IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v13y2022i1d10.1038_s41467-022-30158-1.html
   My bibliography  Save this article

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
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-022-30158-1
    File Function: Abstract
    Download Restriction: no
    File URL: https://libkey.io/10.1038/s41467-022-30158-1?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    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.
    Full references (including those not matched with items on IDEAS)

    Citations

    Citations are extracted by the CitEc Project, subscribe to its RSS feed for this item.
    as


    Cited by:

    1. 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.
    2. 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.

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Xianle Shi & Yanjing Li & Hongwei Zhou & Xiukun Hou & Jihong Yang & Vikas Malik & Francesco Faiola & Junjun Ding & Xichen Bao & Miha Modic & Weiyu Zhang & Lingyi Chen & Syed Raza Mahmood & Effie Apost, 2024. "DDX18 coordinates nucleolus phase separation and nuclear organization to control the pluripotency of human embryonic stem cells," Nature Communications, Nature, vol. 15(1), pages 1-21, December.
    2. Avik Samanta & Maximilian Hörner & Wei Liu & Wilfried Weber & Andreas Walther, 2022. "Signal-processing and adaptive prototissue formation in metabolic DNA protocells," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
    3. Siddharth Agarwal & Dino Osmanovic & Mahdi Dizani & Melissa A. Klocke & Elisa Franco, 2024. "Dynamic control of DNA condensation," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
    4. Chongrui Zhang & Xufei Liu & Jiang Gong & Qiang Zhao, 2023. "Liquid sculpture and curing of bio-inspired polyelectrolyte aqueous two-phase systems," Nature Communications, Nature, vol. 14(1), pages 1-10, December.
    5. Johanna Luige & Alexandros Armaos & Gian Gaetano Tartaglia & Ulf Andersson Vang Ørom, 2024. "Predicting nuclear G-quadruplex RNA-binding proteins with roles in transcription and phase separation," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
    6. Etienne Jambon-Puillet & Andrea Testa & Charlotta Lorenz & Robert W. Style & Aleksander A. Rebane & Eric R. Dufresne, 2024. "Phase-separated droplets swim to their dissolution," Nature Communications, Nature, vol. 15(1), pages 1-12, December.
    7. Giuseppe Sicoli & Daniel Sieme & Kerstin Overkamp & Mahdi Khalil & Robin Backer & Christian Griesinger & Dieter Willbold & Nasrollah Rezaei-Ghaleh, 2024. "Large dynamics of a phase separating arginine-glycine-rich domain revealed via nuclear and electron spins," Nature Communications, Nature, vol. 15(1), pages 1-12, December.
    8. Alexa B. R. McIntyre & Adrian Beat Tschan & Katrina Meyer & Severin Walser & Arpan Kumar Rai & Keisuke Fujita & Lucas Pelkmans, 2025. "Phosphorylation of a nuclear condensate regulates cohesion and mRNA retention," Nature Communications, Nature, vol. 16(1), pages 1-20, December.
    9. Aidan M. Fenix & Yuichiro Miyaoka & Alessandro Bertero & Steven M. Blue & Matthew J. Spindler & Kenneth K. B. Tan & Juan A. Perez-Bermejo & Amanda H. Chan & Steven J. Mayerl & Trieu D. Nguyen & Caitli, 2021. "Gain-of-function cardiomyopathic mutations in RBM20 rewire splicing regulation and re-distribute ribonucleoprotein granules within processing bodies," Nature Communications, Nature, vol. 12(1), pages 1-14, December.
    10. Zhaowei Yu & Qi Wang & Qichen Zhang & Yawen Tian & Guo Yan & Jidong Zhu & Guangya Zhu & Yong Zhang, 2024. "Decoding the genomic landscape of chromatin-associated biomolecular condensates," Nature Communications, Nature, vol. 15(1), pages 1-16, December.
    11. Sarah Rösing & Fabian Ullrich & Susann Meisterfeld & Franziska Schmidt & Laura Mlitzko & Marijana Croon & Ryan G Nattrass & Nadia Eberl & Julia Mahlberg & Martin Schlee & Anja Wieland & Philipp Simon , 2024. "Chronic endoplasmic reticulum stress in myotonic dystrophy type 2 promotes autoimmunity via mitochondrial DNA release," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
    12. Ebru Aydin & Silke Schreiner & Jacqueline Böhme & Birte Keil & Jan Weber & Bojan Žunar & Timo Glatter & Cornelia Kilchert, 2024. "DEAD-box ATPase Dbp2 is the key enzyme in an mRNP assembly checkpoint at the 3’-end of genes and involved in the recycling of cleavage factors," Nature Communications, Nature, vol. 15(1), pages 1-20, December.
    13. Federica Raguseo & Yiran Wang & Jessica Li & Marija Petrić Howe & Rubika Balendra & Anouk Huyghebaert & Devkee M. Vadukul & Diana A. Tanase & Thomas E. Maher & Layla Malouf & Roger Rubio-Sánchez & Fra, 2023. "The ALS/FTD-related C9orf72 hexanucleotide repeat expansion forms RNA condensates through multimolecular G-quadruplexes," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
    14. Zhefan Stephen Chen & Mingxi Ou & Stephanie Taylor & Ruxandra Dafinca & Shaohong Isaac Peng & Kevin Talbot & Ho Yin Edwin Chan, 2023. "Mutant GGGGCC RNA prevents YY1 from binding to Fuzzy promoter which stimulates Wnt/β-catenin pathway in C9ALS/FTD," Nature Communications, Nature, vol. 14(1), pages 1-19, December.
    15. Miriam Linsenmeier & Maria Hondele & Fulvio Grigolato & Eleonora Secchi & Karsten Weis & Paolo Arosio, 2022. "Dynamic arrest and aging of biomolecular condensates are modulated by low-complexity domains, RNA and biochemical activity," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
    16. Ofer Kimchi & Ella M. King & Michael P. Brenner, 2023. "Uncovering the mechanism for aggregation in repeat expanded RNA reveals a reentrant transition," Nature Communications, Nature, vol. 14(1), pages 1-9, December.
    17. Sudarsan Mugunthan & Lan Li Wong & Fernaldo Richtia Winnerdy & Stephen Summers & Muhammad Hafiz Ismail & Yong Hwee Foo & Tavleen Kaur Jaggi & Oliver W. Meldrum & Pei Yee Tiew & Sanjay H. Chotirmall & , 2023. "RNA is a key component of extracellular DNA networks in Pseudomonas aeruginosa biofilms," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
    18. Sheung Chun Ng & Abin Biswas & Trevor Huyton & Jürgen Schünemann & Simone Reber & Dirk Görlich, 2023. "Barrier properties of Nup98 FG phases ruled by FG motif identity and inter-FG spacer length," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
    19. Bing-Ze Yang & Mei-Yin Liu & Kuan-Lin Chiu & Yuh-Ling Chien & Ching-An Cheng & Yu-Lin Chen & Li-Yu Tsui & Keng-Ru Lin & Hsueh-Ping Catherine Chu & Ching-Shyi Peter Wu, 2024. "DHX9 SUMOylation is required for the suppression of R-loop-associated genome instability," Nature Communications, Nature, vol. 15(1), pages 1-18, December.
    20. Momčilo Gavrilov & Joshua Y. C. Yang & Roger S. Zou & Wen Ma & Chun-Ying Lee & Sonisilpa Mohapatra & Jimin Kang & Ting-Wei Liao & Sua Myong & Taekjip Ha, 2022. "Engineered helicase replaces thermocycler in DNA amplification while retaining desired PCR characteristics," Nature Communications, Nature, vol. 13(1), pages 1-14, December.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-30158-1. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.