Systematic identification of fragile sites via genome-wide location analysis of γ-H2AX

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Abstract
H2AX phosphorylation is an early response to DNA damage and is mediated by the ATM/ATR kinases. By examining the genome-wide location of γ-H2A in wild type and mutant S. cerevisiae strains, loci that tend to engage ATR (Mec1) and ATM (Tel1) are identified as a route to mapping fragile sites in this genome. Phosphorylation of histone H2AX is an early response to DNA damage in eukaryotes. In Saccharomyces cerevisiae, DNA damage or replication-fork stalling results in phosphorylation of histone H2A yielding γ-H2A (yeast γ-H2AX) in a Mec1 (ATR)- and Tel1 (ATM)-dependent manner. Here, we describe the genome-wide location analysis of γ-H2A as a strategy to identify loci prone to engaging the Mec1 and Tel1 pathways. Notably, γ-H2A enrichment overlaps with loci prone to replication-fork stalling and is caused by the action of Mec1 and Tel1, indicating that these loci are prone to breakage. Moreover, about half the sites enriched for γ-H2A map to repressed protein-coding genes, and histone deacetylases are necessary for formation of γ-H2A at these loci. Finally, our work indicates that high-resolution mapping of γ-H2AX is a fruitful route to map fragile sites in eukaryotic genomes.