Mediator facilitates transcription initiation at most promoters via a Tail-independent mechanism [RNA-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. Newly synthesized RNAs were labeled with 4-thioU, purified and analyzed with RNA-seq. Depletion of selected factors was achieved either thorugh targeted degradation (auxin-degron system) or gene deletion. For degron experiments, corresponding control and treatment sample files are labeled DMSO and 3IAA (3-indolacetic acid), respectively. Control samples for deletion experiments are indicated in the Methods section of the accompanying manuscript. All experiments were done in three replicates (A,B,C).