Mediator is a common target of DNA-binding transcription factors and also interacts with various components within the macromolecular Pre-Initiation Complex (PIC, which consists of TFIIA, TFIIB, TFIID, TFIIE, TFIIF, TFIIH, Mediator itself, and pol II).  As a central integrator of both general and activator-specific regulatory signals, Mediator plays a prominent role in controlling transcription on a genome-wide scale.  Because Mediator interacts with both DNA-binding activators and the general transcription machinery (including RNA polymerase II), Mediator acts as a molecular bridge to link these factors and facilitate activator-dependent regulation.  Yet Mediator is clearly more than just a general bridging factor.  In fact, Mediator appears to tailor its response in activator-specific ways.  Analysis of Mediator using electron microscopy indicates that Mediator undergoes dramatic structural changes when it binds an activator.  These structural changes appear to play key roles in regulating Mediator function, but their precise mechanistic roles remain incompletely understood.  An equally significant observation is that when different activators (which regulate distinct subsets of genes) bind Mediator, they induce different conformational states in the complex.  These activator-specific structural states may direct gene-specific regulatory events; in other words, Mediator—a general transcription factor—appears to acquire gene-specific functions that are triggered by activator binding.  Coupled with the fact that Mediator subunit composition can change depending upon context, it is clear that Mediator has enormous regulatory potential; such versatility likely underlies the Mediator requirement for transcription genome-wide.

In addition to structural changes triggered by activator binding, Mediator undergoes substantial structural shifts upon interaction with the CDK8 module (CDK8, Cyclin C, MED12, MED13) or the pol II enzyme.  These structural changes expose different surfaces within the Mediator complex, and these surfaces may serve as docking sites for co-regulatory factors that regulate different stages of transcription (e.g. PIC assembly, pol II elongation, or mRNA processing).  A continuing focus of our lab is to define the mechanistic role of Mediator conformational changes, including how they alter Mediator interactions at the promoter or enhancer, whether they trigger new Mediator-cofactor interactions, or allow regulation of transcription elongation or mRNA processing events.

Lab publications related to Mediator structural shifts:
Knuesel, MT; Meyer, KD; Bernecky, C; Taatjes, DJ. The human CDK8 subcomplex is a molecular switch that controls Mediator co-activator function.  Genes & Dev 2009, 23: 439-451.
Ebmeier, CC; Taatjes, DJ. Activator-Mediator binding regulates Mediator-cofactor interactions. PNAS 2010, 107: 11283-11288.
Meyer, KD; Lin, S; Bernecky, C; Gao, Y; Taatjes, DJ. p53 activates transcription by directing structural shifts in Mediator. Nature SMB 2010, 17: 753-760.
Knuesel, MT; Taatjes, DJ. Mediator and post-recruitment regulation of RNA polymerase II.  Transcription 2011, 2: 28-31.
Bernecky, C; Grob, P; Ebmeier, CC; Nogales, E; Taatjes, DJ. Molecular architecture of the human Mediator-RNA polymerase II-TFIIF assembly. PLoS Biol 2011, 9: e1000603.