Requirements for RNA polymerase II preinitiation complex formation in vivo

  1. Natalia Petrenko
  2. Yi Jin
  3. Liguo Dong
  4. Koon Ho Wong  Is a corresponding author
  5. Kevin Struhl  Is a corresponding author
  1. Harvard Medical School, United States
  2. University of Macau, Macau

Abstract

Transcription by RNA polymerase II requires assembly of a preinitiation complex (PIC) composed of general transcription factors (GTFs) bound at the promoter. In vitro, some GTFs are essential for transcription, whereas others are not required under certain conditions. PICs are stable in the absence of nucleotide triphosphates, and subsets of GTFs can form partial PICs. By depleting individual GTFs in yeast cells, we show that all GTFs are essential for TBP binding and transcription, suggesting that partial PICs do not exist at appreciable levels in vivo. Depletion of FACT, a histone chaperone that travels with elongating Pol II, strongly reduces PIC formation and transcription. In contrast, TBP-associated factors (TAFs) contribute to transcription of most genes, but TAF-independent transcription occurs at substantial levels, preferentially at promoters containing TATA elements. PICs are absent in cells deprived of uracil, and presumably UTP, suggesting that transcriptionally inactive PICs are removed from promoters in vivo.

Data availability

Sequencing data has been deposited in GEO under the accession number GSE122734

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

Article and author information

Author details

  1. Natalia Petrenko

    Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, United States
    Competing interests
    No competing interests declared.
  2. Yi Jin

    Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, United States
    Competing interests
    No competing interests declared.
  3. Liguo Dong

    Faculty of Health Sciences, University of Macau, Macau, Macau
    Competing interests
    No competing interests declared.
  4. Koon Ho Wong

    Faculty of Health Sciences, University of Macau, Macau, Macau
    For correspondence
    KoonHoWong@umac.mo
    Competing interests
    No competing interests declared.
  5. Kevin Struhl

    Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, United States
    For correspondence
    kevin@hms.harvard.edu
    Competing interests
    Kevin Struhl, Senior editor, eLife.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-4181-7856

Funding

National Institutes of Health (GM 30186)

  • Natalia Petrenko
  • Yi Jin
  • Koon Ho Wong
  • Kevin Struhl

Universidade de Macau (MYRG2015-00186 FHS)

  • Liguo Dong
  • Koon Ho Wong

Croucher Foundation

  • Koon Ho Wong

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Reviewing Editor

  1. Michael R Green, Howard Hughes Medical Institute, University of Massachusetts Medical School, United States

Publication history

  1. Received: November 14, 2018
  2. Accepted: January 25, 2019
  3. Accepted Manuscript published: January 25, 2019 (version 1)
  4. Version of Record published: February 7, 2019 (version 2)

Copyright

© 2019, Petrenko 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. Natalia Petrenko
  2. Yi Jin
  3. Liguo Dong
  4. Koon Ho Wong
  5. Kevin Struhl
(2019)
Requirements for RNA polymerase II preinitiation complex formation in vivo
eLife 8:e43654.
https://doi.org/10.7554/eLife.43654

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