title: Approaches to link RNA secondary structures with splicing regulation.
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 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 chapter 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' splice site (3'ss).
authors.affiliation: Department of Biology, The Bioinformatics Centre, University of Copenhagen, Copenhagen, Denmark.
authors.forename: Mireya
authors.initials: M
authors.lastname: Plass
authors.forename: Eduardo
authors.initials: E
authors.lastname: Eyras
mesh_terms: D017398:Alternative Splicing / Q000235:genetics*; D008967:Molecular Biology / Q000379:methods*; D009690:Nucleic Acid Conformation; D012313:RNA / Q000235:genetics; D022821:RNA Splice Sites / Q000235:genetics; D017411:Ribonucleoproteins, Small Nuclear / Q000235:genetics; D012441:Saccharomyces cerevisiae / Q000235:genetics
chemical_list: D022821:RNA Splice Sites; D017411:Ribonucleoproteins, Small Nuclear; D012313:RNA