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

Abstract

Among acetyltransferases, the MYST family enzyme Esa1p is distinguished for its essential function and contribution to transcriptional activation and DNA double-stranded break repair. Here we report that Esa1p also plays a key role in silencing RNA polymerase II (Pol II)-transcribed genes at telomeres and within the ribosomal DNA (rDNA) of the nucleolus. These effects are mediated through Esa1p's HAT activity and correlate with changes within the nucleolus. Esa1p is enriched within the rDNA, as is the NAD-dependent protein deacetylase Sir2p, and the acetylation levels of key Esa1p histone targets are reduced in the rDNA in esa1 mutants. Although mutants of both ESA1 and SIR2 have enhanced rates of rDNA recombination, esa1 effects are more modest yet result in distinct structural changes of rDNA chromatin. Surprisingly, increased expression of ESA1 can bypass the requirement for Sir2p in rDNA silencing, suggesting that these two enzymes with seemingly opposing activities both contribute to achieve optimal nucleolar chromatin structure and function. INTRODUCTIONHistone modifications such as phosphorylation, methylation, acetylation, and deacetylation provide a mechanism by which chromatin structure is modulated to affect gene expression both positively and negatively (for reviews see Strahl and Allis, 2000;Iizuka and Smith, 2003;Kurdistani and Grunstein, 2003). The acetylation of lysine residues on histone N-terminal tails is classically linked to increases in gene expression and more directly to roles in transcriptional activation. By contrast, deacetylation of histones is most frequently correlated with transcriptionally silent chromatin. As more is learned about the enzymes catalyzing these modifications, the histone acetyltransferases (HATs) and histone deacetylases (HDACs), simple functional distinctions between acetylation and deacetylation of histones do not hold (Iizuka and Smith, 2003). For example, in several organisms, mutations in RPD3, a gene encoding a deacetylase, lead to increases in silencing rather than the expected decreases (DeRubertis et al., 1996;Rundlett et al., 1996). This brings forward the possibility that histone acetylation may play an important part in both silent and active chromatin. In addition, coactivator proteins, such as the histone acetyltransferases p300 and CBP and nuclear hormone receptors, appear to have roles in transcriptional repression through acetylation and association with particular binding partners (for examples, see Chen and Li, 1998;Waltzer and Bienz, 1998;Baluchamy et al., 2003;Girdwood et al., 2003;Rajabi et al., 2005). Thus, understanding of multiple roles for acetylation in controlling gene expression is expanding.In Saccharomyces cerevisiae, there are three regions of the genome controlled by chromatin-mediated transcriptional silencing: telomeres, the silent mating-type loci HMR and HML, and the rDNA array. Many factors are important for transcriptional silencing at subsets of these loci including the four core histones, the repressor activator protein Rap1...

Collaboration Between the Essential Esa1 Acetyltransferase and the Rpd3 Deacetylase Is Mediated by H4K12 Histone Acetylation in Saccharomyces cerevisiae

“…In a study directly examining Esa1's functions in rDNA silencing, a surprising relationship was discovered between Esa1 and the class III HDAC Sir2 (Clarke et al 2006). When either ESA1 or SIR2 is overexpressed, each suppresses the rDNA silencing defects of the other mutant.…”

“…In a somewhat opposing role, Esa1 is required for transcriptional silencing at the telomeres and the rDNA. Specifically, Pol II reporter genes that are normally repressed when inserted at the telomeres and the rDNA display increased expression in esa1 mutants (Clarke et al 2006).…”

The glucanosyltransferase Gas1 functions in transcriptional silencing

“…GAS1 also exhibited a growth defect with deletion of EAF1 or a conditional allele of ESA1 (15), which both encode subunits of the nucleosomal acetylation of H4 (NuA4) complex (reviewed in ref. 16) that functions in silencing at the telomeres and rDNA (17). The basis for these interactions has not been pursued, but they suggest that GAS1 and ORC2, ESA1, and EAF1 may contribute to parallel processes that are critical for cellular function and viability.…”

Differential Requirement of DNA Replication Factors for Subtelomeric ARS Consensus Sequence Protosilencers in Saccharomyces cerevisiae

“…Hence, silencing of the telomeres is mediated by similar, but not identical mechanisms to these employed at the mating loci. The growing list of factors engaged in silencing also includes the histone acetyl transferase NuA4 (Babiarz et al 2006;Clarke et al 2006), the histone chaperone CAF-1 (Tamburini et al 2006), cohesin (Suter et al 2004;Chang et al 2005), SUM1 (Irlbacher et al 2005), and SCP160 (Marsellach et al 2006).…”