Abstract

Transcription by RNA Polymerase II (Pol II) is initiated by the hierarchical assembly of the Pre-Initiation Complex onto promoter DNA. Decades of research have shown that the TATA-box binding protein (TBP) is essential for Pol II loading and initiation. Here, we report instead that acute depletion of TBP in mouse embryonic stem cells has no global effect on ongoing Pol II transcription. In contrast, acute TBP depletion severely impairs RNA Polymerase III initiation. Furthermore, Pol II transcriptional induction occurs normally upon TBP depletion. This TBP-independent transcription mechanism is not due to a functional redundancy with the TBP paralog TRF2, though TRF2 also binds to promoters of transcribed genes. Rather, we show that the TFIID complex can form and, despite having reduced TAF4 and TFIIA binding when TBP is depleted, the Pol II machinery is sufficiently robust in sustaining TBP-independent transcription.

Data availability

All sequencing data have been deposited in Gene Expression Omnibus (Accession number GSE172401). All mass spectrometry data have been deposited to ProteomeExchange (PXD034171) through MassIVE (MSV000089562). All other data are available in the manuscript or in the supplementary materials.

The following data sets were generated

Article and author information

Author details

  1. James ZJ Kwan

    Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, Canada
    Competing interests
    The authors declare that no competing interests exist.
  2. Thomas F Nguyen

    Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, Canada
    Competing interests
    The authors declare that no competing interests exist.
  3. Anuli C Uzozie

    Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
    Competing interests
    The authors declare that no competing interests exist.
  4. Marek A Budzynski

    Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, Canada
    Competing interests
    The authors declare that no competing interests exist.
  5. Jieying Cui

    Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, Canada
    Competing interests
    The authors declare that no competing interests exist.
  6. Joseph MC Lee

    Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, Canada
    Competing interests
    The authors declare that no competing interests exist.
  7. Filip Van Petegem

    Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, Canada
    Competing interests
    The authors declare that no competing interests exist.
  8. Philipp F Lange

    Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, Canada
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-1171-5864
  9. Sheila S Teves

    Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, Canada
    For correspondence
    sheila.teves@ubc.ca
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-1220-2414

Funding

Canadian Institutes of Health Research (PJT-162289)

  • Filip Van Petegem

Natural Sciences and Engineering Research Council of Canada (RGPIN-2020-06106)

  • Sheila S Teves

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

Reviewing Editor

  1. Irwin Davidson, Institut de Génétique et de Biologie Moléculaire et Cellulaire, France

Version history

  1. Preprint posted: March 29, 2021 (view preprint)
  2. Received: September 29, 2022
  3. Accepted: March 29, 2023
  4. Accepted Manuscript published: March 30, 2023 (version 1)
  5. Version of Record published: May 11, 2023 (version 2)

Copyright

© 2023, Kwan 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. James ZJ Kwan
  2. Thomas F Nguyen
  3. Anuli C Uzozie
  4. Marek A Budzynski
  5. Jieying Cui
  6. Joseph MC Lee
  7. Filip Van Petegem
  8. Philipp F Lange
  9. Sheila S Teves
(2023)
RNA Polymerase II transcription independent of TBP
eLife 12:e83810.
https://doi.org/10.7554/eLife.83810

Share this article

https://doi.org/10.7554/eLife.83810

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