ArticleGenome research2013
DNA damage induces targeted, genome-wide variation of poly(A) sites in budding yeast.
Article in Genome research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.
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Who cites it
36 citing papers in PubMed.
- Comprehensive mapping of the 5' and 3' untranslated regions ofRNA (New York, N.Y.) · 2026Article
- The yeast checkpoint kinase Mec1p functions in transcription termination by facilitating recruitment of Pcf11p and regulating the torpedo exonuclease Rat1p.Scientific reports · 2025Article
- Review
- Delineating yeast cleavage and polyadenylation signals using deep learning.Genome research · 2024Article
- Article
- Members of the CUGBP Elav-like family of RNA-binding proteins are expressed in distinct populations of primary sensory neurons.The Journal of comparative neurology · 2023Article
- Hydroxyurea and inactivation of checkpoint kinase MEC1 inhibit transcription termination and pre-mRNA cleavage at polyadenylation sites in budding yeast.Scientific reports · 2023Article
- Artifacts and biases of the reverse transcription reaction in RNA sequencing.RNA (New York, N.Y.) · 2023Review
- RNA polymerase II transcription attenuation at the yeast DNA repair gene DEF1 is biologically significant and dependent on the Hrp1 RNA-recognition motif.G3 (Bethesda, Md.) · 2023Article
- Macrophage differentiation is marked by increased abundance of the mRNA 3' end processing machinery, altered poly(A) site usage, and sensitivity to the level of CstF64.Frontiers in immunology · 2023Article
- Internal oligo(dT) priming introduces systematic bias in bulk and single-cell RNA sequencing count data.NAR genomics and bioinformatics · 2022Article
- Divergence in the Regulation of the Salt Tolerant Response BetweenFrontiers in plant science · 2022Article
- The Bidirectional Link Between RNA Cleavage and Polyadenylation and Genome Stability: Recent Insights From a Systematic Screen.Frontiers in genetics · 2022Review
- DEF1: Much more than an RNA polymerase degradation factor.DNA repair · 2021Review
- RNA-biology ruling cancer progression? Focus on 3'UTRs and splicing.Cancer metastasis reviews · 2020Review
- Article
- Regulation of alternative polyadenylation in the yeast Saccharomyces cerevisiae by histone H3K4 and H3K36 methyltransferases.Nucleic acids research · 2020Article
- Regulation of the Ysh1 endonuclease of the mRNA cleavage/polyadenylation complex by ubiquitin-mediated degradation.RNA biology · 2020Article
- Connections between 3' end processing and DNA damage response: Ten years later.Wiley interdisciplinary reviews. RNA · 2020Review
- Alternative Polyadenylation of Mammalian Transcripts Is Generally Deleterious, Not Adaptive.Cell systems · 2018Article
Corrections and comments
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Authors and funding
7 authors.
Funding
Abstract
Systemic response to DNA damage and other stresses is a complex process that includes changes in the regulation and activity of nearly all stages of gene expression. One gene regulatory mechanism used by eukaryotes is selection among alternative transcript isoforms that differ in polyadenylation [poly(A)] sites, resulting in changes either to the coding sequence or to portions of the 3' UTR that govern translation, stability, and localization. To determine the extent to which this means of regulation is used in response to DNA damage, we conducted a global analysis of poly(A) site usage in Saccharomyces cerevisiae after exposure to the UV mimetic, 4-nitroquinoline 1-oxide (4NQO). Two thousand thirty-one genes were found to have significant variation in poly(A) site distributions following 4NQO treatment, with a strong bias toward loss of short transcripts, including many with poly(A) sites located within the protein coding sequence (CDS). We further explored one possible mechanism that could contribute to the widespread differences in mRNA isoforms. The change in poly(A) site profile was associated with an inhibition of cleavage and polyadenylation in cell extract and a decrease in the levels of several key subunits in the mRNA 3'-end processing complex. Sequence analysis identified differences in the cis-acting elements that flank putatively suppressed and enhanced poly(A) sites, suggesting a mechanism that could discriminate between variable and constitutive poly(A) sites. Our analysis indicates that variation in mRNA length is an important part of the regulatory response to DNA damage.
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