2014 Articles

Using Pre-mRNA Secondary Structure to Predict Splicing

Maity, Alisha P.

Recently, scientists have tried to explain the mechanisms of post-transcriptional splicing. Developments have been made in mRNA secondary structure prediction programs that use thermodynamics to construct possible structural models of mRNA sequences (Seetin and Mathews 2012). Although splicing is a complex process that is affected by multiple interactive variables, attempts have been made to use pre-mRNA secondary structure to explain how splicing decisions are made. Here we show that there does exist some relationship between structure and splicing. Our analysis reveals that in certain areas of an optimized window of Wilms’ Tumor gene exon 5 with flanks, a significant correlation exists between regions of structural pairedness and splicing. Our results specifically point to a strong stem in the exon studied that retains its double-strandedness in the presence of mutations and is associated with high splicing. These findings advance our understanding of the influence of secondary structure on mRNA-protein interactions and encourage us to delve deeper into the complexities of splice site recognition.