Transcriptomics

Dataset Information

299

Widespread Use of Non-Productive Alternative Splice Sites in Saccharomyces cerevisiae


ABSTRACT: Using RNA-Seq analysis of nonsense-mediated mRNA decay (NMD) mutant strains, we show that many Saccharomyces cerevisiae intron-containing genes exhibit usage of alternative splice sites, but most transcripts generated by splicing from these sites are non-functional because they introduce premature termination codons leading to transcript 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. The use of non-productive alternative splice sites can limit the expression of some transcripts and can be increased in stress conditions in a promoter-dependent manner, contributing to the down-regulation of genes during stress. These results reveal that alternative splicing is frequent in S.cerevisiae but masked by RNA degradation and that the use of alternative splice sites is mostly aimed at controlling transcript levels rather than increasing proteome diversity. mRNA-Seq profiling of 3 mutants in the nonsense-mediated mRNA decay pathway and wildtype yeast

ORGANISM(S): Saccharomyces cerevisiae BY4741  

SUBMITTER: Tadashi R Kawasima   Guillaume F Chanfreau  Stephen M Douglass  Stephen Douglass  Matteo Pellegrini 

PROVIDER: E-GEOD-55213 | ArrayExpress | 2014-02-21

SECONDARY ACCESSION(S): SRP038701GSE55213PRJNA238899

REPOSITORIES: GEO, ArrayExpress, ENA

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Publications

Widespread use of non-productive alternative splice sites in Saccharomyces cerevisiae.

Kawashima Tadashi T   Douglass Stephen S   Gabunilas Jason J   Pellegrini Matteo M   Chanfreau Guillaume F GF  

PLoS genetics 20140410 4


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  ...[more]

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