Mediator facilitates transcription initiation at most promoters via a Tail-independent mechanism [ChEC-seq]

Mediator (MED) is a conserved factor with important roles in basal and activated transcription. Here, we investigate the genome-wide roles of yeast MED by rapid depletion of its activator-binding domain (Tail) and monitoring changes in nascent transcription. Rapid Tail depletion surprisingly reduces transcription from only a small subset of genes. At most of these Tail-dependent genes, in unperturbed conditions, MED is detected at both the UASs and promoters. In contrast, at most Tail-independent genes, we find MED primarily at promoters but not at the UASs. These results suggest that MED Tail and activator-mediated MED recruitment regulate only a small subset of genes. Further, we define three classes of genes that differ in PIC assembly pathways and the requirements for MED Tail, SAGA, TFIID and BET factors Bdf1/2. Our combined results have broad implications for the roles of MED, other coactivators, and mechanisms of transcriptional regulation at different gene classes. ChEC-seq method was used to map genome-wide binding of selected subunits of coactivator complexes. Where indicated, samples were treated with either DMSO or 3-indolacetic acid (IAA), which was used to induce degradation of selected proteins. Experiments were done in two, three or four (A,B,C,D) biological replicates.