RNA structure drives interaction with proteins

Natalia Sanchez de Groot, Alexandros Armaos, Ricardo Graña-Montes, Marion Alriquet, Giulia Calloni, R. Martin Vabulas () and Gian Gaetano Tartaglia ()
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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
Marion Alriquet: Goethe University Frankfurt
Giulia Calloni: Goethe University Frankfurt
R. Martin Vabulas: Goethe University Frankfurt
Gian Gaetano Tartaglia: The Barcelona Institute for Science and Technology

Nature Communications, 2019, vol. 10, issue 1, 1-13

Abstract: 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.

Date: 2019
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DOI: 10.1038/s41467-019-10923-5

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