Transcription elongation is finely tuned by dozens of regulatory factors
- Harvard Medical School, United States
Abstract
Understanding the complex network that regulates transcription elongation requires the quantitative analysis of RNA polymerase II (Pol II) activity in a wide variety of regulatory environments. We performed native elongating transcript sequencing (NET-seq) in 41 strains of S. cerevisiae lacking known elongation regulators, including RNA processing factors, transcription elongation factors, chromatin modifiers, and remodelers. We found that the opposing effects of these factors balance transcription elongation and antisense transcription. Different sets of factors tightly regulate Pol II progression across gene bodies so that Pol II density peaks at key points of RNA processing. These regulators control where Pol II pauses with each obscuring large numbers of potential pause sites that are primarily determined by DNA sequence and shape. Antisense transcription varies highly across the regulatory landscapes analyzed, but antisense transcription in itself does not affect sense transcription at the same locus. Our findings collectively show that a diverse array of factors regulate transcription elongation by precisely balancing Pol II activity.
Data availability
The accession number for the Illumina sequencing reported in this paper is Gene Expression Omnibus (GEO): GSE159603.
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Dynamics of transcription elongation are finely-tuned by dozens of regulatory factorsNCBI Gene Expression Omnibus, GSE98397.
Article and author information
Author details
L Stirling Churchman
Funding
National Institutes of Health (R01-HG007173)
- L Stirling Churchman
National Institutes of Health (F31 HG010570)
- Kate C Lachance
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Reviewing Editor
- Jerry L Workman, Stowers Institute for Medical Research, United States
Version history
- Preprint posted: August 15, 2021 (view preprint)
- Received: March 25, 2022
- Accepted: May 15, 2022
- Accepted Manuscript published: May 16, 2022 (version 1)
- Accepted Manuscript updated: May 17, 2022 (version 2)
- Version of Record published: May 31, 2022 (version 3)
Copyright
© 2022, Couvillion 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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Transcription elongation is finely tuned by dozens of regulatory factors
eLife 11:e78944.
https://doi.org/10.7554/eLife.78944
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Splicing is the stepwise molecular process by which introns are removed from pre-mRNA and exons are joined together to form mature mRNA sequences. The ordering and spatial distribution of these steps remain controversial, with opposing models suggesting splicing occurs either during or after transcription. We used single-molecule RNA FISH, expansion microscopy, and live-cell imaging to reveal the spatiotemporal distribution of nascent transcripts in mammalian cells. At super-resolution levels, we found that pre-mRNA formed clouds around the transcription site. These clouds indicate the existence of a transcription-site-proximal zone through which RNA move more slowly than in the nucleoplasm. Full-length pre-mRNA undergo continuous splicing as they move through this zone following transcription, suggesting a model in which splicing can occur post-transcriptionally but still within the proximity of the transcription site, thus seeming co-transcriptional by most assays. These results may unify conflicting reports of co-transcriptional versus post-transcriptional splicing.
