The human Mediator complex: a versatile, genome-wide regulator of transcription

Abstract

The Mediator complex interacts extensively with the RNA polymerase II enzyme and regulates its ability to express protein-coding genes. The mechanisms by which Mediator regulates gene expression remain poorly understood, in part because the structure of Mediator and even its composition can change, depending upon the promoter context. Combined with the sheer size of the human Mediator complex (26 subunits, 1.2 MDa), this structural adaptability bestows seemingly unlimited regulatory potential within the complex. Recent efforts to understand Mediator structure and function have identified expanded roles that include control of both pre- and post-initiation events; it is also evident that Mediator performs both general and gene-specific roles to regulate gene expression.

Box 1, Figure I

The transcription initiation machinery. Each PEC component is shown at a scale that approximates the relative sizes of each factor. *TFIIA can be proteolytically processed into 3 subunits; **the subunit composition of TFIID is variable.

Box 2, Figure I

MED12 and MED13 subunits

Figure 1

A universal mechanism for activated transcription? Shown are Mediator structures without an activator bound (unliganded Mediator), or bound to the activation domain of the vitamin D receptor (VDR–Mediator) or VP16 (VP16–Mediator). The pol II enzyme is shown to scale in red. Note that activator binding causes major structural re-organization within Mediator and that VDR induces a distinct structural state relative to VP16. Despite the structural differences between VDR-Mediator and VP16-Mediator, a prominent, shared feature is a large “pocket” domain (arrows) that is of sufficient size and shape to accommodate the pol II enzyme. In fact, pol II binds at this site within yeast and human Mediator [24,27]. In contrast to the activator-bound structures, the unliganded Mediator structure lacks this pocket domain. Interestingly, the VDR–Mediator and VP16–Mediator structures can each strongly activate transcription [31,79], whereas the unliganded Mediator structure does not [24], indicating that activator-dependent formation of the pol II “pocket” domain within Mediator might represent a common means by which activators activate transcription. It is currently not known why the pocket domain forms in different orientations within Mediator (e.g. pol II binds from a different face with VDR–Mediator compared with VP16–Mediator). One simple explanation is that it could enable divergent transcription (sense and anti-sense) from gene promoters [68,69].

Figure 2

Structural differences between Mediator and CDK8-Mediator. Shown are different views of the Mediator (blue) or CDK8-Mediator structures (white), and also an overlay of the structures. Each structure is bound to the activation domain of VP16. The 600 kDa CDK8 submodule comprises the “foot” domain within CDK8-Mediator [29]. Upon binding to Mediator, the CDK8 subcomplex also induces a structural shift within the head/body region (arrows). Within Mediator itself, this region corresponds to the pol II binding site (i.e. the “pocket” domain that interfaces extensively with the pol II enzyme); however, upon binding the CDK8 submodule, this site becomes occluded and pol II does not bind [29].

Figure 3

A framework for understanding how Mediator might function to regulate transcription. A) CDK8-Mediator provides a platform for multiple, functionally divergent events. Upon binding the TRRAP and GCN5L polypeptides, this assembly (provisionally called T/G-Mediator) can modify chromatin templates [33], perhaps to facilitate recruitment of additional activities such as chromatin remodeling complexes or STAGA [52], that help establish an environment favorable for transcription and PEC assembly. Note that CDK8 might also phosphorylate transcription factors (green) at this stage, which might coordinately activate the transcription factor and target it for subsequent degradation [45,47]. B) At some point prior to full PEC assembly, the CDK8 submodule (red) and perhaps other bound factors (e.g. TRRAP/GCN5L) must dissociate. Mediator can then serve as the central scaffold about which the PEC assembles. C) Further remodeling of the promoter region is required, together with assembly of the PEC (Mediator, pol II, TFIIA, TFIIB, TFIID, TFIIE, TFIIF, TFIIH). The precise mechanisms by which this occurs are not known. At this stage, pol II can exist in a number of possible functional states, including a stalled state in which pol II has engaged the promoter but has not initiated elongation [70]. D) With the appropriate signal (e.g. Mediator structural shift, post-translational modifications, etc.), pol II clears the promoter and initiates productive elongation. The remaining scaffold assembly can then recruit additional pol II complexes and re-initiate transcription. Alternatively, the CDK8 submodule could bind at this stage to block re-initiation [29]. At a later time, CDK8 might dissociate from Mediator to again allow re-activation of transcription (red arrow). At a subset of genes, the CDK8 submodule might also positively impact pol II elongation events via functional interactions with elongation factors such as P-TEFb [50]. E) If CDK8-Mediator occupancy is sustained (i.e. dissociation of the CDK8 submodule no longer occurs), activated transcription can be shut down. At this stage, dis-assembly of other PEC factors (e.g. TFIID, TFIIH) might occur and/or transcription factors might dissociate from the promoter and be degraded. The chromatin architecture at the promoter might also be altered, returning the locus to a more basal state. F) Long-term repression might be further enforced via CDK8-Mediator interactions with chromatin remodeling/modifying factors such as the G9a methyltransferase [32]. Note that many regulatory factors are not included in this scheme for clarity and also to better highlight Mediator-specific regulatory functions; this schematic also does not formally propose that each regulatory event shown occurs at every protein-coding gene.