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

Approaches to link RNA secondary structures with splicing regulation