Transcription elongation is finely tuned by dozens of regulatory factors

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.

The following data sets were generated
The following previously published data sets were used

Article and author information

Author details

  1. Mary Couvillion

    Department of Genetics, Harvard Medical School, Boston, United States
    Competing interests
    No competing interests declared.
  2. Kevin M Harlen

    Department of Genetics, Harvard Medical School, Boston, United States
    Competing interests
    No competing interests declared.
  3. Kate C Lachance

    Department of Genetics, Harvard Medical School, Boston, United States
    Competing interests
    No competing interests declared.
  4. Kristine L Trotta

    Department of Genetics, Harvard Medical School, Boston, United States
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-8166-7696
  5. Erin Smith

    Department of Genetics, Harvard Medical School, Boston, United States
    Competing interests
    No competing interests declared.
  6. Christian Brion

    Department of Genetics, Harvard Medical School, Boston, United States
    Competing interests
    No competing interests declared.
  7. Brendan M Smalec

    Department of Genetics, Harvard Medical School, Boston, United States
    Competing interests
    No competing interests declared.
  8. L Stirling Churchman

    Department of Genetics, Harvard Medical School, Boston, United States
    For correspondence
    churchman@genetics.med.harvard.edu
    Competing interests
    L Stirling Churchman, Reviewing editor, eLife.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-3888-2574

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

  1. Jerry L Workman, Stowers Institute for Medical Research, United States

Publication history

  1. Preprint posted: August 15, 2021 (view preprint)
  2. Received: March 25, 2022
  3. Accepted: May 15, 2022
  4. Accepted Manuscript published: May 16, 2022 (version 1)
  5. Accepted Manuscript updated: May 17, 2022 (version 2)
  6. 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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  1. Mary Couvillion
  2. Kevin M Harlen
  3. Kate C Lachance
  4. Kristine L Trotta
  5. Erin Smith
  6. Christian Brion
  7. Brendan M Smalec
  8. L Stirling Churchman
(2022)
Transcription elongation is finely tuned by dozens of regulatory factors
eLife 11:e78944.
https://doi.org/10.7554/eLife.78944

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