|Title:||Predicting in vivo binding sites of RNA-binding proteins using mRNA secondary structure|
Department of Computer Science, ChiBi, University of British Columbia
mRNA and protein are the two main products from the genome. Their interactions widely exists in the cell, and are as important as DNA-protein interactions for determining the state of a living cell and play key roles in post-transcriptional regulation of gene expression. Unlike DNA-protein interactions which are dominated by primary sequence motifs in canonical double stranded DNA molecule, RNA-protein interactions usually involve secondary structure features of the single stranded RNA molecule. Previous studies have shown that: sequence-specific RNA-binding proteins (RBPs) either recognize and bind to unstructured single-stranded RNA or require at least some of their RNA binding sites to be unpaired. Such single-strandness is defined as accessibility of that RNA sequence. In this talk, I will present our recent progress on utilizing mRNA secondary structure to assess the accessibility of putative RBP binding sites in vivo.