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RNA structure drives interaction with proteins

Author

Listed:
  • Natalia Sanchez de Groot

    (The Barcelona Institute for Science and Technology)

  • Alexandros Armaos

    (The Barcelona Institute for Science and Technology)

  • Ricardo Graña-Montes

    (The Barcelona Institute for Science and Technology
    University of Zürich)

  • Marion Alriquet

    (Goethe University Frankfurt
    Goethe University Frankfurt)

  • Giulia Calloni

    (Goethe University Frankfurt
    Goethe University Frankfurt)

  • R. Martin Vabulas

    (Goethe University Frankfurt
    Goethe University Frankfurt)

  • Gian Gaetano Tartaglia

    (The Barcelona Institute for Science and Technology
    ICREA 23 Passeig Lluis Companys 08010 and Universitat Pompeu Fabra (UPF)
    Sapienza University of Rome
    Istituto Italiano di Tecnologia)

Abstract

The combination of high-throughput sequencing and in vivo crosslinking approaches leads to the progressive uncovering of the complex interdependence between cellular transcriptome and proteome. Yet, the molecular determinants governing interactions in protein-RNA networks are not well understood. Here we investigated the relationship between the structure of an RNA and its ability to interact with proteins. Analysing in silico, in vitro and in vivo experiments, we find that the amount of double-stranded regions in an RNA correlates with the number of protein contacts. This relationship —which we call structure-driven protein interactivity— allows classification of RNA types, plays a role in gene regulation and could have implications for the formation of phase-separated ribonucleoprotein assemblies. We validate our hypothesis by showing that a highly structured RNA can rearrange the composition of a protein aggregate. We report that the tendency of proteins to phase-separate is reduced by interactions with specific RNAs.

Suggested Citation

  • Natalia Sanchez de Groot & Alexandros Armaos & Ricardo Graña-Montes & Marion Alriquet & Giulia Calloni & R. Martin Vabulas & Gian Gaetano Tartaglia, 2019. "RNA structure drives interaction with proteins," Nature Communications, Nature, vol. 10(1), pages 1-13, December.
    • Handle: RePEc:nat:natcom:v:10:y:2019:i:1:d:10.1038_s41467-019-10923-5
    DOI: 10.1038/s41467-019-10923-5
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    Cited by:

    1. Prakash Kharel & Marta Fay & Ekaterina V. Manasova & Paul J. Anderson & Alexander V. Kurkin & Junjie U. Guo & Pavel Ivanov, 2023. "Stress promotes RNA G-quadruplex folding in human cells," Nature Communications, Nature, vol. 14(1), pages 1-10, December.
    2. Elsa Zacco & Owen Kantelberg & Edoardo Milanetti & Alexandros Armaos & Francesco Paolo Panei & Jenna Gregory & Kiani Jeacock & David J. Clarke & Siddharthan Chandran & Giancarlo Ruocco & Stefano Gusti, 2022. "Probing TDP-43 condensation using an in silico designed aptamer," Nature Communications, Nature, vol. 13(1), pages 1-13, December.

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