ArticleProceedings of the National Academy of Sciences of the United States of America2013
Species-specific factors mediate extensive heterogeneity of mRNA 3' ends in yeasts.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers.
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Who cites it
39 citing papers in PubMed.
- Genetic analysis of polyadenylation patterns reveals distinct classes of yeast genes and local chromatin effects on Pol II elongation.Genetics · 2026Article
- PolyAseqTrap: a universal tool for genome-wide identification and quantification of polyadenylation sites from different 3' end sequencing data.Genome biology · 2026Article
- Location of polyadenylation sites within 3' untranslated regions is linked to biological function in yeast.Genetics · 2024Article
- Delineating yeast cleavage and polyadenylation signals using deep learning.Genome research · 2024Article
- Chromatin regulates alternative polyadenylation via the RNA polymerase II elongation rate.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- How is polyadenylation restricted to 3'-untranslated regions?Yeast (Chichester, England) · 2024Review
- Structured 3' UTRs destabilize mRNAs in plants.Genome biology · 2024Article
- Functional analysis of a random-sequence chromosome reveals a high level and the molecular nature of transcriptional noise in yeast cells.Molecular cell · 2023Article
- Condition-specific 3' mRNA isoform half-lives and stability elements in yeast.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Genome-Wide Mapping of 5' Isoforms with 5'-Seq.Current protocols · 2023Article
- Article
- 3' Untranslated Regions Are Modular Entities That Determine Polyadenylation Profiles.Molecular and cellular biology · 2022Article
- A compensatory link between cleavage/polyadenylation and mRNA turnover regulates steady-state mRNA levels in yeast.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Learning the Regulatory Code of Gene Expression.Frontiers in molecular biosciences · 2021Review
- Deep learning suggests that gene expression is encoded in all parts of a co-evolving interacting gene regulatory structure.Nature communications · 2020Article
- Article
- Additional Layer of Regulation via Convergent Gene Orientation in Yeasts.Molecular biology and evolution · 2020Article
- Probing In Vivo Structure of Individual mRNA 3' Isoforms Using Dimethyl Sulfate.Current protocols in molecular biology · 2019Article
- Extensive Structural Differences of Closely Related 3' mRNA Isoforms: Links to Pab1 Binding and mRNA Stability.Molecular cell · 2018Article
- Article
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5 authors.
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Abstract
Most eukaryotic genes express mRNAs with alternative polyadenylation sites at their 3' ends. Here we show that polyadenylated 3' termini in three yeast species (Saccharomyces cerevisiae, Kluyveromyces lactis, and Debaryomyces hansenii) are remarkably heterogeneous. Instead of a few discrete 3' ends, the average yeast gene has an "end zone," a >200 bp window with >60 distinct poly(A) sites, the most used of which represents only 20% of the mRNA molecules. The pattern of polyadenylation within this zone varies across species, with D. hansenii possessing a higher focus on a single dominant point closer to the ORF terminus. Some polyadenylation occurs within mRNA coding regions with a strong bias toward the promoter. The polyadenylation pattern is determined by a highly degenerate sequence over a broad region and by a local sequence that relies on A residues after the cleavage point. Many dominant poly(A) sites are predicted to adopt a common secondary structure that may be recognized by the cleavage/polyadenylation machinery. We suggest that the end zone reflects a region permissive for polyadenylation, within which cleavage occurs preferentially at the A-rich sequence. In S. cerevisiae strains, D. hansenii genes adopt the S. cerevisiae polyadenylation profile, indicating that the polyadenylation pattern is mediated primarily by species-specific factors.
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