High-resolution patterns of meiotic recombination across the human major histocompatibility complex

Abstract

Definitive characteristics of meiotic recombination events over large (i.e., >1 Mb) segments of the human genome remain obscure, yet they are essential for establishing the haplotypic structure of the genome and for efficient mapping of complex traits. We present a high-resolution map of recombination at the kilobase level across a 3.3-Mb interval encompassing the major histocompatibility complex (MHC). Genotyping of 20,031 single sperm from 12 individuals resulted in the identification and fine mapping of 325 recombinant chromosomes within genomic intervals as small as 7 kb. Several principal characteristics of recombination in this region were observed: (1) rates of recombination can differ significantly between individuals; (2) intense hot spots of recombination occur at least every 0.8 Mb but are not necessarily evenly spaced; (3) distribution in the location of recombination events can differ significantly among individuals; (4) between hot spots, low levels of recombination occur fairly evenly across 100-kb segments, suggesting the presence of warm spots of recombination; and (5) specific sequence motifs associate significantly with recombination distribution. These data provide a plausible model for recombination patterns of the human genome overall.

Figure 1

Summary of steps involved in recombination fine mapping. A, The MHC was surveyed for recombinants through use of PEP-amplified sperm DNA and the polymorphic markers MOGCA at the telomeric end and either D6S439 (red) or D6S291 (blue) at the centromeric end (depending on heterozygosity in each donor). Four hundred sperm containing a single crossover in the 4.14-Mb segment from MOGCA to D6S439 and 176 sperm containing a single crossover within an overlapping 5.7-Mb segment from MOGCA to D6S291 were identified. Of the 576 recombinants, 325 mapped within the MHC, as determined by typing all recombinants with two additional closely spaced markers (indicated with an asterisk [*]). Forty-eight STRs were used to localize 325 MHC crossovers within the smallest possible interval bordered by adjacent markers. Limited amounts of PEP-DNA restricted the number of markers typed for each recombinant to only those markers that would narrow the segment in which the recombinant occurred (4–11 markers typed per recombinant). B, Numbers representing recombinants identified over the entire region initially screened (red and blue indicate recombinants from MOGCA to D6S439 and MOGCA to D6S291, respectively), recombinants within the MHC, number of informative sperm, and the distance-normalized recombination rate within the MHC. C, Histogram of individual variation in the rates of recombination among 12 donors. Donors A, B, C, and G are unrelated (black). Donors L and E share one parental HLA haplotype (green), donors S and T are HLA-identical siblings (blue), and donors X and Y and donors V and W are two sets of MZ twins (red). Frequency of recombination plus 1 SD is shown.

Figure 2

Map of the MHC in which 325 recombinant chromosomes were fine mapped by single-sperm typing. The relative positions of 19 MHC genes (red arrows) and 37 polymorphic STRs used to partition the MHC into 30 segments, illustrated as the region between the fine horizontal lines, are shown. The location in which each recombination breakpoint occurred is depicted as a colored box. The number in each box indicates the number of recombinants fine mapped within the area covered by the box. Black boxes represent those recombinants that occurred within a single segment; green, within two adjacent segments (each segment is therefore credited one-half the number of recombinants); red, within three adjacent segments (each segment is credited one-third the number of recombinants); yellow, within four adjacent segments (each segment is credited one-fourth the number of recombinants); and gray, within a segment >395 kb (each segment is therefore credited 1/n the number of recombinants, where n is the number of segments spanned by the recombinant). The total number of potential recombination breakpoints identified in each of the 30 segments (numbered) is listed to the right in boldface type.

Figure 3

Recombination intensity across the MHC. A, The MHC was subdivided into 30 segments. Segments displaying an excess of recombination are represented as a red bar, which is proportional in length to the increase in recombination over the expected (0.49 cM/Mb). One SD is shown for the six segments where excess recombination was observed. Numbers adjacent to the bars indicate the increase in recombination over the expected. Three segments displayed significantly higher rates of recombination over that expected, after correction for multiple tests (where a superscript “P” is <10⁻⁵ and a superscript “PP” is <10⁻¹⁵). Blue bars to the left represent segments displaying a reduction in recombination over that expected, none of which were statistically significant. A distance-normalized scale of recombination rates (in cM/Mb), which allows direct comparison of rates between segments of varied size, is shown at the bottom. White bars straddling the center line represent a 1–1.1× deviation in recombination from the expected. White bars flanking the center line represent a 1.1–1.35× deviation from the expected. B, Recombination intensity across the MHC class II region was compared using data from 88 sperm-based class II recombinants (present study) and previously reported class II recombinants identified in families (Cullen et al. 1997); 22 crossovers of maternal origin (hatched bars) and the complete data set of 31 maternally and paternally derived crossovers (solid bars). The expected number of recombinants for the sperm-based class II recombination profile was based on 88 recombinants evenly distributed across a 635-kb genomic segment and therefore is not identical to the class II profile shown in 3A. No crossovers were identified between DRB1 and DRA in the family data. However, crossovers of paternal origin were identified between DQB1 and DRB1 in the family data.

Figure 4

Variation among individuals in the distribution of recombination events. Individual levels of recombination exceeding that expected, given an overall MHC rate of 0.49 cM/Mb (1×), were plotted for each of 30 segments as excess in recombination activity (range = 1–8×). The magnitude of the increase in recombination is represented as an arrow relative to the scale on the ordinate, and each donor is represented by a unique color. The minimum threshold rate for a hot spot (red horizontal line) is twice the baseline rate of 0.49 cM/Mb. The six peaks in recombination intensity identified in the pooled donor recombination data (fig. 3A) corresponded with segments 1, 4, 7, 14, 28, and 30. Only segments 1, 4, and 14 exhibited highly significant increases in recombination after correction for multiple tests (see fig. 3A). Segments 7 and 28 (light gray) were not as robust, with only 3 of 12 donors exceeding the 2× threshold. Although segment 30 did not undergo significant levels of recombination over the expected after correction for multiple tests, 7 of 12 donors exhibited hot spot levels in this segment. The relative locations of 18 classical and nonclassical HLA genes are shown, and the three gray segments (2–3, 5–13, and 15–29) represent three major haplotypic blocks. Gray and black boxes in the lower 12×30 grid represent MHC segments that exhibit hot spot (⩾2×) levels of recombination for each individual.

Figure 5

Relationship between recombination intensity and (GT)_⩾20 repeat density. The four major hot spots are labeled 1–4 and are illustrated by red bars. The MHC extends from map position 250 kb to 3550 kb on the X-axis. The total number of (GT)_⩾20 repeat loci was based on the sum of all tandem (GT)_n or (CA)_n repeat units (n⩾20) per marker per segment, as determined from MHC sequence data (available on the MHC sequence database) and illustrated as black bars. The number of tandem repeats per marker used to determine the repeat length plotted in the histogram reflects the most common allele size within a population of 36 HTCs (M. Cullen, A. Harding, and M. Carrington, unpublished data). The graph insert shows a plot of recombination intensity by (GT) repeat intensity used in the linear regression analysis.