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

• Published in: Molecular cell 2018-06, Vol.70 (5), p.854-867.e9
• Main Authors: Dominguez, Daniel, Freese, Peter, Alexis, Maria S., Su, Amanda, Hochman, Myles, Palden, Tsultrim, Bazile, Cassandra, Lambert, Nicole J., Van Nostrand, Eric L., Pratt, Gabriel A., Yeo, Gene W., Graveley, Brenton R., Burge, Christopher B.
• Format: Article
• Language: English
• Subjects: alternative splicing; Base Sequence; Binding Sites; High-Throughput Nucleotide Sequencing; Humans; KH domain; mRNA stability; Nucleic Acid Conformation; Nucleotide Motifs; Protein Binding; Pum domain; RBNS; RNA - chemistry; RNA - genetics; RNA - metabolism; RNA binding protein; RNA context; RNA recognition motif; RNA Recognition Motif Proteins - chemistry; RNA Recognition Motif Proteins - genetics; RNA Recognition Motif Proteins - metabolism; RNA secondary structure; Structure-Activity Relationship; zinc finger
• ISSN: 1097-2765; 1097-4164
• DOI: 10.1016/j.molcel.2018.05.001

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. [Display omitted] •In vitro specificity of 78 human RNA binding proteins determined by deep sequencing•RBP motifs have low diversity, compositional complexity, and RNA structure potential•RBPs that bind similar motifs often differ in their sequence context preferences•Many favor specific “bipartite” motifs, flanking base composition, or RNA structures Dominguez et al. describe in vitro binding specificities of 78 human RNA binding proteins (RBPs) to RNA sequences and structures. They find that many RBPs bind similar RNA motifs but differ in affinity for spaced “bipartite” motifs, flanking composition, and RNA structure, supporting the model that distinct motif occurrences are often discriminated based on sequence context.