Histone Deacetylases RPD3 and HOS2 Regulate the Transcriptional Activation of DNA Damage-Inducible Genes

Abstract

DNA microarray and genetic studies of Saccharomyces cerevisiae have demonstrated that histone deacetylases (HDACs) are required for transcriptional activation and repression, but the mechanism by which they activate transcription remains poorly understood. We show that two HDACs, RPD3 and HOS2, are required for the activation of DNA damage-inducible genes RNR3 and HUG1. Using mutants specific for the Rpd3L complex, we show that the complex is responsible for regulating RNR3. Furthermore, unlike what was described for the GAL genes, Rpd3L regulates the activation of RNR3 by deacetylating nucleosomes at the promoter, not at the open reading frame. Rpd3 is recruited to the upstream repression sequence of RNR3, which surprisingly does not require Tup1 or Crt1. Chromatin remodeling and TFIID recruitment are largely unaffected in the ⌬rpd3/⌬hos2 mutant, but the recruitment of RNA polymerase II is strongly reduced, arguing that Rpd3 and Hos2 regulate later stages in the assembly of the preinitiation complex or facilitate multiple rounds of polymerase recruitment. Furthermore, the histone H4 acetyltransferase Esa1 is required for the activation of RNR3 and HUG1. Thus, reduced or unregulated constitutive histone H4 acetylation is detrimental to promoter activity, suggesting that HDAC-dependent mechanisms are in place to reset promoters to allow high levels of transcription.Although the correlation between histone modifications and gene expression was established many years ago (2), the underlying mechanism by which they affect transcription is still largely unknown. Histone acetyltransferases (HATs) and histone deacetylases (HDACs) function in an antagonistic manner to regulate the balance of histone acetylation and gene activity (25,37,42). It is widely accepted that histone acetylation by HAT correlates with gene expression, while histone deacetylation by HDACs is associated with gene repression (25,37,42).Histone deacetylases catalyze the removal of acetyl groups from the amino-terminal tails of the core histones, making chromatin inaccessible to the transcriptional machinery (11,25,42). Two families of HDACs are found in yeast (Saccharomyces cerevisiae), and each family is classified based upon sequence homology among its members. Five HDACs, namely Hda1, Rpd3, Hos1, Hos2, and Hos3, belong to one family, and the other includes Sir2 and Hst1 to Hst4 (25). Two mechanisms have been proposed for how HDACs regulate transcription: targeted and nontargeted. The targeting mechanism involves the direct recruitment of HDACs to promoters by DNA binding proteins or corepressors, such as Ume6 or Tup1, respectively (21,22,23,36,38,46,47). This mechanism results in targeted deacetylation, spanning approximately two nucleosomes over the DNA binding site (22,38,47). The second mechanism is poorly understood and results in untargeted, genome-wide histone deacetylation (26,44,47), including deacetylation within coding regions. The mechanism of targeted versus global deacetylation was illuminated partly by the discovery of two Rpd3-cont...

Toggle involving cis -interfering noncoding RNAs controls variegated gene expression in yeast

“…This paradox is unresolved in the literature. At some gene targets, Rpd3L displays the net repressive effect on transcription expected of an HDAC (36)(37)(38), but at others, it has an unexpected net activating effect on transcription (39)(40)(41)(42). In this report, we demonstrate that Rpd3L activates FLO11 transcription via its repressive effects on one of the cis-acting ncRNAs that itself negatively regulates FLO11 transcription.…”

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

“…One role is to participate in the transcriptional response through the activation of DNA repair genes. For example, Esa1 and Rpd3 are both required for transcriptional activation of the damage-inducible genes HUG1 and RNR3 (Sharma et al 2007). The identification of these as shared targets for activation raises a useful distinction because rpd3 cannot suppress esa1's sensitivity to DNA damage.…”

“…In contrast, there are several transcripts that require Rpd3 for their activation (de Nadal et al 2004;Sertil et al 2007). For example, Rpd3 is required for expression of the DNA damage inducible genes HUG1 and RNR3 (Sharma et al 2007). In line with Rpd3 having a role in DNA repair, rpd3 mutants are defective in nonhomologous end joining ( Jazayeri et al 2004).…”

Chromatin Modulation at the FLO11 Promoter of Saccharomyces cerevisiae by HDAC and Swi/Snf Complexes

“…Pho23, but not HDACs Rpd3 and Hos2, has a clear role in generating a nucleosome-depleted FLO11 promoter region Rpd3 mainly deacetylates histones H4 and H3 (Kurdistani and Grunstein 2003a), acting redundantly with Hos2 in the case of histone H4 (Sharma et al 2007). If Hos2 and Rpd3 are the catalytic subunits of the complexes involved in FLO11 activation, we would expect to see changes in histone acetylation at the FLO11 promoter in single or double mutants for these catalytic subunits, as well as in pho23D mutants.…”

“…However, both deacetylases have been shown to act redundantly to positively regulate the expression of DNA damage-inducible genes (Sharma et al 2007). Here we have observed a strong reduction of FLO11 expression in the 133d strain when both RPD3 and HOS2 were deleted.…”