Widespread use of non-productive alternative splice sites in Saccharomyces cerevisiae.
Saccharomyces cerevisiae has been used as a model system to investigate the mechanisms of pre-mRNA splicing but only a few examples of alternative splice site usage have been described in this organism. Using RNA-Seq analysis of nonsense-mediated mRNA decay (NMD) mutant strains, we show that many S. cerevisiae intron-containing genes exhibit usage of alternative splice sites, but many transcripts generated by splicing at these sites are non-functional because they introduce premature termination codons, leading to degradation by NMD. Analysis of splicing mutants combined with NMD inactivation revealed the role of specific splicing factors in governing the use of these alternative splice sites and identified novel functions for Prp17p in enhancing the use of branchpoint-proximal upstream 3' splice sites and for Prp18p in suppressing the usage of a non-canonical AUG 3'-splice site in GCR1. The use of non-productive alternative splice sites can be increased in stress conditions in a promoter-dependent manner, contributing to the down-regulation of genes during stress. These results show that alternative splicing is frequent in S. cerevisiae but masked by RNA degradation and that the use of alternative splice sites in this organism is mostly aimed at controlling transcript levels rather than increasing proteome diversity.
Department of Chemistry and Biochemistry and the Molecular Biology Institute, UCLA, Los Angeles, California, United States of America.
Tadashi
T
Kawashima
Bioinformatics Interdepartmental Program, UCLA, Los Angeles, California, United States of America.
Stephen
S
Douglass
Department of Chemistry and Biochemistry and the Molecular Biology Institute, UCLA, Los Angeles, California, United States of America.
Jason
J
Gabunilas
Department of Molecular, Cellular and Developmental Biology, UCLA, Los Angeles, California, United States of America.
Matteo
M
Pellegrini
Department of Chemistry and Biochemistry and the Molecular Biology Institute, UCLA, Los Angeles, California, United States of America.
Guillaume F
GF
Chanfreau
D017398:Alternative Splicing / Q000235:genetics*; D018797:Cell Cycle Proteins / Q000235:genetics; D018389:Codon, Nonsense / Q000235:genetics; D004268:DNA-Binding Proteins / Q000235:genetics; D015536:Down-Regulation / Q000235:genetics; D059365:Nonsense Mediated mRNA Decay / Q000235:genetics*; D011401:Promoter Regions, Genetic / Q000235:genetics; D012313:RNA / Q000235:genetics; D022821:RNA Splice Sites / Q000235:genetics*; D012326:RNA Splicing / Q000235:genetics*; D000072260:RNA Splicing Factors; D020871:RNA Stability / Q000235:genetics; D016601:RNA-Binding Proteins / Q000235:genetics; D017415:Ribonucleoprotein, U5 Small Nuclear / Q000235:genetics; D012441:Saccharomyces cerevisiae / Q000235:genetics*; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics; D014157:Transcription Factors / Q000235:genetics
C093570:CDC40 protein, S cerevisiae; D018797:Cell Cycle Proteins; D018389:Codon, Nonsense; D004268:DNA-Binding Proteins; C076227:GCR1 protein, S cerevisiae; C080779:PRP18 protein, S cerevisiae; D022821:RNA Splice Sites; D000072260:RNA Splicing Factors; D016601:RNA-Binding Proteins; D017415:Ribonucleoprotein, U5 Small Nuclear; D029701:Saccharomyces cerevisiae Proteins; D014157:Transcription Factors; D012313:RNA