Global mapping of meiotic recombination hotspots and coldspots in the yeast Saccharomyces cerevisiae

Abstract

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...

Inverted repeat of a large segment unveiled on the right arm of Saccharomyces cerevisiae chromosome II

“…However, our preliminary chromosome-walking data contradict this explanation. In this regard, we are interested in the recent observation that the recombination frequency differs markedly depending on the distance from the centromere; in general, the closer to the centromere, the more recombination is suppressed (Gerton et al, 2000). Our data are in accordance with this notion.…”

The histone methylase Set2p and the histone deacetylase Rpd3p repress meiotic recombination at the HIS4 meiotic recombination hotspot in Saccharomyces cerevisiae

“…Chromosome III is depicted in the lower part of the figure. The short vertical lines represent the positions of meiotic recombination hotspots determined by microarray analysis (15). Cell extracts were prepared from the same diploid strains that were analyzed for DSBs: FX1 (wild-type, white bars), JDM1093 (set2, striped bars), JDM1095 (rpd3, black bars), and JDM1096 (set2 rpd3, stippled bars).…”

“…In our genetic background, the HIS4 gene is one of the strongest recombination hotspots in the S. cerevisiae genome (15) and is associated with a high-frequency DSB located upstream of HIS4 (16,17). In cells sporulated at 25°, this DSB is responsible for initiating about half of HIS4 conversion events (16).…”

Relationship between G+C content, ORF‐length and mRNA concentration in Saccharomyces cerevisiae

“…Finally it should be mentioned that a significant correlation between G+C content and meiotic recombination exists (Sharp and Lloyd, 1993;Gerton et al, 2000). In addition, it has been suggested that recombination could drive G+C content through GC-biased mismatch repair within the heteroduplexes formed during recombination (Birdsell, 2002).…”