Trends in Cell Biology
Volume 27, Issue 10, October 2017, Pages 765-783
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Review
The Mediator Complex: At the Nexus of RNA Polymerase II Transcription

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Trends

Mediator is implicated in most aspects of gene expression, including nearly all steps of the transcription reaction, in addition to mRNA processing, higher-order chromatin organization, and genome stability.

The dynamic composition and structure of Mediator have recently begun to be elucidated through both structural work and in vivo protein–DNA interaction mapping.

The Kinase module has both positive and negative roles in gene expression regulation.

Mediator is an essential, large, multisubunit, transcriptional co-activator highly conserved across eukaryotes. Mediator interacts with gene-specific transcription factors at enhancers as well as with the RNA polymerase II (RNAPII) transcription machinery bound at promoters. It also interacts with several other factors involved in various aspects of transcription, chromatin regulation, and mRNA processing. Hence, Mediator is at the nexus of RNAPII transcription, regulating its many steps and connecting transcription with co-transcriptional events. To achieve this flexible role, Mediator, which is divided into several functional modules, reorganizes its conformation and composition while making transient contacts with other components. Here, we review the mechanisms of action of Mediator and propose a unifying model for its function.

Section snippets

Mediator: A Universal Eukaryotic Coactivator

Originally purified from budding yeast as a large multisubunit complex mediating activated transcription by DNA-binding transcription factors (TFs), Mediator is now implicated in nearly all aspects of gene transcription across eukaryotes 1, 2, 3, 4, 5. Mediator also regulates chromatin looping [4] and higher-order chromatin folding [6] (Box 1) as well as mRNA processing [7] and export [8], and transcriptional memory [9] and re-initiation [10]. In addition, Mediator has roles beyond gene

Mediator Redefined: Down to the Essentials

Early electron microscopy (EM) studies suggested that Mediator had a Head and Tail interconnected by a Middle module [24]. However, two recent EM analyses redefined the organization of the Mediator modules 20, 25. In this revised structure, the Head and Middle modules are tightly bound together, with the Tail sitting at the base of the complex (Figure 1A and Box 3). Previous studies provided the subunit organization and structure of the free Kinase module, which comprises the Cdk8-CycC pair,

Bridging Enhancers to Promoters: The Kinase Module Has to Go

In metazoans, chromatin immunoprecipitation followed by sequencing (ChIP-seq) studies revealed that Mediator occupies active enhancers and superenhancers genome-wide 35, 36. In yeast, where the mechanism of Mediator function has been most studied, the genomic location of Mediator has been a matter of debate, mainly due to high gene density in the yeast genome and inherent background generated in most ChIP protocols. The use of high-resolution ChIP followed by DNA microarrays (ChIP-chip) or

Targeting Mediator to Chromatin: The Tail’s Business, with a Little Help from Its Friends

In yeast, deletion of a combination of Tail subunits abrogates Mediator binding to UAS regions genome-wide 29, 33, consistent with UAS-bound TFs recruiting Mediator via contact with subunits in the Tail module. In metazoans, several DNA-binding TFs contact Mediator via subunits located in other modules 1, 2, 56. Notably, the Middle subunit Med1 is an important target for nuclear receptors in mammalian cells 57, 58, 59. Since Med1 is adjacent to the Tail within Mediator 20, 21, it is perhaps not

A Role in Preinitiation, Initiation, and Promoter Clearance: The Ancient Function of Mediator

Perhaps the best-described function of Mediator is to stabilize the PIC formed by RNAPII and the GTFs at core promoters. Recent structural and chemical crosslinking studies revealed that Mediator makes several contacts with components of the PIC, including RNAPII, TFIIB, TFIIE, TFIIF, TFIIH, and TFIIS 19, 21, 22, 31. Several mutations within the yeast Mediator Middle and Head subunits have been recently characterized to better understand how Mediator coordinates PIC assembly in vivo 70, 71.

Role in Promoter-Proximal Pausing: A Recently Acquired Function of Mediator

In metazoans, RNAPII often pauses 30–60 nucleotides after the initiation site. This pause is induced by DSIF (Spt4 and Spt5) and NELF, and released upon the phosphorylation of these two factors by P-TEFb, a CDK9-containing positive transcription elongation factor (reviewed in 79, 80, 81). At many genes, pause release is the rate-limiting step and gene expression is regulated by the recruitment of pause-release factors, such as P-TEFb or the P-TEFb-containing super elongation complex (SEC).

A Unifying Model of Mediator Function

Mediator interacts with an array of factors, from TFs and PIC components, to elongation factors, such as SEC. The compositional and conformational dynamics of Mediator, as well as the dynamics and regulation of its interacting partners, constrain these interactions. These constraints allow us to propose a dynamic model for the sequential functions of Mediator in the transcription cycle. For instance, the Mediator–RNAPII interaction is disrupted by CTD phosphorylation, suggesting that Mediator

Concluding Remarks

In recent years, detailed analyses of Mediator occupancy and function in yeast cells, as well as the solving of several structures of Mediator-containing complexes, have led to a better understanding of its role in transcription initiation. Work in higher eukaryotes has highlighted additional roles for Mediator in postinitiation events, while the number of Mediator subunit mutations and misexpression in human diseases has grown exponentially. In coming years, efforts should be made to integrate

Acknowledgments

We apologize to those authors whose important work could not be cited owing to space restrictions. We are grateful to Nicole Francis for commenting on the manuscript. Work in our laboratory on Mediator is supported by a grant from the Canadian Institutes of Health Research (MOP-133648).

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