In the yeast Saccharomyces cerevisiae, meiotic recombination is initiated by double-strand DNA breaks (DSBs). Meiotic DSBs occur at relatively high frequencies in some genomic regions (hotspots) and relatively low frequencies in others (coldspots). We used DNA microarrays to estimate variation in the level of nearby meiotic DSBs for all 6,200 yeast genes. Hotspots were nonrandomly associated with regions of high G ؉ C base composition and certain transcriptional profiles. Coldspots were nonrandomly associated with the centromeres and telomeres. Hotspots are genomic regions with unusually high levels of recombination (1). From studies in yeast, several generalizations concerning hotspots can be made. First, most hotspots are intergenic rather than intragenic (2). Second, genetically defined hotspots are associated with local double-strand DNA breaks (DSBs) (1). Third, DSBs usually occur in DNase Isensitive regions (3). Fourth, activity of the HIS4 hotspot in Saccharomyces cerevisiae requires the binding of transcription factors in the hotspot region (4-6), but does not require high levels of meiosis-specific transcription (7). Hotspots that require transcription factor binding are called ␣ hotspots (8). Fifth, certain DNA sequences result in hotspots (␤ hotspots) that do not require the binding of known transcription factors (9).Meiotic DSB formation requires Spo11p, a topoisomerase II-related protein that is transiently covalently attached to the 5Ј ends of the DNA fragments (10, 11). In wild-type yeast cells, the Spo11p is removed to allow subsequent steps in recombination. In strains with the rad50S mutation, however, Spo11p stays covalently attached to the broken DNA ends (11).Coldspots in yeast have received less attention than hotspots. Lambie and Roeder (12) showed that the centromere of chromosome III reduced crossing-over and gene conversion of nearby markers, and Baudat and Nicolas (13) noted a lack of DSB sites near the centromere. Several researchers have found a relative lack of DSB sites in rad50S strains near the telomeres (13,14).Although observations concerning individual hotspots and coldspots have given clues as to the mechanism of recombination initiation, our ability to predict hotspots and coldspots from DNA sequence information is very limited. A complementary approach is to map hotspots and coldspots globally and to determine whether they share common DNA sequences and͞or structural elements. Such mapping studies have been performed to map DSB sites to single-gene resolution on chromosome III (13) and to the resolution of a pulsed-field gel on chromosomes I, III, and VI (14,15). By using DNA samples enriched for meiosis-specific DSBs as hybridization probes on DNA microarrays, we extended these analyses to measure the global distribution of DSBs at single-gene resolution. Materials and MethodsYeast Strains. FX4, FX6, and QFY105 are diploid rad50S strains that have been described (4). These strains (used in the microarray analysis) are isogenic except for changes introduced by transformati...

The postreplicative repair of double-strand breaks (DSBs) is thought to require sister chromatid cohesion, provided by the cohesin complex along the chromosome arms. A further specialized role for cohesin in DSB repair is suggested by its de novo recruitment to regions of DNA damage in mammals. Here, we show in budding yeast that a single DSB induces the formation of a approximately 100 kb cohesin domain around the lesion. Our analyses suggest that the primary DNA damage checkpoint kinases Mec1p and Tel1p phosphorylate histone H2AX to generate a large domain, which is permissive for cohesin binding. Cohesin binding to the phospho-H2AX domain is enabled by Mre11p, a component of a critical repair complex, and Scc2p, a component of the cohesin loading machinery that is necessary for sister chromatid cohesion. We also provide evidence that the DSB-induced cohesin domain functions in postreplicative repair.

Both Mec1p and Tel1p can respond to a DSB, with distinct roles for these checkpoint kinases at different phases of the cell cycle. Part of this response involves histone phosphorylation over large chromosomal domains; however, the distinct distributions of gamma-H2AX and repair proteins near DSBs indicate that localization of repair proteins to breaks is not likely to be the main function of this histone modification.