Article Methods Cell lines Cell lines were purchased from ATCC and were not formally authenticated, but confirmation of expected gene expression patterns were performed for RNA-seq and eCLIP experiments. Cell lines were routinely tested for mycoplasma contamination (MycoAlert, Lonza).

Genomes encompass all the information necessary to specify the development and function of an organism. In addition to genes, genomes also contain a myriad of functional elements that control various steps in gene expression. A major class of these elements function only when transcribed into RNA as they serve as the binding sites for RNA binding proteins (RBPs) which act to control post-transcriptional processes including splicing, cleavage and polyadenylation, RNA editing, RNA localization, translation, and RNA stability. Despite the importance of these functional RNA elements encoded in the genome, they have been much less studied than genes and DNA elements. Here, we describe the mapping and characterization of RNA elements recognized by a large collection of human RBPs in K562 and HepG2 cells. These data expand the catalog of functional elements encoded in the human genome by addition of a large set of elements that function at the RNA level through interaction with RBPs.Van Nostrand et al.

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.

Production of functional cellular RNAs involves multiple processing and regulatory steps principally mediated by RNA binding proteins (RBPs). Here we present the affinity landscapes of 78 human RBPs using an unbiased assay that determines the sequence, structure, and context preferences of an RBP in vitro from deep sequencing of bound RNAs. Analyses of these data revealed several interesting patterns, including unexpectedly low diversity of RNA motifs, implying frequent convergent evolution of binding specificity toward a relatively small set of RNA motifs, many with low compositional complexity. Offsetting this trend, we observed extensive preferences for contextual features outside of core RNA motifs, including spaced "bipartite" motifs, biased flanking nucleotide context, and bias away from or towards RNA structure.These contextual features are likely to enable targeting of distinct subsets of transcripts by different RBPs that recognize the same core motif. Our results enable construction of "RNA maps" of RBP activity without requiring crosslinking-based assays, and provide unprecedented depth of information on the interaction of RBPs with RNA..

Summary Splicing dysregulation is one of the molecular hallmarks of cancer. However, the underlying molecular mechanisms remain poorly defined. Here we report the splicing factor RBM4 suppresses proliferation and migration of various cancer cells by specifically controlling cancer-related splicing. Particularly, RBM4 regulates Bcl-x splicing to induce apoptosis, and co-expression of Bcl-xL partially reverses the RBM4-mediated tumor suppression. Moreover, RBM4 antagonizes an oncogenic splicing factor, SRSF1, to inhibit mTOR activation. Strikingly, RBM4 expression is dramatically decreased in cancer patients, and RBM4 level is positively correlated with improved survival. In addition to providing mechanistic insights of cancer-related splicing dysregulation, this study establishes RBM4 as a tumor suppressor with therapeutic potentials and clinical values as a prognostic factor.