This schematic illustrates that as the structure of Mediator changes, its ability to interact with other regulatory proteins may also change. Such structural transitions could enable the same Mediator complex to adopt distinct functions at the appropriate stages of transcription (for example, initiation vs. elongation). Also, the model allows for some cofactors to bind Mediator in several different structural states. a) Upon binding a transcription factor (TF), Mediator undergoes structural changes that facilitate interactions with additional transcription regulators. Structural changes associated with TF-Mediator binding also appear to promote stable association with pol II, and correlate with activation of transcription. b) Binding of pol II triggers distinct structural changes throughout Mediator^,; these might be important for functional interactions between Mediator and factors that promote pol II initiation and/or elongation, such as TFIIS, TFIIF, or POLR2M^,,,. c) CDK8 module–Mediator binding also induces structural changes in Mediator that prevent pol II binding^,; further, CDK8-Mediator associates with elongation factors such as the SEC^,, which may regulate the timing of SEC recruitment at some genes.

a) Mediator plays key roles in the assembly of the Pre-initiation Complex (PIC). Mediator helps recruit pol II and other PIC factors to the promoter. At this stage, the pol II CTD is not highly phosphorylated. During transcription initiation, the pol II CTD becomes highly phosphorylated by TFIIH, and the pol II enzyme begins to transcribe the gene. At some genes, pol II may pause after transcribing about 60 nucleotides; whether this “paused pol II” remains associated with Mediator is not known. b) The CDK8 module may associate with Mediator after pol II-Mediator contacts are broken, and this may regulate pol II elongation or release from a paused state at some genes. CDK8-Mediator may regulate the recruitment or activity of the super elongation complex (SEC) to promote pol II pause release and elongation^,. c) Because CDK8-Mediator cannot interact with pol II, re-initiation of transcription requires release of the CDK8 module. A scaffold PIC complex, which may be stabilized by a transcription factor, could facilitate rapid re-initiation.

The cooperative interactions between Mediator and transcription factors (TF), cohesin and non-coding RNAs (ncRNA) appear to stabilize enhancer-promoter loops^,,,. An expanding set of factors influence the formation and stability of enhancer-promoter loops and the formation of such structures correlates with high levels of transcription^-. Because the CDK8 module must dissociate from Mediator to allow pol II–Mediator binding^,, a potential ncRNA–CDK8 module interaction, perhaps via the CDK8 module subunit MED12, may tether the CDK8 module near the PIC. This could facilitate re-formation of CDK8-Mediator complexes following pol II promoter escape.

Four representative, simplified signaling pathways are shown. Each pathway is activated by different signals; for instance, p53 signaling is activated during cell stress, toll like receptors (TLR) are activated in response to infection, and the sterol regulatory element binding protein (SREBP) is activated in response to metabolic cues. Each pathway converges on a distinct transcription factor that targets a different Mediator subunit, helping to recruit and regulate Mediator activity at select genomic loci. The end result is transcription factor-dependent activation (or repression) of a specific set of genes that are important for the response to the stimulus. Due to Mediator's role in relaying and integrating these signals directly to the transcription machinery (including the pol II enzyme itself), Mediator can be considered an endpoint of signaling cascades.