rnacontext a new method for learning the sequence and structure binding preferences of rna-binding proteinsrnacontext学习的一种新方法的序列和结构绑定偏好rna结合蛋白.pdfVIP

RNAcontext: A New Method for Learning the Sequence and Structure Binding Preferences of RNA-Binding Proteins 1 2 3 2,3,4 1,2,3,4 Hilal Kazan , Debashish Ray , Esther T. Chan , Timothy R. Hughes , Quaid Morris * 1 Department of Computer Science, University of Toronto, Toronto, Ontario, Canada, 2 Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, Canada, 3 Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada, 4 Donnelley Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada 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 SF