Nucleotide-level linkage of transcriptional elongation and polyadenylation
- Harvard Medical School, United States
- University of Colorado Anschutz Medical Campus, United States
Abstract
Alternative polyadenylation yields many mRNA isoforms whose 3' termini occur disproportionately in clusters within 3' UTRs. 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., 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 the nucleotide level within clusters, but not between them. Pol II occupancy increases just downstream of the most speed-sensitive 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.
Data availability
Sequencing data for the yeast experiment have been previously deposited in GEO (GSE151196). Sequencing for the human experiment has been deposited in GEO (GSE214095).
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Nucleotide-level linkage of transcriptional elongation and polyadenylationNCBI Gene Expression Omnibus, GSE214095.
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The transcriptional elongation rate regulates alternative polyadenylation in yeastNCBI Gene Expression Omnibus, GSE151196.
Article and author information
Author details
Funding
National Institutes of Health (GM30186)
- Kevin Struhl
National Institutes of Health (GM131801)
- Kevin Struhl
National Institutes of Health (GM118051)
- David Bentley
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Reviewing Editor
- Eric J Wagner, University of Rochester Medical Center, United States
Version history
- Preprint posted: September 5, 2022 (view preprint)
- Received: September 5, 2022
- Accepted: November 22, 2022
- Accepted Manuscript published: November 24, 2022 (version 1)
- Version of Record published: December 5, 2022 (version 2)
Copyright
© 2022, Geisberg et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
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Nucleotide-level linkage of transcriptional elongation and polyadenylation
eLife 11:e83153.
https://doi.org/10.7554/eLife.83153
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