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Identification of New Branch Points and Unconventional Introns in Saccharomyces cerevisiae

ABSTRACT: Spliced messages constitute one-fourth of expressed mRNAs in the yeast Saccharomyces cerevisiae, and most mRNAs in metazoans. Splicing requires 5' splice site (5'SS), branch point (BP), and 3' splice site (3'SS) elements, but the role of the BP in splicing control is poorly understood because BP identification remains difficult. We developed a high-throughput method, Branch-seq, to map BP and 5'SS of isolated RNA lariats. Applied to S. cerevisiae, Branch-seq detected 76% of expressed, annotated BPs and identified a comparable number of novel BPs. We used RNA-seq to confirm associated 3'SS locations, identifying some 200 novel splice junctions, including an AT-AC intron. We show that several yeast introns use two or even three different BPs, with effects on 3'SS choice, protein coding potential, or RNA stability and identify novel introns whose splicing changes during meiosis or in response to stress. Together, these findings reveal BP-based regulation and demonstrate unanticipated complexity of splicing in yeast.

ORGANISM(S): Saccharomyces cerevisiae S288C Saccharomyces cerevisiae

PROVIDER: GSE68022 | GEO | 2016/08/01

SECONDARY ACCESSION(S): PRJNA281544

REPOSITORIES: GEO

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Identification of New Branch Points and Unconventional Introns in Saccharomyces cerevisiae

Project description:Spliced messages constitute one-fourth of expressed mRNAs in the yeast Saccharomyces cerevisiae, and most mRNAs in metazoans. Splicing requires 5' splice site (5'SS), branch point (BP), and 3' splice site (3'SS) elements, but the role of the BP in splicing control is poorly understood because BP identification remains difficult. We developed a high-throughput method, Branch-seq, to map BP and 5'SS of isolated RNA lariats. Applied to S. cerevisiae, Branch-seq detected 76% of expressed, annotated BPs and identified a comparable number of novel BPs. We used RNA-seq to confirm associated 3'SS locations, identifying some 200 novel splice junctions, including an AT-AC intron. We show that several yeast introns use two or even three different BPs, with effects on 3'SS choice, protein coding potential, or RNA stability and identify novel introns whose splicing changes during meiosis or in response to stress. Together, these findings reveal BP-based regulation and demonstrate unanticipated complexity of splicing in yeast. 1 Lariat-seq experiment library. 3 barcoded Branch-seq libraries that make up one experiment. 26 RNA-seq samples, 2 biological replicates of each.

2016-08-01 | E-GEOD-68022 | biostudies-arrayexpress

Cancer associated SF3B1 hotspot mutations induce cryptic 3' splice site selection through use of a different branch point

Project description:Recurrent mutations in the spliceosome are observed in several human cancers but their functional and therapeutic significance remain elusive. SF3B1, the most frequently mutated component of the spliceosome in cancer, is involved in the recognition of the branch point sequence (BPS) during selection of the 3’ splice site (ss) in RNA splicing. Here, we report that common and tumor-specific splicing aberrations are induced by SF3B1 mutations and establish aberrant 3’ ss selection as the most frequent splicing defect. Strikingly, mutant SF3B1 utilizes a BPS that differs from that used by wild-type SF3B1 and requires the canonical 3’ ss to enable aberrant splicing during the second step. Approximately 50% of the aberrantly spliced mRNAs are subjected to nonsense-mediated decay resulting in downregulation of gene and protein expression. These findings ascribe functional significance to the consequences of SF3B1 mutations in cancer. 72 samples, including two sets of patient data and cell lines with two additional technical replicates each

2015-09-08 | E-GEOD-72790 | biostudies-arrayexpress

A comprehensive map of intron branchpoints and lariat RNAs in plants

Project description:Lariat is formed by excised intron, in which the 5' splice site joints with the branchpoint (BP) during splicing. Although lariat RNAs are usually degraded by DBR1 (RNA debranching enzyme 1), recent findings in animals showed that many lariat RNAs were widely detected under physiological conditions. In contrast, the features of BPs and to what extent lariat RNAs accumulate naturally are largely unexplored in plants. Here, we analyzed 948 RNA sequencing datasets to document plant BPs and lariat RNAs on a genome-wide scale. In total, we identified 13872, 5199, 29582, and 13478 BPs in Arabidopsis, tomato, rice, and maize, respectively. Features of plant BPs are highly similar to those in yeast and human, in that BPs are adenine-preferred and flanked by uracil-enriched sequences. Intriguingly, ~20% of introns harbor multiple BPs, and BP usage is tissue-specific. Furthermore, 10580 lariat RNAs accumulate in wild type Arabidopsis plants, and most of these lariat RNAs originate from longer or retroelement-depleted introns, and the expression of these lariat RNAs significantly correlated with the incidence of back-splicing of parent exons. Collectively, our results provide the first comprehensive map of intron BPs and lariat RNAs in plants, and uncover a novel link between lariat turnover and splicing.

2019-04-17 | GSE117416 | GEO

Cancer associated SF3B1 hotspot mutations induce cryptic 3' splice site selection through use of a different branch point

2015-09-08 | GSE72790 | GEO

Intron evolution in Saccharomycetaceae

Project description:Purpose: Saccharomyceatacea yeast are intron-poor species and they contain on average 300 introns in their genomes. We designed RNAseq experiment to investigate if splicing patterns in related yeast species are similar. Methods: Total RNA was extracted from wild type cells and processed by the RiboMinus Transcriptome Isolation Kit for Yeast and Bacteria (Invitrogen) to deplete the rRNA. cDNA libraries were prepared according to manufacturer's protocol and sequenced by SOLiD. Sequence reads were filtered and processed by TopHat. Results: We found 216, 163, 200 and 155 predicted introns with canonical splice signals in S. cerevisiae, S. kudriavzevii, S. bayanus and N. castellii respectively. Three introns in S. cerevisiae, four in S. bayanus and ten in S. castellii are novel compared to Saccharomyces Genome Database (SGD) annotations. The expression of introns and splicing shows very high correlation between species. Conclusion: Transcripts with introns in yeast species tested show similar levels of expression and splicing. We found few novel introns, which are conserved in yeast genomes.

2014-09-15 | GSE58884 | GEO

The impact of Prp18p on splicing fidelity and efficiency in budding yeast

Project description:Fidelity of 3´-splice site (3´SS) selection by the spliceosome is critical for proper gene expression but is a daunting task considering the low complexity of the 3´SS consensus YAG. Here we show that loss of the splicing factor Prp18p in budding yeast activates a diverse array of alternative 3´SS at more than half of all introns. Some alternative sites highly diverge from the YAG consensus, demonstrating a critical role for Prp18p in promoting spliceosome fidelity. Usage of alternative 3´SS is determined by distance from the branchpoint, local RNA secondary structures, upstream poly(U) content, and adenosine enrichment in exons. The 3´SS fidelity function of Prp18p can be genetically uncoupled from its role in splicing efficiency and is promoted by interactions with Slu7p and Prp8p. Taken together, these results provide a comprehensive mechanism into how the spliceosome achieves specificity of 3´SS selection and how it prevents aberrant activation of non-canonical splice sites.

2020-05-25 | GSE131797 | GEO

Novel RNA-binding Proteins Bind U1 snRNA to Promote Splicing of Weak 5' Splice Sites

Project description:Removal of introns during pre-mRNA splicing, which is central to gene expression, initiates by base pairing of U1 snRNA with a 5' splice site (5'SS). In mammals, many introns contain weak 5'SSs that are not efficiently recognized by the canonical U1 snRNP, suggesting alternative mechanisms exist. Here, we develop a cross-linking immunoprecipitation coupled to a high-throughput sequencing method, BCLIP-seq, to identify NRDE2 (Nuclear RNAi defective-2) and CCDC174 (Coiled-Coil Domain-Containing 174) as novel RNA-binding proteins in mouse ES cells that associate with U1 snRNA and unspliced 5'SSs. Both proteins bind directly to U1 snRNA independently of canonical U1 snRNP specific proteins, and they are required for the selection and effective processing of weak 5'SSs. Our results reveal that mammalian cells use non-canonical splicing factors bound directly to U1 snRNA to effectively select suboptimal 5'SS sequences in hundreds of genes, promoting proper splice site choice and accurate pre-mRNA splicing.

2023-09-07 | PXD029392 | Pride

Prp4 Kinase Grants the License to Splice: Control of Weak Splice Sites during Spliceosome Activation

Project description:The genome of the fission yeast Schizosaccharomyces pombe encodes 17 kinases that are essential for cell growth. These include the cell-cycle regulator Cdc2, as well as several kinases that coordinate cell growth, polarity, and morphogenesis during the cell cycle. In this study, we further characterized another of these essential kinases, Prp4, and showed that the splicing of many introns is dependent on Prp4 kinase activity. For detailed characterization, we chose the genes res1 and ppk8, each of which contains one intron of typical size and position. Splicing of the res1 intron was dependent on Prp4 kinase activity, whereas splicing of the ppk8 intron was not. Extensive mutational analyses of the 5’ splice site of both genes revealed that proper transient interaction with the 5’ end of snRNA U1 governs the dependence of splicing on Prp4 kinase activity. Proper transient interaction between the branch sequence and snRNA U2 was also important. Therefore, the Prp4 kinase is required for recognition and efficient splicing of introns displaying weak exon1/5’ splice sites and weak branch sequences.

2015-12-01 | GSE75517 | GEO

Global analysis of binding sites of U2AF1 and ZRSR2 reveals RNA elements required for mutually exclusive splicing by the U2- and U12-type spliceosome

Project description:Eukaryotic nuclear introns have been dichotomously classified into common U2-type introns and rare U12-type introns. Because the highly conserved consensus sequences for the 5’ splice site and the branch point are found within all U12-type introns, weighted matrices for these motifs are used for prediction of U12-type introns. However, the U12-type consensus sequences per se are also recognized by the U2-type spliceosome. To better understand how distinct splicing systems recognize their authentic splice sites, we determined the binding sites of splicing factors, U2AF1 and ZRSR2, and found that ZRSR2 binding is mostly limited to U12-type introns. Our results reveal RNA elements contributing to selection of U2-type and U12-type splice sites in a mutually exclusive manner.

2022-05-24 | GSE203531 | GEO

Excised linear introns regulate growth in yeast

Project description:Spliceosomal introns are ubiquitous non-coding RNAs typically destined for rapid debranching and degradation. Here, we describe 34 excised Saccharomyces cerevisiae introns that, although rapidly degraded in log-phase growth, accumulate as linear RNAs under either saturated-growth conditions or other stresses that cause prolonged inhibition of TORC1, a key integrator of growth signaling. Introns that become stabilized remain associated with components of the spliceosome and differ from other spliceosomal introns in having a short distance between their lariat branch point and 3´ splice site, which is necessary and sufficient for their stabilization. Deletion of these unusual introns is disadvantageous in saturated conditions and causes aberrantly high growth rates of yeast chronically challenged with the TORC1 inhibitor rapamycin. Reintroduction of native or engineered stable introns suppresses this aberrant rapamycin response. Thus, excised introns function within the TOR growth-signaling network of S. cerevisiae, and more generally, excised spliceosomal introns can have biological functions.

2018-10-29 | GSE121765 | GEO

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