Saccharomyces cerevisiae Sin3p facilitates DNA double-strand break repair

Abstract

There are two main pathways in eukaryotic cells for the repair of DNA double-strand breaks: homologous recombination and nonhomologous end joining. Because eukaryotic genomes are packaged in chromatin, these pathways are likely to require the modulation of chromatin structure. One way to achieve this is by the acetylation of lysine residues on the N-terminal tails of histones. Here we demonstrate that Sin3p and Rpd3p, components of one of the predominant histone deacetylase complexes of Saccharomyces cerevisiae, are required for efficient nonhomologous end joining. We also show that lysine 16 of histone H4 becomes deacetylated in the proximity of a chromosomal DNA doublestrand break in a Sin3p-dependent manner. Taken together, these results define a role for the Sin3p͞Rpd3p complex in the modulation of DNA repair.I n eukaryotic cells, the genome is compacted into chromatin.The basic unit of chromatin is the nucleosome, which is composed of the conserved core histones H2A, H2B, H3, and H4. The structure of nucleosomal DNA is further compacted by a range of other factors, including proteins such as the linker histone H1 that binds to DNA between the nucleosome repeats (1). Various DNA-templated processes such as transcription, replication, and DNA repair take place in the context of chromatin and so must involve the manipulation of nucleosomes. One way to achieve this is through the reversible acetylation, phosphorylation, ubiquitination, or ADP-ribosylation of the histone tails that extend to the accessible surface of the nucleosome core particle (2). It has been proposed that combinations of these modifications create a ''histone code'' that is recognized by other proteins to bring about specific downstream events (3).The most extensive body of data has been accumulated for the effect of nucleosome modifications in transcription (4). However, there is growing evidence that there is cross-talk between chromatin and DNA damage response and repair pathways. This is particularly well established for nucleotide excision repair (NER), in which several chromatin remodeling and modification factors have been implicated (ref. 5 and references therein). As discussed further below, there is also evidence for the importance of chromatin modification in the repair of DNA doublestrand breaks (DSBs), which are generated by ionizing radiation and a range of chemotherapeutic agents. Given the highly recombinogenic and cytotoxic nature of such lesions (6, 7), the impact of chromatin on DSB repair is likely to be of considerable biological importance.There are two principle mechanisms for the repair of DNA DSBs: homologous recombination (HR) and nonhomologous end joining (NHEJ). The former requires genes in the RAD52 epistasis group and relies on extensive homology between the damaged DNA and an undamaged partner [sister chromatid or homologous chromosome (8)]. By contrast, NHEJ requires little or no homology between the recombining molecules (9). Key components of the NHEJ machinery in mammals include the Ku70͞Ku80 heterodimer an...

Histone deacetylase inhibitors and genomic instability

“…In addition, RPD3 deacetylates lysine 16 on histone H4 in the vicinity of a DSB that can only be repaired by NHEJ. Consequently, RPD3 mutants also disrupt NHEJ, indicating that HDAC activity is also involved in the NHEJ-mediated DSB repair [59]. Time-course chromatin immunoprecipitation data suggest that HDACs are involved in restoring chromatin to its original conformation during the final steps of the DSB repair process [60].…”

NAD+-dependent deacetylation of H4 lysine 16 by class III HDACs

“…For instance, DNA repair after ultraviolet irradiation is related to acetylation of H3K9 and H3K14 in the affected loci (Yu et al, 2005), and H4K8Ac has been linked to HR of DSB (Downs et al, 2004). Additionally, H4K16Ac was detected at DSB sites in yeast (Jazayeri et al, 2004). Male absent on the first (MOF), the main HAT responsible for H4K16Ac in higher eukaryotes (Dou et al, 2005;Smith et al, 2005;Taipale et al, 2005) that is involved in male dosage compensation in Drosophila (Hilfiker et al, 1997), binds to ataxiatelangiectasia mutated protein (ATM), a kinase that triggers the response to DNA damage in DSB by its phosphorylation of targets involved in DNA repair, cellcycle control and apoptosis (Gupta et al, 2005).…”

Orchestration of chromatin-based processes: mind the TRRAP

“…Following DNA repair, acetyl marks may be removed (deacetylation) by the action of histone deacetylases. Although such a possibility awaits experimental proof, histone deacetylases were shown to be required for efficient DNA repair (Jazayeri et al, 2004;Tamburini and Tyler, 2005). In addition, it was shown that histone H3 and H4 were acetylated during homology-directed repair and that deacetylation occurs after DNA repair is completed (Tamburini and Tyler, 2005).…”