Genome-wide bioinformatic and molecular analysis of introns in Saccharomyces cerevisiae
Open accessAbstract
Introns have typically been discovered in an ad hoc fashion: introns are found as a gene is characterized for other reasons. As complete eukaryotic genome sequences become available, better methods for predicting RNA processing signals in raw sequence will be necessary in order to discover genes and predict their expression. Here we present a catalog of 228 yeast introns, arrived at through a combination of bioinformatic and molecular analysis. Introns annotated in the Saccharomyces Genome Database (SGD) were evaluated, questionable introns were removed after failing a test for splicing in vivo, and known introns absent from the SGD annotation were added. A novel branchpoint sequence, AAUUAAC, was identified within an annotated intron that lacks a six-of-seven match to the highly conserved branchpoint consensus UACUAAC. Analysis of the database corroborates many conclusions about pre-mRNA substrate requirements for splicing derived from experimental studies, but indicates that splicing in yeast may not be as rigidly determined by splice-site conservation as had previously been thought. Using this database and a molecular technique that directly displays the lariat intron products of spliced transcripts (intron display), we suggest that the current set of 228 introns is still not complete, and that additional intron-containing genes remain to be discovered in yeast. The database can be accessed at http://www.cse.ucsc.edu/research/compbi o/yeast_introns.html.
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Yeast Saccharomyces cerevisiae has a large number of fungal genomes, a relatively small genome (6,000 genes total), and relatively little mRNA splicing.
“To mitigate the first three challenges, we chose to predict protein complexes for yeast Saccharomyces cerevisiae as the starting point because there are a large number of fungal genomes (16), the genome is relatively small (6,000 genes total), and there is relatively little mRNA splicing (17).”
From Computed structures of core eukaryotic protein complexes (2021) · cites this paper as [17]
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- Authors
- SPINGOLA, M., GRATE, L., HAUSSLER, D., & ARES, M.
- Affiliations
- University of California, Santa Cruz (US)
- Venue
- RNA
- Publisher
- Cold Spring Harbor Laboratory
- Published
- 1999-02
- Volume
- 5
- Issue
- 2
- Pages
- 221-234
- ISSN
- 1355-8382 (ISSN-L)
- PMC
- PMC1369754
- OpenAlex
- W2134232237
- Cited by
- 316
- References
- 90
- Citations by year
- 2026: 7 · 2025: 7 · 2024: 7 · 2023: 6 · 2022: 7 · 2021: 5 · 2020: 5 · 2019: 17 · 2018: 9 · 2017: 9 · 2016: 17 · 2015: 18 · 2014: 11 · 2013: 9 · 2012: 13
- FWCI
- 6.21
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- RNA (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- IRL - University of Missouri, St. Louis (University of Missouri–St. Louis) (submittedVersion)
- Funders
- National Institutes of Health (5r21ca077813-02)
- National Cancer Institute (R21 CA77813)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Fungal and yeast genetics research
- Keywords
- introns, Saccharomyces cerevisiae, pre-mRNA splicing, Saccharomyces Genome Database, gene discovery
- MeSH terms
- Introns, Markov Chains, Ribosomal Proteins, RNA Precursors, RNA Splicing, RNA, Small Nuclear, Saccharomyces cerevisiae, Genome, Fungal, Spliceosomes, Computational Biology, Databases as Topic
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