  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.
