Global histone acetylation and deacetylation in yeast

Abstract

Histone acetyltransferases and deacetylases can be targeted to promoters to activate or repress genes. For example, the histone acetyltransferase GCN5 is part of a yeast multiprotein complex that is recruited by the DNA-binding activator protein GCN4 (refs 1-3). The histone deacetylase RPD3 complex is recruited to DNA by the repressor UME6 (refs 4, 5); similar mechanisms exist in other eukaryotes. However, deletion of RPD3 also increases expression of the PHO5 gene that is repressed by nucleosomes, and regulated by GCN5 (ref. 10) but not by UME6. We have determined whether acetylation and deacetylation are promoter specific at PHO5, by using antibodies against acetylated lysine residues and chromatin immunoprecipitation to examine the acetylation state of a 4.25-kilobase region surrounding the PHO5 gene. Here we show that this region is acetylated extensively by ESA1 and GCN5 and deacetylated by HDA1 and RPD3, and that widespread histone modification affects three separate chromosomal regions examined, which total 22kb. Our data indicate that targeted modification occurs in a background of global acetylation and deacetylation that not only reduces basal transcription, but also allows a rapid return to the initial state of acetylation when targeting is removed.

Distinct Roles for the Essential MYST Family HAT Esa1p in Transcriptional Silencing

“…By both chromatin immunoprecipitation and fluorescence localization studies, Esa1p has been defined for its general nuclear roles and distribution (Galarneau et al, 2000;Reid et al, 2000;Vogelauer et al, 2000;Huh et al, 2003). Viewed collectively, the previously observed defects in nucleolar structure , in addition to the rDNA silencing, recombination and PFGE analyses reported here all suggested that ESA1 also contributes to normal nucleolar structure and function.…”

“…Biochemical studies demonstrate that Esa1p is the catalytic subunit of the NuA4 complex that includes other essential subunits such as Tra1p and Act3p and other key subunits with connections to growth control and epigenetic elements of transcriptional activation (Allard et al, 1999;Galarneau et al, 2000). Indeed, a number of distinct transcriptional targets have been identified for Esa1p, along with genome-wide validation of its role as a global H4 HAT (Galarneau et al, 2000;Reid et al, 2000;Vogelauer et al, 2000;Nourani et al, 2001). More extensive expression analysis suggests nearly equal numbers of positively and negatively affected transcriptional targets for Esa1p (Mnaimneh et al, 2004).…”

“…Because Esa1p regulates global levels of acetylation in yeast and these modifications are not restricted to promoterproximal regions Vogelauer et al, 2000), we considered that Esa1p may have additional roles in genomic regulation. We found that Esa1p contributes to locus-specific transcriptional silencing and appears to have a prominent role within the rDNA of the nucleolus.…”

“…Tip60 has been linked to DNA repair (Ikura et al, 2000) and a role for Esa1p and the Yng2p NuA4 subunit was found in replication-coupled DNA double-stranded break repair (Bird et al, 2002;Choy and Kron, 2002). Indeed, several subunits of NuA4 are shared with the Swr1 chromatin remodeling complex and are linked at additional levels to chromosomal stability (Kobor et al, 2004;Krogan et al, 2004;Mizuguchi et al, 2004).Because Esa1p regulates global levels of acetylation in yeast and these modifications are not restricted to promoterproximal regions Vogelauer et al, 2000), we considered that Esa1p may have additional roles in genomic regulation. We found that Esa1p contributes to locus-specific transcriptional silencing and appears to have a prominent role within the rDNA of the nucleolus.…”

“…In previous ChIP experiments to evaluate promoter occupancy, Esa1p was found at many ribosomal protein gene promoters (Reid et al, 2000). It is also known that ESA1 influences total levels of H4 acetylation and that much of this global acetylation is not restricted to promoter regions (Vogelauer et al, 2000). We performed ChIP experiments using a fully functional Esa1-HA epitope-tagged strain and compared recovery of rDNA sequences to a control untagged strain (Figure 3, A and B).…”