ArticleRNA (New York, N.Y.)2012
RNA secondary structure mediates alternative 3'ss selection in Saccharomyces cerevisiae.
Article in RNA (New York, N.Y.), 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed, 44 citations in OpenAlex.
- Control of gene output by intron RNA structure.bioRxiv : the preprint server for biology · 2025Article
- Sex-dependent epigenetic disruption of YY1 binding by prenatal BPA exposure downregulates Matr3 and alters Agap1 splicing in the offspring hippocampus.Biology of sex differences · 2025Article
- From benign to pathogenic variants and vice versa: pyrimidine transitions at position -3 of TAG and CAG 3' splice sites.Journal of human genetics · 2025Article
- Impact on splicing inRNA (New York, N.Y.) · 2023Article
- Splicing factor Prp18p promotes genome-wide fidelity of consensus 3'-splice sites.Nucleic acids research · 2023Article
- Transcriptomic Analysis Reveals That Rho GTPases Regulate Trap Development and Lifestyle Transition of the Nematode-Trapping FungusMicrobiology spectrum · 2022Article
- Group II Introns: Flexibility and Repurposing.Frontiers in molecular biosciences · 2022Article
- Improved recognition of splice sites in3 Biotech · 2021Article
- A broad analysis of splicing regulation in yeast using a large library of synthetic introns.PLoS genetics · 2021Article
- Direct Nanopore Sequencing of mRNA Reveals Landscape of Transcript Isoforms in Apicomplexan Parasites.mSystems · 2021Article
- Article
- Transcription rate strongly affects splicing fidelity and cotranscriptionality in budding yeast.Genome research · 2018Article
- RNAStructuromeDB: A genome-wide database for RNA structural inference.Scientific reports · 2017Article
- Structure of the yeast spliceosomal postcatalytic P complex.Science (New York, N.Y.) · 2017Article
- The effects of structure on pre-mRNA processing and stability.Methods (San Diego, Calif.) · 2017Review
- Cancer-associated SF3B1 mutants recognize otherwise inaccessible cryptic 3' splice sites within RNA secondary structures.Oncogene · 2017Article
- RNA structure in splicing: An evolutionary perspective.RNA biology · 2016Review
- Novel Intronic RNA Structures Contribute to Maintenance of Phenotype in Saccharomyces cerevisiae.Genetics · 2016Article
- IntSplice: prediction of the splicing consequences of intronic single-nucleotide variations in the human genome.Journal of human genetics · 2016Article
- Parallel computation of genome-scale RNA secondary structure to detect structural constraints on human genome.BMC bioinformatics · 2016Article
Corrections and comments
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Authors and funding
5 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Alternative splicing is the mechanism by which different combinations of exons in the pre-mRNA give rise to distinct mature mRNAs. This process is mediated by splicing factors that bind the pre-mRNA and affect the recognition of its splicing signals. Saccharomyces species lack many of the regulatory factors present in metazoans. Accordingly, it is generally assumed that the amount of alternative splicing is limited. However, there is recent compelling evidence that yeast have functional alternative splicing, mainly in response to environmental conditions. We have previously shown that sequence and structure properties of the pre-mRNA could explain the selection of 3' splice sites (ss) in Saccharomyces cerevisiae. In this work, we extend our previous observations to build a computational classifier that explains most of the annotated 3'ss in the CDS and 5' UTR of this organism. Moreover, we show that the same rules can explain the selection of alternative 3'ss. Experimental validation of a number of predicted alternative 3'ss shows that their usage is low compared to annotated 3'ss. The majority of these alternative 3'ss introduce premature termination codons (PTCs), suggesting a role in expression regulation. Furthermore, a genome-wide analysis of the effect of temperature, followed by experimental validation, yields only a small number of changes, indicating that this type of regulation is not widespread. Our results are consistent with the presence of alternative 3'ss selection in yeast mediated by the pre-mRNA structure, which can be responsive to external cues, like temperature, and is possibly related to the control of gene expression.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.