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.

RNA structure drives interaction with proteins / Sanchez de Groot, N.; Armaos, A.; Grana-Montes, R.; Alriquet, M.; Calloni, G.; Vabulas, R. M.; Tartaglia, G. G.. - In: NATURE COMMUNICATIONS. - ISSN 2041-1723. - 10:1(2019), pp. 1-13. [10.1038/s41467-019-10923-5]

RNA structure drives interaction with proteins

Tartaglia G. G.
2019

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.
2019
Algorithms; Binding Sites; Gene Ontology; HeLa Cells; High-Throughput Nucleotide Sequencing; Humans; Models, Molecular; Protein Binding; Proteome; RNA; RNA-Binding Proteins; Transcriptome; Nucleic Acid Conformation; Protein Domains
01 Pubblicazione su rivista::01a Articolo in rivista
RNA structure drives interaction with proteins / Sanchez de Groot, N.; Armaos, A.; Grana-Montes, R.; Alriquet, M.; Calloni, G.; Vabulas, R. M.; Tartaglia, G. G.. - In: NATURE COMMUNICATIONS. - ISSN 2041-1723. - 10:1(2019), pp. 1-13. [10.1038/s41467-019-10923-5]
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Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/11573/1451123
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