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

Overview

Journal Mol Cell

Publisher Cell Press

Specialty Cell Biology

Date 2018 Jun 9

PMID 29883606

Citations 264

Authors

Daniel Dominguez

Peter Freese

Maria S Alexis

Amanda Su

Myles Hochman

Tsultrim Palden

Cassandra Bazile

Nicole J Lambert

Eric L Van Nostrand

Gabriel A Pratt

Gene W Yeo

Brenton R Graveley

Christopher B Burge

Affiliations

Soon will be listed here.

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.

Citing Articles

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