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.

Figure 1

Characterization of DSB-enriched probe. (a) Map of the HIS4 recombination hotspot in FX4. An insertion of telomeric DNA with three Rap1 binding sites results in high levels of meiosis-specific DSBs at the position indicated by the arrow (4). The position of the probe (pDN42; 4) used in b is shown by the vertical line adjacent to the map. (b) Southern analysis of FX4 meiotic DNA samples used in the microarray experiments. Lanes 1 and 2 contain BglII-treated DSB-enriched DNA (P2) isolated by using glass fiber filters (11), and BglII-treated total genomic DNA (P1), respectively. Lane 3 contains HindIII-treated λ DNA. Arrows indicate the position of the intact 2.9-kb HIS4-BIK1 BglII fragment and the 1.9-kb fragment resulting from the meiosis-specific DSB.

Figure 2

Hotspot activity of yeast ORFs. To estimate DSB formation adjacent to each ORF, we measured the ratio of hybridization to a DSB-enriched probe (P2) to a total genomic probe (P1) in seven microarrays. The log of the median hybridization ratio for each of the 6,200 ORFs is graphed; ratios were grouped into bins of 0.015 log units. An arrow marks the separation between the ORFs with hybridization ratios ranked in the top eighth from those in the bottom seven-eighths.

Figure 3

Chromosomal map positions of the hotspots (red) and coldspots (green). Ovals indicate centromeres. Blue lines represent peaks of G + C base composition that are 3% higher than the average for the chromosome.

Figure 4

Comparison of different methods of mapping hotspots and coldspots on chromosome III. (a) Summary of hybridization ratios using microarrays for all chromosome III ORFs. These data were based on yeast strains FX4 and FX6, except for the HIS4 locus for which only the FX6 data were used. Each ORF was assigned the median hybridization ratio of the seven microarrays and we graphed the log function of this value. The 182 ORFs represented in the analysis (left to right on the x axis) are (inclusive Stanford Genome Database numbering system): YCL076W-YCL073C, YCL069W-YCL016C, YCL014W-YCL001W, YCR001W-YCR020C, YCR020C-A, YCR021C-YCR024C, YCR024C-A, YCR025C-YCR029C, YCR029C-A, YCR030C-YCR077C, YCR079W-YCR097WA, and YCR097WB-YCR107W. The hotspot labels correspond to those listed in Table 1. (b) Summary of data of Baudat and Nicolas (13). These researchers monitored DSBs in an SK1 derivative by Southern analysis. (c) Analysis of hotspots in an SK1 derivative using DNA from immunoprecipitated Spo11p/hemagglutinin-DNA complexes as a probe of nylon filters containing chromosome III ORFs. The y axis shows the log of the average normalized ratio of hybridization (DSB-enriched probe/total genomic DNA probe). Gaps on the x axis reflect ORFs that were not present on the nylon filters. (d) Analysis of hotspots in FX6 using macroarrays. In this experiment, the probe was prepared by the method used in a.

Figure 5

Correlation of hotspots with peaks of high G + C content on chromosome III. (Upper) A scan of base composition at 1-kb intervals (5-kb sliding window). The marked peaks have a G + C base composition ≥ 3% above the average for chromosome III (38.7%). In addition, we show the log values of the median hybridization ratio (DSB-enriched probe/total genomic DNA). (Lower) The ORFs (two lines of black rectangles) and the positions of a number of structural chromosomal elements are indicated.