SONAR Discovers RNA-Binding Proteins from Analysis of Large-Scale Protein-Protein Interactomes

Abstract

RNA metabolism is controlled by an expanding, yetincomplete, catalog of RNA-binding proteins (RBPs), many of which lack characterized RNA binding domains. Approaches to expand the RBP repertoire to discover non-canonical RBPs are currently needed. Here, HaloTag fusion pull down of 12 nuclearand cytoplasmic RBPs followed by quantitative mass spectrometry (MS) demonstrates that proteins interacting with multiple RBPs in an RNA-dependentmanner are enriched for RBPs. This motivated SONAR, a computational approach that predicts RNA binding activity by analyzing large-scale affinityprecipitation-MS protein-protein interactomes. Without relying on sequence or structure information, SONARidentifies 1,923 human, 489 fly, and 745 yeast RBPs,including over 100 human candidate RBPs that contain zinc finger domains. Enhanced CLIP confirms RNA binding activity and identifies transcriptome-wide RNA binding sites for SONAR-predicted RBPs, revealing unexpected RNA binding activity for disease-relevant proteins and DNA binding proteins.