensional localization precision of single molecule images using adaptive optics2021

    • Author(s)
      Xiang Zhou, Yuma Ito, Makio Tokunaga
    • Organizer
      第59回 日本生物物理学会年会
    • Related Report
      2021 Annual Research Report
  • [Presentation] Single-molecule analysis of state-specific histone mobility in chromatin subcompartments with different epigenetic modifications2021

    • Author(s)
      Masanori Hirose, Yuma Ito, Makio Tokunaga
    • Organizer
      第59回 日本生物物理学会年会
    • Related Report
      2021 Annual Research Report
  • [Presentation] Single-molecule imaging analysis of RNA-dependent dynamics of phase-separated nucleolar protens in living cells2021

    • Author(s)
      Yuma Ito, Supanut Sirisukhodom, Makio Tokunaga
    • Organizer
      第59回 日本生物物理学会年会
    • Related Report
      2021 Annual Research Report
  • [Presentation] Single-molecule super-resolution analysis for nano-scale interaction between RNA polymerase II and chromatin2021

    • Author(s)
      Yuma Ito, Makio Tokunaga
    • Organizer
      第59回 日本生物物理学会年会
    • Related Report
      2021 Annual Research Report
  • [Presentation] Structural changes in heterochromatin involved in cell cycle using single-molecule and super-resolution imaging2021

    • Author(s)
      Masanori Nakano, Yuma Ito, Makio Tokunaga
    • Organizer
      第59回 日本生物物理学会年会
    • Related Report
      2021 Annual Research Report
  • [Presentation] Visualizing and quantifying single-molecule dynamics in living cells2021

    • Author(s)
      Ito Y, Tokunaga M
    • Organizer
      The 9th Tokyo Tech International Symposium on Life Science and Technology
    • Related Report
      2020 Research-status Report
    • Int'l Joint Research / Invited
  • [Presentation] Nano-scale localization analysis of histone variants in living cells using single-molecule super-resolution imaging2020

    • Author(s)
      Ito Y, Tokunaga M
    • Organizer
      第58回日本生物物理学会年会
    • Related Report
      2020 Research-status Report
  • [Presentation] Quantification of dynamics and kinetics using single-molecule and super-resolution imaging in living cells2020

    • Author(s)
      Ito Y, Tokunaga M
    • Organizer
      第58回日本生物物理学会年会
    • Related Report
      2020 Research-status Report
  • [Presentation] Multicolor single-molecule imaging analysis of the nucleolar proteins2020

    • Author(s)
      Sirisukhodom S, Ito Y, Saitoh N, Tokunaga M
    • Organizer
      第58回日本生物物理学会年会
    • Related Report
      2020 Research-status Report
  • [Presentation] Dynamics of Heterochromatin protein 1α inside and outside chromocenter domain in living cells using single-molecule imaging2020

    • Author(s)
      Nakano M, Ito Y, Maeda T, Obuse C, Tokunaga M
    • Organizer
      第58回日本生物物理学会年会
    • Related Report
      2020 Research-status Report
  • [Presentation] Light field simulation of single-molecule imaging for aberration correction using adaptive optics2020

    • Author(s)
      Zhou X, Ito Y, Tokunaga M
    • Organizer
      第58回日本生物物理学会年会
    • Related Report
      2020 Research-status Report

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Published: 2020-04-28   Modified: 2023-01-30  

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