Sequence, Structure, and Context Preferences of Human RNA Binding Proteins

TLDR

RNA binding proteins (RBPs) orchestrate the production, processing, and function of mRNAs. The study aims to map the sequence, structure, and context preferences of 78 human RBPs through an unbiased in vitro assay. The authors employed deep sequencing of bound RNAs in an unbiased assay to generate affinity landscapes and construct RNA maps of RBP activity without crosslinking. The analysis revealed a surprisingly low diversity of RNA motifs, indicating convergence toward a small set of motifs, yet uncovered extensive contextual preferences such as bipartite motifs, flanking nucleotide biases, and structure biases that likely allow RBPs sharing the same linear motif to target distinct transcript subsets.

Abstract

RNA binding proteins (RBPs) orchestrate the production, processing, and function of mRNAs. Here, we present the affinity landscapes of 78 human RBPs using an unbiased assay that determines the sequence, structure, and context preferences of these proteins in vitro by deep sequencing of bound RNAs. These data enable construction of "RNA maps" of RBP activity without requiring crosslinking-based assays. We found an unexpectedly low diversity of RNA motifs, implying frequent convergence of binding specificity toward a relatively small set of RNA motifs, many with low compositional complexity. Offsetting this trend, however, we observed extensive preferences for contextual features distinct from short linear RNA motifs, including spaced "bipartite" motifs, biased flanking nucleotide composition, and bias away from or toward RNA structure. Our results emphasize the importance of contextual features in RNA recognition, which likely enable targeting of distinct subsets of transcripts by different RBPs that recognize the same linear motif.