Role of the pre-initiation complex in Mediator recruitment and dynamics

Abstract
Data availability
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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

1. Knoll ER
2. Zhu ZI
3. Sarkar D
4. Landsman D
5. Morse RH
(2018) Data from ChIP-seq and RNA-seq experiments
Short Read Archive, PRJNA413080.

https://www.ncbi.nlm.nih.gov/bioproject/PRJNA413080/

Article and author information

Author details

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.

"This ORCID iD identifies the author of this article:" 0000-0002-1083-6472
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.
Debasish Sarkar

Wadsworth Center, New York State Department of Health, Albany, United States

Competing interests
The authors declare that no competing interests exist.
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.

"This ORCID iD identifies the author of this article:" 0000-0002-9819-6675
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.

"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.

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.