The packaging of newly replicated and repaired DNA into chromatin is crucial for the maintenance of genomic integrity. Acetylation of histone H3 core domain lysine 56 (H3K56ac) has been shown to play a crucial role in compaction of DNA into chromatin following replication and repair in Saccharomyces cerevisiae. However, the occurrence and function of such acetylation has not been reported in mammals. Here we show that H3K56 is acetylated and that this modification is regulated in a cell cycle-dependent manner in mammalian cells. We also demonstrate that the histone acetyltransferase p300 acetylates H3K56 in vitro and in vivo, whereas hSIRT2 and hSIRT3 deacetylate H3K56ac in vivo. Further we show that following DNA damage H3K56 acetylation levels increased, and acetylated H3K56, which is localized at the sites of DNA repair. It also colocalized with other proteins involved in DNA damage signaling pathways such as phospho-ATM, CHK2, and p53. Interestingly, analysis of occurrence of H3K56 acetylation using ChIP-on-chip revealed its genome-wide spread, affecting genes involved in several pathways that are implicated in tumorigenesis such as cell cycle, DNA damage response, DNA repair, and apoptosis.

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...