A two-step regulatory mechanism dynamically controls histone H3 acetylation by SAGA complex at growth-related promoters

Acetylation of histone H3 at residue K9 (H3K9ac) is a dynamically regulated mark associated with transcriptionally active promoters in eukaryotes. However, our understanding of the relation-ship between H3K9ac and gene expression remains largely correlative. In this study, we identify a large suite of growth-related genes in yeast that undergo a particularly strong down-regulation of both transcription and H3K9ac upon stress, and delineate the roles of transcriptional activa-tors, repressors, SAGA histone acetyltransferase, and RNA-polymerase II in this response. We demonstrate that H3K9 acetylation states are orchestrated by a two-step mechanism driven by the dynamic binding of transcriptional repressors and activators, that is independent of tran-scription. In response to stress, promoter release of transcriptional activators at growth-related genes is a prerequisite for rapid reduction of H3K9ac, whereas binding of transcriptional re-pressors is required to establish a hypo-acetylated, strongly repressed state. Overall design: Histone H3 acetylation level and RNA Polymerase II occupancies were measured by ChIP of H3K9ac and Rbp1, respectively. The ChIP experiments were performed with the samples treated- or non-treated with rapamycin for 20 min in wild type, stb3?dot6?tod6?, CRF1 expressing strains as well and upon nuclear depletion of TBP, Sfp1 and Ifh1. Stb3 and Rpd3 occupancies were measured by ChIP in Stb3-Flag and Rpd3-Myc tagged wild type and CRF1 expressing strains following 20 min rapamycin stress.