1. Chromosomes and Gene Expression
  2. Genetics and Genomics
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Role of the pre-initiation complex in Mediator recruitment and dynamics

  1. Elisabeth R Knoll
  2. Z Iris Zhu
  3. Debasish Sarkar
  4. David Landsman
  5. Randall H Morse  Is a corresponding author
  1. University at Albany School of Public Health, United States
  2. National Center for Biotechnology Information, National Library of Medicine, National Institute of Health, United States
  3. New York State Department of Health, United States
Research Article
  • Cited 12
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Cite this article as: eLife 2018;7:e39633 doi: 10.7554/eLife.39633

Abstract

The Mediator complex stimulates the cooperative assembly of a pre-initiation complex (PIC) and recruitment of RNA Polymerase II (Pol II) for gene activation. The core Mediator complex is organized into head, middle, and tail modules, and in budding yeast (Saccharomyces cerevisiae), Mediator recruitment has generally been ascribed to sequence-specific activators engaging the tail module triad of Med2-Med3-Med15 at upstream activating sequences (UASs). We show that yeast lacking Med2-Med3-Med15 are viable and that Mediator and PolII are recruited to promoters genome-wide in these cells, albeit at reduced levels. To test whether Mediator might alternatively be recruited via interactions with the PIC, we examined Mediator association genome-wide after depleting PIC components. We found that depletion of Taf1, Rpb3, and TBP profoundly affected Mediator association at active gene promoters, with TBP being critical for transit of Mediator from UAS to promoter, while Pol II and Taf1 stabilize Mediator association at proximal promoters.

Data availability

Data from ChIP-seq and RNA-seq experiments have been deposited at the NCBI Short Read Archive under project number PRJNA413080.

The following data sets were generated

Article and author information

Author details

  1. Elisabeth R Knoll

    Department of Biomedical Sciences, University at Albany School of Public Health, Albany, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-1083-6472
  2. Z Iris Zhu

    Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institute of Health, Bethesda, United States
    Competing interests
    The authors declare that no competing interests exist.
  3. Debasish Sarkar

    Wadsworth Center, New York State Department of Health, Albany, United States
    Competing interests
    The authors declare that no competing interests exist.
  4. David Landsman

    Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institute of Health, Bethesda, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-9819-6675
  5. Randall H Morse

    Department of Biomedical Sciences, University at Albany School of Public Health, Albany, United States
    For correspondence
    randall.morse@health.ny.gov
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-0000-8718

Funding

National Science Foundation (MCB1516839)

  • Elisabeth R Knoll
  • Debasish Sarkar
  • Randall H Morse

National Institutes of Health (Intramural program)

  • Z Iris Zhu
  • David Landsman

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

Reviewing Editor

  1. Alan G Hinnebusch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, United States

Publication history

  1. Received: June 28, 2018
  2. Accepted: December 12, 2018
  3. Accepted Manuscript published: December 12, 2018 (version 1)
  4. Version of Record published: January 7, 2019 (version 2)

Copyright

This is an open-access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication.

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Further reading

    1. Chromosomes and Gene Expression
    2. Genetics and Genomics
    Natalia Petrenko, Kevin Struhl
    Research Article Updated

    The preinitiation complex (PIC) for transcriptional initiation by RNA polymerase (Pol) II is composed of general transcription factors that are highly conserved. However, analysis of ChIP-seq datasets reveals kinetic and compositional differences in the transcriptional initiation process among eukaryotic species. In yeast, Mediator associates strongly with activator proteins bound to enhancers, but it transiently associates with promoters in a form that lacks the kinase module. In contrast, in human, mouse, and fly cells, Mediator with its kinase module stably associates with promoters, but not with activator-binding sites. This suggests that yeast and metazoans differ in the nature of the dynamic bridge of Mediator between activators and Pol II and the composition of a stable inactive PIC-like entity. As in yeast, occupancies of TATA-binding protein (TBP) and TBP-associated factors (Tafs) at mammalian promoters are not strictly correlated. This suggests that within PICs, TFIID is not a monolithic entity, and multiple forms of TBP affect initiation at different classes of genes. TFIID in flies, but not yeast and mammals, interacts strongly at regions downstream of the initiation site, consistent with the importance of downstream promoter elements in that species. Lastly, Taf7 and the mammalian-specific Med26 subunit of Mediator also interact near the Pol II pause region downstream of the PIC, but only in subsets of genes and often not together. Species-specific differences in PIC structure and function are likely to affect how activators and repressors affect transcriptional activity.

    1. Chromosomes and Gene Expression
    2. Structural Biology and Molecular Biophysics
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    Research Article Updated

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