GSE109235
Distinct patterns of histone acetyltransferase and Mediator deployment at yeast protein-coding genes
The transcriptional co-activators Mediator and two histone acetyltransferase (HAT) complexes, NuA4 and SAGA, play global roles in transcriptional activation. Here we explore the relative contributions of these factors to RNA polymerase II association at specific genes and gene classes by rapid nuclear depletion of key complex subunits. We show that the NuA4 HAT Esa1 differentially affects certain groups of genes, whereas the SAGA HAT Gcn5 has a weaker but more uniform effect. Relative dependence on Esa1 and Tra1, a shared component of NuA4 and SAGA, distinguishes two large groups of co-regulated growth-promoting genes. In contrast, we show that the activity of Mediator is particularly important at a separate, small set of highly transcribed TATA box-containing genes. Our analysis indicates that at least three distinct combinations of co-activator deployment are used to generate moderate or high transcription levels, and suggests that each may be associated with distinct forms of regulation. Overall design: Histone acetylation, nucleosome occupancy, RNA Polymerase II binding as well as metabolic labeled RNA was measured upon nuclear depletion of Esa1, Gcn5, Tra1 and Med17. Med8 binding was measured by ChEC-Seq upon nuclear depletion of Med17, Esa1 and Gcn5.  IMPORTANT: The S.pombe spike control normalization of the metabolic labeled RNA-Seq (4-tU RNA-Seq) data revealed to be unreliable due to the reduced number of reads uniquely assigned to the S.pombe transcriptome. Therefore, we advise against making any quantitative interpretation of the data. Furthermore, the 4-tU RNA-Seq experiment has been performed only once. For these reasons, the 4-tU RNA-Seq data are not included in the publication linked to this study. Nevertheless, we think these data could be potentially useful for the scientific community and we deposit them here to make them publicly available.