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....
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2014-04-01
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| Series: | PLoS Genetics |
| Online Access: | http://europepmc.org/articles/PMC3983031?pdf=render |
| _version_ | 1818056159405277184 |
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| author | Tadashi Kawashima Stephen Douglass Jason Gabunilas Matteo Pellegrini Guillaume F Chanfreau |
| author_facet | Tadashi Kawashima Stephen Douglass Jason Gabunilas Matteo Pellegrini Guillaume F Chanfreau |
| author_sort | Tadashi Kawashima |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-12-10T12:24:24Z |
| format | Article |
| id | doaj.art-a42f1981e279433ebcd2a3a48115efb1 |
| institution | Directory Open Access Journal |
| issn | 1553-7390 1553-7404 |
| language | English |
| last_indexed | 2024-12-10T12:24:24Z |
| publishDate | 2014-04-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS Genetics |
| spelling | doaj.art-a42f1981e279433ebcd2a3a48115efb12022-12-22T01:49:00ZengPublic Library of Science (PLoS)PLoS Genetics1553-73901553-74042014-04-01104e100424910.1371/journal.pgen.1004249Widespread use of non-productive alternative splice sites in Saccharomyces cerevisiae.Tadashi KawashimaStephen DouglassJason GabunilasMatteo PellegriniGuillaume F ChanfreauSaccharomyces 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.http://europepmc.org/articles/PMC3983031?pdf=render |
| spellingShingle | Tadashi Kawashima Stephen Douglass Jason Gabunilas Matteo Pellegrini Guillaume F Chanfreau Widespread use of non-productive alternative splice sites in Saccharomyces cerevisiae. PLoS Genetics |
| title | Widespread use of non-productive alternative splice sites in Saccharomyces cerevisiae. |
| title_full | Widespread use of non-productive alternative splice sites in Saccharomyces cerevisiae. |
| title_fullStr | Widespread use of non-productive alternative splice sites in Saccharomyces cerevisiae. |
| title_full_unstemmed | Widespread use of non-productive alternative splice sites in Saccharomyces cerevisiae. |
| title_short | Widespread use of non-productive alternative splice sites in Saccharomyces cerevisiae. |
| title_sort | widespread use of non productive alternative splice sites in saccharomyces cerevisiae |
| url | http://europepmc.org/articles/PMC3983031?pdf=render |
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