Title: | Predicting in vivo binding sites of RNA-binding proteins using mRNA secondary structure |
Speaker: |
Shu Yang Department of Computer Science, ChiBi, University of British Columbia |
Abstract |
Abstract 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. |