ArticleGenome biology2010
Detection and analysis of alternative splicing in Yarrowia lipolytica reveal structural constraints facilitating nonsense-mediated decay of intron-retaining transcripts.
Article in Genome biology, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
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35 citing papers in PubMed, 74 citations in OpenAlex.
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- Intron location and sequence modulate gene expression in Yarrowia lipolytica.Nucleic acids research · 2026Article
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- Using Euf1 transcription factor as a titrator of erythritol-inducible promoters in Yarrowia lipolytica; insight into the structure, splicing, and regulation mechanism.FEMS yeast research · 2024Article
- Replicative aging in yeast involves dynamic intron retention patterns associated with mRNA processing/export and protein ubiquitination.Microbial cell (Graz, Austria) · 2024Article
- Refactoring the architecture of a polyketide gene cluster enhances docosahexaenoic acid production in Yarrowia lipolytica through improved expression and genetic stability.Microbial cell factories · 2023Article
- Insights into the Genomic and Phenotypic Landscape of the Oleaginous YeastJournal of fungi (Basel, Switzerland) · 2023Article
- Analysis of Fungal Genomes Reveals Commonalities of Intron Gain or Loss and Functions in Intron-Poor Species.Molecular biology and evolution · 2021Article
- The RNA binding protein FgRbp1 regulates specific pre-mRNA splicing via interacting with U2AF23 in Fusarium.Nature communications · 2021Article
- Recent Advances in the Synthetic Biology of Natural Drugs.Frontiers in bioengineering and biotechnology · 2021Review
- Yeast-Based Biosynthesis of Natural Products From Xylose.Frontiers in bioengineering and biotechnology · 2021Review
- CRISPR-Cas12a/Cpf1-assisted precise, efficient and multiplexed genome-editing inMetabolic engineering communications · 2020Article
- Exon junction complex components Y14 and Mago still play a role in budding yeast.Scientific reports · 2019Article
- Refining the Ambush Hypothesis: Evidence That GC- and AT-Rich Bacteria Employ Different Frameshift Defence Strategies.Genome biology and evolution · 2018Article
- Adenine Enrichment at the Fourth CDS Residue in Bacterial Genes Is Consistent with Error Proofing for +1 Frameshifts.Molecular biology and evolution · 2017Article
- YaliBricks, a versatile genetic toolkit for streamlined and rapid pathway engineering inMetabolic engineering communications · 2017Article
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Authors and funding
8 authors at 4 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundHemiascomycetous yeasts have intron-poor genomes with very few cases of alternative splicing. Most of the reported examples result from intron retention in Saccharomyces cerevisiae and some have been shown to be functionally significant. Here we used transcriptome-wide approaches to evaluate the mechanisms underlying the generation of alternative transcripts in Yarrowia lipolytica, a yeast highly divergent from S. cerevisiae.
resultsExperimental investigation of Y. lipolytica gene models identified several cases of alternative splicing, mostly generated by intron retention, principally affecting the first intron of the gene. The retention of introns almost invariably creates a premature termination codon, as a direct consequence of the structure of intron boundaries. An analysis of Y. lipolytica introns revealed that introns of multiples of three nucleotides in length, particularly those without stop codons, were underrepresented. In other organisms, premature termination codon-containing transcripts are targeted for degradation by the nonsense-mediated mRNA decay (NMD) machinery. In Y. lipolytica, homologs of S. cerevisiae UPF1 and UPF2 genes were identified, but not UPF3. The inactivation of Y. lipolytica UPF1 and UPF2 resulted in the accumulation of unspliced transcripts of a test set of genes.
conclusionsY. lipolytica is the hemiascomycete with the most intron-rich genome sequenced to date, and it has several unusual genes with large introns or alternative transcription start sites, or introns in the 5' UTR. Our results suggest Y. lipolytica intron structure is subject to significant constraints, leading to the under-representation of stop-free introns. Consequently, intron-containing transcripts are degraded by a functional NMD pathway.
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