Approaches to link RNA secondary structures with splicing regulation

TL;DR

This paper reviews how RNA secondary structures influence splicing regulation in eukaryotes and yeast, highlighting analysis methods and the potential regulatory roles of RNA folding in splicing processes.

Contribution

It provides a comprehensive overview of approaches to analyze RNA secondary structures and their impact on splicing regulation, emphasizing yeast as a model.

Findings

RNA secondary structures can facilitate or hinder splicing factor interactions

Structural features of pre-mRNA influence splice site recognition

Analysis methods help elucidate structure-function relationships in splicing

Abstract

In higher eukaryotes, alternative splicing is usually regulated by protein factors, which bind to the pre-mRNA and affect the recognition of splicing signals. There is recent evidence that the secondary structure of the pre-mRNA may also play an important role in this process, either by facilitating or by hindering the interaction with factors and small nuclear ribonucleoproteins (snRNPs) that regulate splicing. Moreover, the secondary structure could play a fundamental role in the splicing of yeast species, which lack many of the regulatory splicing factors present in metazoans. This review describes the steps in the analysis of the secondary structure of the pre-mRNA and its possible relation to splicing. As a working example, we use the case of yeast and the problem of the recognition of the 3-prime splice site.