Schizosaccharomyces pombe Hst4 Functions in DNA Damage Response by Regulating Histone H3 K56 Acetylation

Abstract

The packaging of eukaryotic DNA into chromatin is likely to be crucial for the maintenance of genomic integrity. Histone acetylation and deacetylation, which alter chromatin accessibility, have been implicated in DNA damage tolerance. Here we show that Schizosaccharomyces pombe Hst4, a homolog of histone deacetylase Sir2, participates in S-phase-specific DNA damage tolerance. Hst4 was essential for the survival of cells exposed to the genotoxic agent methyl methanesulfonate (MMS) as well as for cells lacking components of the DNA damage checkpoint pathway. It was required for the deacetylation of histone H3 core domain residue lysine 56, since a strain with a point mutation of its catalytic domain was unable to deacetylate this residue in vivo. Hst4 regulated the acetylation of H3 K56 and was itself cell cycle regulated. We also show that MMS treatment resulted in increased acetylation of histone H3 lysine 56 in wild-type cells and hst4⌬ mutants had constitutively elevated levels of histone H3 K56 acetylation. Interestingly, the level of expression of Hst4 decreased upon MMS treatment, suggesting that the cell regulates access to the site of DNA damage by changing the level of this protein. Furthermore, we find that the phenotypes of both K56Q and K56R mutants of histone H3 were similar to those of hst4⌬ mutants, suggesting that proper regulation of histone acetylation is important for DNA integrity. We propose that Hst4 is a deacetylase involved in the restoration of chromatin structure following the S phase of cell cycle and DNA damage response.DNA in eukaryotes is packaged into chromatin, and this packaging affects processes such as transcription, replication, repair, and recombination (14, 29). Compaction of DNA into chromatin reduces accessibility of DNA to various factors involved in these processes; therefore, cells have evolved different ways to counteract this inhibitory effect of chromatin (2, 45). Chromatin accessibility can be altered by posttranslational modifications of the histones, such as acetylation, ubiquitination, and phosphorylation (32, 55). These modifications are thought to alter chromatin structure, thereby regulating DNA metabolic processes. It has also been proposed that these modifications create a "histone code" that is utilized by nonhistone proteins targeting these proteins to sites of modification (49).Acetylation of histones has been linked to transcriptionally active chromatin, but recent studies have demonstrated that this modification is also important in the DNA damage response and repair pathways (26,36,45,55). In the budding yeast Saccharomyces cerevisiae, the histone acetyltransferase Esa1 acetylates the N-terminal tails of histone H4. This enzyme is also required for double-strand break repair via the nonhomologous end-joining pathway. Strikingly, the mammalian Esa1 homolog Tip60 is also required for DNA doublestrand break repair (5, 27), suggesting conservation of the mechanism. Similarly, the SAGA acetyltransferase acetylates the N-terminal tails of histone H3, and this...

Mapping genomic hotspots of DNA damage by a single-strand-DNA-compatible and strand-specific ChIP-seq method

“…Deacetylation of H3K56Ac is mediated by the sirtuin-family deacetylase Hst4. Loss of Hst4 caused growth defect and hypersensitivity to genotoxic agents (Haldar and Kamakaka 2008). To better understand the consequences of H3K56 hyperacetylation, we examined the Rad52 enrichment profile in hst4D by SPI-seq.…”

Interplay Between Histone H3 Lysine 56 Deacetylation and Chromatin Modifiers in Response to DNA Damage

“…Such ubiquitination events are believed to release new histones from Asf1, thereby increasing the availability of free histones for downstream chaperones (Han et al 2013). However, as a result of DNA damage-induced Hst3 degradation (Thaminy et al 2007;Haldar and Kamakaka 2008), K56-acetylated H3 molecules incorporated into chromatin retain their acetylation until DNA damage has been repaired (Masumoto et al 2005). In addition, several distinct mutations suppress the phenotypes of hst3D hst4D cells without modulating H3K56Ac levels, suggesting that abnormal persistence of H3K56Ac throughout the cell cycle may cause defects in processes linked to DNA replication and repair (Collins et al 2007;Celic et al 2008).…”

“…In yeast, H3K56Ac is present in virtually all newly synthesized H3 molecules deposited throughout the genome during S phase (Celic et al 2006) but is much less abundant in preexisting histones (Masumoto et al 2005). H3K56Ac is catalyzed by Rtt109 acetyltransferase in concert with the histone-binding protein Asf1 (Celic et al 2006;Schneider et al 2006;Driscoll et al 2007;Han et al 2007a, b;Tsubota et al 2007), while deacetylation of this residue depends, in a largely redundant manner, on the sirtuins Hst3 and Hst4 (Celic et al 2006;Maas et al 2006;Thaminy et al 2007;Haldar and Kamakaka 2008). Hst3 and Hst4 are absent during S phase, and as a result, H3K56Ac progressively accumulates in nascent chromatin during replication and reaches maximal levels after completion of DNA synthesis (Masumoto et al 2005;Maas et al 2006;Kaplan et al 2008).…”

Autoacetylation of the Histone Acetyltransferase Rtt109

“…Although in vitro characterization has not been possible, Hst3 and Hst4 are likely the candidate deacetylases in vivo, as yeast cells deleted of Hst3 and Hst4 genes have increased H3 Lys-56 acetylation (30,31,(53)(54)(55). Potentially, in addition to deacetylating H3 Lys-56 following S-phase, Hst3 and Hst4 may deacetylate and inactivate Rtt109, thereby lowering the overall Lys-56 acetylation levels.…”