Widespread and precise epigenomic reprogramming in response to heat shock

Gene expression is controlled by a variety of proteins (the epigenome) whose precise organization and mechanism of action at every promoter remains to be worked out. Here we examine a functionally diverse subset of these proteins: RSC (Rsc9), SAGA (Spt3), Hsf1, general transcription factors (GTFs), FACT (Spt16), and RNA polymerase (Pol) II, under normal and acute heat shock conditions, using the ultra-high resolution genome-wide ChIP-exo assay. Our findings indicate that canonically organized proteins reside at most genes and are rapidly reorganized upon heat shock. This includes association of SAGA with Hsf1 at upstream promoters regions, RSC movement from gene bodies to promoters, and Pol II accumulation at pre-existing melted promoter DNA. Surprisingly, most of these events are not coupled to changes in gene expression. In contrast, GTF occupancy tracks with gene expression level. Together, these findings reveal that the epigenome is reprogrammed by signaling events far beyond what is indicated by gene expression changes. Genome-wide analysis of yeast general regulatory factors by heatshock stress condition