Abstract
Metazoan genomes encode hundreds of RNA-binding proteins (RBPs). These proteins regulate post-transcriptional gene expression and have critical roles in numerous cellular processes including mRNA splicing, export, stability and translation. Despite their ubiquity and importance, the binding preferences for most RBPs are not well characterized. In vitro and in vivo studies, using affinity selection-based approaches, have successfully identified RNA sequence associated with specific RBPs; however, it is difficult to infer RBP sequence and structural preferences without specifically designed motif finding methods. In this study, we introduce a new motif-finding method, RNAcontext, designed to elucidate RBP-specific sequence and structural preferences with greater accuracy than existing approaches. We evaluated RNAcontext on recently published in vitro and in vivo RNA affinity selected data and demonstrate that RNAcontext identifies known binding preferences for several control proteins including HuR, PTB, and Vts1p and predicts new RNA structure preferences for SF2/ASF, RBM4, FUSIP1 and SLM2. The predicted preferences for SF2/ASF are consistent with its recently reported in vivo binding sites. RNAcontext is an accurate and efficient motif finding method ideally suited for using large-scale RNA-binding affinity datasets to determine the relative binding preferences of RBPs for a wide range of RNA sequences and structures.
Highlights
RNA-binding proteins (RBPs) act in the post-transcriptional regulation (PTR) of gene expression by binding to target RNAs to control splicing, stability, localization and translation
Recognition occurs by the binding of the RBP to the phrase
The set of phrases bound by a particular RBP is defined by the RNA base content of the binding site as well as the 3D configuration of these bases
Summary
RBPs act in the post-transcriptional regulation (PTR) of gene expression by binding to target RNAs to control splicing, stability, localization and translation. Recent draft networks of RBPtranscript physical interaction in yeast [1], fruit flies [2], and humans [3] reveal a complex and combinatorial pattern of RBP targeting and supports an RNA regulon model [4] in which cisregulatory transcript sequence dictates the post-transcriptional fate of an mRNA at multiple, distinct stages of regulation. Deciphering this operon code as well as the role of individual RBPs in posttranscriptional regulation requires the detailed characterization of the binding preferences of RBPs. We have recently introduced the RNAcompete assay [5], a microarray-based in vitro method to estimate the binding affinity of selected RBPs to a defined population of short RNA sequences. This step can prove challenging because many RBPs show a preference for both specific sequences and secondary structure contexts in their binding sites [8,9,10,11,12]
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