Promoter-driven splicing regulation in fission yeast

Moldón, Alberto; Malapeira, Jordi; Gabrielli, Natalia; Gogol, Madelaine; Gómez‐Escoda, Blanca; Ivanova, Tsvetomira; Seidel, Chris; Ayté, José

doi:10.1038/nature07325

Cited by 81 publications

(133 citation statements)

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“…Expression of the two protein isoforms may be promoter dependent: overexpression with either the MET25 (Ramos et al 2000) or the GAL1 inducible promoters produces significantly more mitochondrial Ptc7 s than Ptc7 u (Figure 5 and Figure S1). Promoter-specific alternative splicing has been identified in Schizosaccharomyces pombe (Moldon et al 2008); S. cerevisiae likely shares some of the same regulatory mechanisms.…”

Section: Discussionmentioning

confidence: 99%

Alternative Splicing of PTC7 inSaccharomyces cerevisiaeDetermines Protein Localization

2009

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It is well established that higher eukaryotes use alternative splicing to increase proteome complexity. In contrast, Saccharomyces cerevisiae, a single-cell eukaryote, conducts predominantly regulated splicing through retention of nonfunctional introns. In this article we describe our discovery of a functional intron in the PTC7 (YHR076W) gene that can be alternatively spliced to create two mRNAs that code for distinct proteins. These two proteins localize to different cellular compartments and have distinct cellular roles. The protein translated from the spliced mRNA localizes to the mitochondria and its expression is carbon-source dependent. In comparison, the protein translated from the unspliced mRNA contains a transmembrane domain, localizes to the nuclear envelope, and mediates the toxic effects of Latrunculin A exposure. In conclusion, we identified a definitive example of functional alternative splicing in S. cerevisiae that confers a measurable fitness benefit. I N higher eukaryotes alternative splicing is pervasive; in humans the majority of genes are alternatively spliced to form multiple proteins (Modrek et al. 2001;Johnson et al. 2003). In contrast, only 5% of the genes in Saccharomyces cerevisiae contain introns and .95% of those intron-containing genes possess only a single intron (Nash et al. 2007). The simple architecture of the yeast genome constrains its ability to utilize alternative splicing and has encouraged the view that alternative splicing is absent in S. cerevisiae. Currently no conclusive examples of functional alternative splicing exist; most confirmed instances of alternative splicing in yeast downregulate gene expression, a process that is often referred to as ''regulated splicing.'' In this process, nonfunctional introns are not spliced out of the transcript and premature stop codons are included in the fully processed mRNA. The stop codons activate the nonsense-mediated decay (NMD) pathway and the mRNA is degraded before it can be translated (Gonzalez et al. 2001).The transition from vegetative growth to meiosis illustrates how regulated splicing improves yeast fitness. DNA breakage and recombination could be toxic during vegetative growth, and therefore entrance into meiosis is tightly controlled. Consequently, all 13 meiosis-specific introncontaining genes are regulated post-transcriptionally with splicing repressed during vegetative growth and induced during sporulation (Engebrecht et al. 1991;Nakagawa and Ogawa 1999;Juneau et al. 2007). Other examples of regulated splicing include YRA1 and MTR2 (RNA export) (Preker et al. 2002;Parenteau et al. 2008) and RPL30 (ribosomal) (Li et al. 1996).In contrast to regulated splicing, there is only one example in S. cerevisiae where splicing results in the expression of multiple proteins, SRC1 (Grund et al. 2008). SRC1 contains a single intron located at the 39 end of the pre-mRNA. The intron has two alternative 59-splice sites (Rodriguez-Navarro et al. 2002). Splicing at the most highly conserved 59-splice site (Bon et al. 2003) ...

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Section: Discussionmentioning

confidence: 99%

Alternative Splicing of PTC7 inSaccharomyces cerevisiaeDetermines Protein Localization

2009

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“…However, considering that the HMG box of SRYrelated proteins resembles RNA-binding domains, and that these factors have roles in RNA metabolism (43,44), it is possible that Mc acts in a similar manner to modulate Swi2 and Swi5 protein levels. Indeed, promoter-associated transcription factors have been shown to affect mRNA processing (45). In any case, the elevated levels of the RPC ultimately translate into its increased association with the chromatin and spreading, presumably in a manner similar to dosage-dependent spreading of heterochromatin proteins (11).…”

Section: Discussionmentioning

confidence: 99%

A homolog of male sex-determining factor SRY cooperates with a transposon-derived CENP-B protein to control sex-specific directed recombination

Matsuda

Sugioka-Sugiyama

Mizuguchi

et al. 2011

Proc. Natl. Acad. Sci. U.S.A.

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Schizosaccharomyces pombe cells switch mating type by replacing genetic information at the expressed mat1 locus with sequences copied from mat2-P or mat3-M silent donor loci. The choice of donor locus is dictated by cell type, such that mat2 is the preferred donor in M cells and mat3 is the preferred donor in P cells. Donor choice involves a recombination-promoting complex (RPC) containing Swi2 and Swi5. In P cells, the RPC localizes to a specific DNA element located adjacent to mat3, but in M cells it spreads across the silent mating-type region, including mat2-P. This differential distribution of the RPC regulates nonrandom choice of donors. However, celltype-specific differences in RPC localization are not understood. Here we show that the mat1-M-encoded factor Mc, which shares structural and functional similarities with the male sex-determining factor SRY, is highly enriched at the swi2 and swi5 loci and promotes elevated levels of RPC components. Loss of Mc reduces Swi2 and Swi5 to levels comparable to those in P cells and disrupts RPC spreading across the mat2/3 region. Mc also localizes to loci expressed preferentially in M cells and to retrotransposon LTRs. We demonstrate that Mc localization at LTRs and at swi2 requires Abp1, a homolog of transposon-derived CENP-B protein and that loss of Abp1 impairs Swi2 protein expression and the donor choice mechanism. These results suggest that Mc modulates levels of recombination factors, which is important for mating-type donor selection and for the biased gene conversion observed during meiosis, where M cells serve as preferential donors of genetic information. (1) and mating-type switching in the yeasts Saccharomyces cerevisiae and Schizosaccharomyces pombe (2-5). In these distantly related yeast species, cells alternate between two distinct mating-type alleles by copying genetic information from one of the two silent donor loci to the active mating-type locus via highly orchestrated recombination processes (6-8).The mating-type region of S. pombe contains three linked locimat1, mat2, and mat3-located on chromosome 2. In wild-type homothallic strains, designated h 90 , mat2 is located ∼17 kb centromere-distal to mat1, whereas mat3 is separated from mat2 by an 11-kb interval ( Fig. 1) (8, 9). The mating type of a haploid cell is determined by the presence of P or M information at mat1 (8). Each allele consists of two divergently transcribed genes (10). mat1-P contains the Pc and Pi genes, and mat1-M contains the Mc and Mi genes. mat2 and mat3 contain the same genetic information as mat1-P and mat1-M, respectively, but are maintained in a silent state. These silent mating-type cassettes are embedded in a 20-kb heterochromatin domain surrounded by inverted repeat (IR-R and IR-

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“…Furthermore, cis-acting sequence elements important in splicing regulation in multicellular eukaryotes have been shown to modulate the splicing efficiency of individual S. pombe introns (24), and indeed nonendogenous plant and mammalian intron sequences have been shown to be properly excised in S. pombe (25,26). Nevertheless, although instances of intron-retention have been documented (27,28), no examples of exon skipping have been described in S. pombe. Surprisingly, two recent RNA-seq studies (29,30) failed to detect any instances of exon skipping in S. pombe; however, it was unclear whether this reflected an absence of such splicing events in S. pombe or a limitation of RNA-seq for detecting them.…”

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confidence: 99%

Lariat sequencing in a unicellular yeast identifies regulated alternative splicing of exons that are evolutionarily conserved with humans

Awan

Manfredo

Pleiss

2013

Proc. Natl. Acad. Sci. U.S.A.

114

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Alternative splicing is a potent regulator of gene expression that vastly increases proteomic diversity in multicellular eukaryotes and is associated with organismal complexity. Although alternative splicing is widespread in vertebrates, little is known about the evolutionary origins of this process, in part because of the absence of phylogenetically conserved events that cross major eukaryotic clades. Here we describe a lariat-sequencing approach, which offers high sensitivity for detecting splicing events, and its application to the unicellular fungus, Schizosaccharomyces pombe, an organism that shares many of the hallmarks of alternative splicing in mammalian systems but for which no previous examples of exon-skipping had been demonstrated. Over 200 previously unannotated splicing events were identified, including examples of regulated alternative splicing. Remarkably, an evolutionary analysis of four of the exons identified here as subject to skipping in S. pombe reveals high sequence conservation and perfect length conservation with their homologs in scores of plants, animals, and fungi. Moreover, alternative splicing of two of these exons have been documented in multiple vertebrate organisms, making these the first demonstrations of identical alternative-splicing patterns in species that are separated by over 1 billion y of evolution.pre-mRNA splicing | post-transcriptional gene regulation | phylogeny T he protein coding regions of eukaryotic genes are typically interrupted by noncoding introns that must be removed to produce a translatable mRNA. The removal of introns, catalyzed by the spliceosome, offers a powerful opportunity for an organism to regulate gene expression. In mammals, where individual genes are often interrupted by multiple introns, it is now abundantly clear that the process of intron removal provides a critical regulatory control point for both qualitative and quantitative aspects of gene expression (1). By changing the identity of the exons that are included within the final mRNA, the process of alternative splicing plays a critical role in expanding the diversity of proteins that can be synthesized within a cell (2). Moreover, alternative splicing can direct the production of isoforms of genes that are directly targeted to cellular decay pathways, providing a mechanism to quantitatively regulate gene expression (3, 4).In mammalian organisms the predominant form of alternative splicing is exon skipping, wherein different combinations of exons are included in the final transcript. In contrast, exon skipping is far less prevalent in simpler eukaryotes (5, 6); however, recent studies suggest that splicing in the last eukaryotic common ancestor was similar in many respects to splicing in vertebrates, in so much as it was intron-dense (7-9), had degenerate splice site sequences (10), and likely had many of the proteins involved in alternative splicing (11,12). Intron density correlates positively with the prevalence of alternative splicing across the eukaryotic kingdoms (13), and thus it has...

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Promoter-driven splicing regulation in fission yeast

Cited by 81 publications

References 104 publications

Alternative Splicing of PTC7 inSaccharomyces cerevisiaeDetermines Protein Localization

Alternative Splicing of PTC7 inSaccharomyces cerevisiaeDetermines Protein Localization

A homolog of male sex-determining factor SRY cooperates with a transposon-derived CENP-B protein to control sex-specific directed recombination

Lariat sequencing in a unicellular yeast identifies regulated alternative splicing of exons that are evolutionarily conserved with humans

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