Meiosis-dependent mRNA splicing of the fission yeast Schizosaccharomyces pombe mes1 + gene

Kishida, Masao; Nagai, Tsutomu; Nakaseko, Yukinobu; Shimoda, Chikashi

doi:10.1007/bf00351668

Cited by 37 publications

(33 citation statements)

References 32 publications

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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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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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“…Cells lacking Mei4 arrest before the onset of meiosis I (5,15). Mes1 is one of the many genes under the transcriptional control of Mei4 (20); mes1 null cells are viable but arrest as binucleated cells before the onset of meiosis II (18,31). Genetic and biochemical analyses have shown that the cyclin-dependent kinase Cdc2 is required for progression through the meiotic cell cycle (13,16).…”

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A Meiosis-Specific Cyclin Regulated by Splicing Is Required for Proper Progression through Meiosis

Malapeira

Moldón

Hidalgo

et al. 2005

Molecular and Cellular Biology

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The meiotic cell cycle is modified from the mitotic cell cycle by having a premeiotic S phase which leads to high levels of recombination, a reductional pattern of chromosome segregation at the first division, and a second division with no intervening DNA synthesis. Cyclin-dependent kinases are essential for progression through the meiotic cell cycle, as for the mitotic cycle. Here we show that a fission yeast cyclin, Rem1, is present only during meiosis. Cells lacking Rem1 have impaired meiotic recombination, and Rem1 is required for premeiotic DNA synthesis when Cig2 is not present. rem1 expression is regulated at the level of both transcription and splicing, with Mei4 as a positive and Cig2 a negative factor of rem1 splicing. This regulation ensures the timely appearance of the different cyclins during meiosis, which is required for the proper progression through the meiotic cell cycle. We propose that the meiosis-specific B-type cyclin Rem1 has a central role in bringing about progression through meiosis.During its life cycle, the fission yeast Schizosaccharomyces pombe can undergo either mitotic proliferation or sexual conjugation followed by meiosis. The decision between these two developmental fates occurs in the G 1 phase of the cell cycle. Fission yeast cells proliferate in a haploid state, and when the nitrogen source becomes limiting they arrest in G 1 and conjugate with cells of the opposite mating type (11, 37). The pathway controlling entry into meiosis is quite well understood in S. pombe. Nitrogen starvation induces the expression of several genes, including mei2, which encodes an RNA-binding protein that is inactivated during mitotic growth by direct phosphorylation by the protein kinase Pat1 (25,35,36), and mei3, which encodes an inhibitor of Pat1 protein kinase (26). The temperature-sensitive pat1-114 allele initiates meiosis at the restrictive temperature (17,25,26,29) and can be used to synchronously induce meiosis, even in haploid cells.When diploid zygotes proceed into meiosis, they transiently arrest in G 1 and then initiate one round of DNA replication (premeiotic S phase), leading to cells with a 4C DNA content. Replication is followed by high levels of recombination, chromosome pairing, and two consecutive nuclear divisions, generating four nuclei with a 1C DNA content (for a review, see reference 38). Premeiotic S phase takes longer than mitotic S phase, although, at least in Saccharomyces cerevisiae, the same replication origins are used and the replication forks move at the same rate (8). Although many gene products essential for mitotic DNA synthesis are also required for premeiotic S phase (28), there are some exceptions. For example, in S. cerevisiae, two S-phase cyclins, CLB5 and CLB6, are not required for completion of mitotic DNA synthesis but are essential for premeiotic S phase (34). These differences between mitotic and meiotic DNA synthesis might be related to the period of high recombination that follows premeiotic S phase. In fact, DSBs (double-strand breaks) and thus me...

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“…However, two well-documented instances of regulated splicing have been described in S. cerevisiae, both utilizing intron retention as an on-off switch for protein expression (19,20). The situation is less clear in Schizosaccharomyces pombe, but a similar form of regulation at the level of splicing has been proposed for mes1 pre-mRNA during meiosis (37).…”

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Evidence for Splice Site Pairing via Intron Definition in Schizosaccharomyces pombe

Romfo

Alvarez

Heeckeren

et al. 2000

Molecular and Cellular Biology

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Schizosaccharomyces pombe pre-mRNAs are generally multi-intronic and share certain features with premRNAs from Drosophila melanogaster, in which initial splice site pairing can occur via either exon or intron definition. Here, we present three lines of evidence suggesting that, despite these similarities, fission yeast splicing is most likely restricted to intron definition. First, mutating either or both splice sites flanking an internal exon in the S. pombe cdc2 gene produced almost exclusively intron retention, in contrast to the exon skipping observed in vertebrates. Second, we were unable to induce skipping of the internal microexon in fission yeast cgs2, whereas the default splicing pathway excludes extremely small exons in mammals. Because nearly quantitative removal of the downstream intron in cgs2 could be achieved by expanding the microexon, we propose that its retention is due to steric occlusion. Third, several cryptic 5 junctions in the second intron of fission yeast cdc2 are located within the intron, in contrast to their generally exonic locations in metazoa. The effects of expanding and contracting this intron are as predicted by intron definition; in fact, even highly deviant 5 junctions can compete effectively with the standard 5 splice site if they are closer to the 3 splicing signals. Taken together, our data suggest that pairing of splice sites in S. pombe most likely occurs exclusively across introns in a manner that favors excision of the smallest segment possible.Splice site selection has been most extensively studied in higher eukaryotes (reviewed in reference 11), where abundant evidence indicates that the unit initially recognized by the splicing machinery is the exon, as proposed by Robberson et al. nearly a decade ago (53). Particularly compelling in this regard is the observation that the most common effect of a 5Ј splice site mutation is skipping of the preceding exon rather than inclusion of the mutant intron (61; reviewed in reference 6). Moreover, in the subset of cases in which a 5Ј junction mutation causes activation of a cryptic splice site rather than exon skipping, the new exon-intron boundary is almost invariably located within the preceding exon, again supporting the view that communication occurs across the exon rather than the intron. Finally, there are significant constraints on exon length in vertebrate pre-mRNAs, consistent with the proposal that the 3Ј and 5Ј splice sites on opposite sides of the exon must be recognized concurrently. Not only are the vast majority of natural internal exons in vertebrate pre-mRNAs Ͻ300 nucleotides in length (6), but expanding an exon beyond this size causes it to be skipped (53), particularly if it is surrounded by large introns (60). In contrast to the limitations on exon length, the introns in vertebrate pre-mRNAs can be extremely large (tens of kilobases [29]).Although many questions remain to be answered, several components of the machinery responsible for exon definition have been identified. First, UV cross-linking experiments ...

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Meiosis-dependent mRNA splicing of the fission yeast Schizosaccharomyces pombe mes1 + gene

Cited by 37 publications

References 32 publications

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

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

A Meiosis-Specific Cyclin Regulated by Splicing Is Required for Proper Progression through Meiosis

Evidence for Splice Site Pairing via Intron Definition in Schizosaccharomyces pombe

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