ArticleG3 (Bethesda, Md.)2013
Extensive transcript diversity and novel upstream open reading frame regulation in yeast.
Article in G3 (Bethesda, Md.), 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 46 papers.
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Who cites it
46 citing papers in PubMed, 71 citations in OpenAlex.
- An upstream open reading frame regulates expression of the mitochondrial protein Slm35 and mitophagy flux.FEBS letters · 2026Article
- The patterns of alternative TSS usage explain the highly heterogeneous landscape of 5'UTR lengths in eukaryotes.NAR genomics and bioinformatics · 2025Article
- Deciphering the landscape of cis-acting sequences in natural yeast transcript leaders.Nucleic acids research · 2025Article
- Dual regulation of the levels and function of Start transcriptional repressors drives G1 arrest in response to cell wall stress.Cell communication and signaling : CCS · 2025Article
- Review
- Deciphering thebioRxiv : the preprint server for biology · 2024Article
- The CDK Pho85 inhibits Whi7 Start repressor to promote cell cycle entry in budding yeast.EMBO reports · 2024Article
- Direct analysis of ribosome targeting illuminates thousand-fold regulation of translation initiation.Cell systems · 2022Article
- Combinations of slow-translating codon clusters can increase mRNA half-life inProceedings of the National Academy of Sciences of the United States of America · 2021Article
- The CWI Pathway: A Versatile Toolbox to Arrest Cell-Cycle Progression.Journal of fungi (Basel, Switzerland) · 2021Review
- A standard knockout procedure alters expression of adjacent loci at the translational level.Nucleic acids research · 2021Article
- The budding yeast Start repressor Whi7 differs in regulation from Whi5, emerging as a major cell cycle brake in response to stress.Journal of cell science · 2020Article
- Changes in transcription start sites of Zap1-regulated genes during zinc deficiency: Implications for HNT1 gene regulation.Molecular microbiology · 2020Article
- Impacts of uORF codon identity and position on translation regulation.Nucleic acids research · 2019Article
- The nucleosome position-encoding WW/SS sequence pattern is depleted in mammalian genes relative to other eukaryotes.Nucleic acids research · 2019Article
- Gid10 as an alternative N-recognin of the Pro/N-degron pathway.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- Pervasive and dynamic transcription initiation inGenome research · 2019Article
- A subtelomeric region affects telomerase-negative replicative senescence in Saccharomyces cerevisiae.Scientific reports · 2019Article
- YeasTSS: an integrative web database of yeast transcription start sites.Database : the journal of biological databases and curation · 2019Article
- Conserved non-AUG uORFs revealed by a novel regression analysis of ribosome profiling data.Genome research · 2018Article
Corrections and comments
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Authors and funding
2 authors at 2 institutions in 1 country.
Funding
Abstract
To understand the diversity of transcripts in yeast (Saccharomyces cerevisiae) we analyzed the transcriptional landscapes for cells grown under 18 different environmental conditions. Each sample was analyzed using RNA-sequencing, and a total of 670,446,084 uniquely mapped reads and 377,263 poly-adenylated end tags were produced. Consistent with previous studies, we find that the majority of yeast genes are expressed under one or more different conditions. By directly comparing the 5' and 3' ends of the transcribed regions, we find extensive differences in transcript ends across many conditions, especially those of stationary phase, growth in grape juice, and salt stimulation, suggesting differential choice of transcription start and stop sites is pervasive in yeast. Relative to the exponential growth condition (i.e., YPAD), transcripts differing at the 5' ends and 3' ends are predicted to differ in their annotated start codon in 21 genes and their annotated stop codon in 63 genes. Many (431) upstream open reading frames (uORFs) are found in alternate 5' ends and are significantly enriched in transcripts produced during the salt response. Mutational analysis of five genes with uORFs revealed that two sets of uORFs increase the expression of a reporter construct, indicating a role in activation which had not been reported previously, whereas two other uORFs decreased expression. In addition, RNA binding protein motifs are statistically enriched for alternate ends under many conditions. Overall, these results demonstrate enormous diversity of transcript ends, and that this heterogeneity is regulated under different environmental conditions. Moreover, transcript end diversity has important biological implications for the regulation of gene expression. In addition, our data also serve as a valuable resource for the scientific community.
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Registered trials
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