RNA-dependent interactome allows network-based assignment of RNA-binding protein function

Author:

Fradera-Sola Albert1ORCID,Nischwitz Emily1,Bayer Marie Elisabeth1,Luck Katja2ORCID,Butter Falk1ORCID

Affiliation:

1. Quantitative Proteomics, Institute of Molecular Biology , D-55128 Mainz, Germany

2. Integrative Systems Biology, Institute of Molecular Biology , D-55128 Mainz, Germany

Abstract

Abstract RNA-binding proteins (RBPs) form highly diverse and dynamic ribonucleoprotein complexes, whose functions determine the molecular fate of the bound RNA. In the model organism Sacchromyces cerevisiae, the number of proteins identified as RBPs has greatly increased over the last decade. However, the cellular function of most of these novel RBPs remains largely unexplored. We used mass spectrometry-based quantitative proteomics to systematically identify protein–protein interactions (PPIs) and RNA-dependent interactions (RDIs) to create a novel dataset for 40 RBPs that are associated with the mRNA life cycle. Domain, functional and pathway enrichment analyses revealed an over-representation of RNA functionalities among the enriched interactors. Using our extensive PPI and RDI networks, we revealed putative new members of RNA-associated pathways, and highlighted potential new roles for several RBPs. Our RBP interactome resource is available through an online interactive platform as a community tool to guide further in-depth functional studies and RBP network analysis (https://www.butterlab.org/RINE).

Funder

Deutsche Forschungsgemeinschaft

Publisher

Oxford University Press (OUP)

Subject

Genetics

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