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Characterization of RNA content in individual phase-separated coacervate microdroplets

Author

Listed:
  • Damian Wollny

    (Max Planck Institute for Evolutionary Anthropology
    Friedrich Schiller University
    Leibniz Institute on Aging—Fritz Lipmann Institute (FLI))

  • Benjamin Vernot

    (Max Planck Institute for Evolutionary Anthropology)

  • Jie Wang

    (Max Planck Institute of Molecular Cell Biology and Genetics)

  • Maria Hondele

    (ETH Zurich
    University of Basel)

  • Aram Safrastyan

    (Friedrich Schiller University
    Leibniz Institute on Aging—Fritz Lipmann Institute (FLI))

  • Franziska Aron

    (Friedrich Schiller University
    Leibniz Institute on Aging—Fritz Lipmann Institute (FLI))

  • Julia Micheel

    (Friedrich Schiller University
    Leibniz Institute on Aging—Fritz Lipmann Institute (FLI))

  • Zhisong He

    (University of Basel)

  • Anthony Hyman

    (Max Planck Institute of Molecular Cell Biology and Genetics)

  • Karsten Weis

    (ETH Zurich)

  • J. Gray Camp

    (Roche Innovation Center
    University of Basel)

  • T.‐Y. Dora Tang

    (Max Planck Institute of Molecular Cell Biology and Genetics
    TU Dresden)

  • Barbara Treutlein

    (Max Planck Institute for Evolutionary Anthropology
    ETH Zürich)

Abstract

Condensates formed by complex coacervation are hypothesized to have played a crucial part during the origin-of-life. In living cells, condensation organizes biomolecules into a wide range of membraneless compartments. Although RNA is a key component of biological condensates and the central component of the RNA world hypothesis, little is known about what determines RNA accumulation in condensates and to which extend single condensates differ in their RNA composition. To address this, we developed an approach to read the RNA content from single synthetic and protein-based condensates using high-throughput sequencing. We find that certain RNAs efficiently accumulate in condensates. These RNAs are strongly enriched in sequence motifs which show high sequence similarity to short interspersed elements (SINEs). We observe similar results for protein-derived condensates, demonstrating applicability across different in vitro reconstituted membraneless organelles. Thus, our results provide a new inroad to explore the RNA content of phase-separated droplets at single condensate resolution.

Suggested Citation

  • Damian Wollny & Benjamin Vernot & Jie Wang & Maria Hondele & Aram Safrastyan & Franziska Aron & Julia Micheel & Zhisong He & Anthony Hyman & Karsten Weis & J. Gray Camp & T.‐Y. Dora Tang & Barbara Tre, 2022. "Characterization of RNA content in individual phase-separated coacervate microdroplets," Nature Communications, Nature, vol. 13(1), pages 1-9, December.
    • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-30158-1
    DOI: 10.1038/s41467-022-30158-1
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    References listed on IDEAS

    as
    1. Tina Ukmar-Godec & Saskia Hutten & Matthew P. Grieshop & Nasrollah Rezaei-Ghaleh & Maria-Sol Cima-Omori & Jacek Biernat & Eckhard Mandelkow & Johannes Söding & Dorothee Dormann & Markus Zweckstetter, 2019. "Lysine/RNA-interactions drive and regulate biomolecular condensation," Nature Communications, Nature, vol. 10(1), pages 1-15, December.
    2. Ankur Jain & Ronald D. Vale, 2017. "RNA phase transitions in repeat expansion disorders," Nature, Nature, vol. 546(7657), pages 243-247, June.
    3. Raghav R. Poudyal & Rebecca M. Guth-Metzler & Andrew J. Veenis & Erica A. Frankel & Christine D. Keating & Philip C. Bevilacqua, 2019. "Template-directed RNA polymerization and enhanced ribozyme catalysis inside membraneless compartments formed by coacervates," Nature Communications, Nature, vol. 10(1), pages 1-13, December.
    4. Maria Hondele & Ruchika Sachdev & Stephanie Heinrich & Juan Wang & Pascal Vallotton & Beatriz M. A. Fontoura & Karsten Weis, 2019. "DEAD-box ATPases are global regulators of phase-separated organelles," Nature, Nature, vol. 573(7772), pages 144-148, September.
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    Cited by:

    1. Basusree Ghosh & Patrick M. McCall & Kristian Kyle Vay & Archishman Ghosh & Lars Hubatsch & David T. Gonzales & Jan Brugués & Hannes Mutschler & T-Y. Dora Tang, 2025. "RNA-peptide interactions tune the ribozyme activity within coacervate microdroplet dispersions," Nature Communications, Nature, vol. 16(1), pages 1-15, December.
    2. Jiaxing Yuan & Hajime Tanaka, 2025. "Network-forming phase separation of oppositely charged polyelectrolytes forming coacervates in a solvent," Nature Communications, Nature, vol. 16(1), pages 1-14, December.
    3. Luisa Statello & José Miguel Fernandez-Justel & Jovanna González & Marta Montes & Alessia Ranieri & Enrique Goñi & Aina M. Mas & Maite Huarte, 2024. "The chromatin-associated lncREST ensures effective replication stress response by promoting the assembly of fork signaling factors," Nature Communications, Nature, vol. 15(1), pages 1-17, December.

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