ArticleeLife2022
Nucleotide-level linkage of transcriptional elongation and polyadenylation.
Article in eLife, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
- Spt5's central KOW domains and the Pol II stalk collaborate to regulate chromatin and 3'-end processing in Saccharomyces cerevisiae.G3 (Bethesda, Md.) · 2026Article
- Genetic analysis of polyadenylation patterns reveals distinct classes of yeast genes and local chromatin effects on Pol II elongation.Genetics · 2026Article
- mRNA initiation and termination are spatially coordinated.Science (New York, N.Y.) · 2025Article
- Phenotypic screens identify SCAF1 as critical activator of RNAPII elongation and global transcription.Nucleic acids research · 2025Article
- RNA Polymerase II Activity Control of Gene Expression and Involvement in Disease.Journal of molecular biology · 2025Review
- Challenges in identifying mRNA transcript starts and ends from long-read sequencing data.Genome research · 2024Review
- 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
- Co-transcriptional gene regulation in eukaryotes and prokaryotes.Nature reviews. Molecular cell biology · 2024Review
- 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
- Genome-wide kinetic profiling of pre-mRNA 3' end cleavage.RNA (New York, N.Y.) · 2024Article
- Transcription readthrough is prevalent in healthy human tissues and associated with inherent genomic features.Communications biology · 2024Article
- mRNA initiation and termination are spatially coordinated.bioRxiv : the preprint server for biology · 2024Article
- Regulation of alternative splicing and polyadenylation in neurons.Life science alliance · 2023Review
- Let's make it clear: systematic exploration of mitochondrial DNA- and RNA-protein complexes by complexome profiling.Nucleic acids research · 2023Article
- Pre-mRNA splicing and its cotranscriptional connections.Trends in genetics : TIG · 2023Review
- 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
- Article
- The Advances in Deep Learning Modeling of Polyadenylation Codes.Wiley interdisciplinary reviews. RNAReview
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
Alternative polyadenylation yields many mRNA isoforms whose 3' termini occur disproportionately in clusters within 3' untranslated regions. Previously, we showed that profiles of poly(A) site usage are regulated by the rate of transcriptional elongation by RNA polymerase (Pol) II (Geisberg et al., 2020). Pol II derivatives with slow elongation rates confer an upstream-shifted poly(A) profile, whereas fast Pol II strains confer a downstream-shifted poly(A) profile. Within yeast isoform clusters, these shifts occur steadily from one isoform to the next across nucleotide distances. In contrast, the shift between clusters - from the last isoform of one cluster to the first isoform of the next - is much less pronounced, even over large distances. GC content in a region 13-30 nt downstream from isoform clusters correlates with their sensitivity to Pol II elongation rate. In human cells, the upstream shift caused by a slow Pol II mutant also occurs continuously at single nucleotide resolution within clusters but not between them. Pol II occupancy increases just downstream of poly(A) sites, suggesting a linkage between reduced elongation rate and cluster formation. These observations suggest that (1) Pol II elongation speed affects the nucleotide-level dwell time allowing polyadenylation to occur, (2) poly(A) site clusters are linked to the local elongation rate, and hence do not arise simply by intrinsically imprecise cleavage and polyadenylation of the RNA substrate, (3) DNA sequence elements can affect Pol II elongation and poly(A) profiles, and (4) the cleavage/polyadenylation and Pol II elongation complexes are spatially, and perhaps physically, coupled so that polyadenylation occurs rapidly upon emergence of the nascent RNA from the Pol II elongation complex.
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