Allelic recombination between distinct genomic locations generates copy number diversity in human beta-defensins

Abstract

Beta-defensins are small secreted antimicrobial and signaling peptides involved in the innate immune response of vertebrates. In humans, a cluster of at least 7 of these genes shows extensive copy number variation, with a diploid copy number commonly ranging between 2 and 7. Using a genetic mapping approach, we show that this cluster is at not 1 but 2 distinct genomic loci approximately 5 Mb apart on chromosome band 8p23.1, contradicting the most recent genome assembly. We also demonstrate that the predominant mechanism of change in beta-defensin copy number is simple allelic recombination occurring in the interval between the 2 distinct genomic loci for these genes. In 416 meiotic transmissions, we observe 3 events creating a haplotype copy number not found in the parent, equivalent to a germ-line rate of copy number change of approximately 0.7% per gamete. This places it among the fastest-changing copy number variants currently known.

Fig. 1.

8p23.1 genomic region showing an example of a β-defensin repeat. The 2 olfactory receptor/FAM90A repeat regions REPD and REPP are shown at either end of an inversion (inv) on the chromosome ideogram. An example of a partial β-defensin repeat, based on 1 of the 2 assembled versions in human genome assembly hg18, is shown below the ideogram. RefSeq genes, together with the copy number assays used in this article, are shown. The exact length of the copy number variable β-defensin unit is not known, and the region highlighted corresponds to the class V repeat identified previously (30).

Fig. 2.

CEPH offspring 133306 inherits an altered copy number after recombination between maternal haplotypes. Paternal (red/blue) and maternal (black/cyan) haplotypes in the parents (133301 and 133302) were defined by analysis of grandparental genotypes and of segregation patterns into nonrecombinant offspring (e.g., 133304 and 133308) at the multiallelic indel rs5889219 (Left) and the microsatellite EPEV-3 (Center). Right shows an interpretation of the segregation pattern in which EPEV-3 alleles are shown in rectangles and rs5889219 alleles are shown within ellipses. The appearance of a recombinant C/D haplotype in offspring 133306 coincides with a maternal crossover in the interval, as deduced from CEPH segregation data (see Fig. 4 and Table S1).

Fig. 3.

CEPH offspring 134106 and 134109 inherit different reciprocal maternal crossovers that do not alter copy number. Paternal (red/blue) and maternal (black/cyan) haplotypes in the parents (134101 and 134102) were defined by segregation patterns into nonrecombinant offspring, including 134104 and 134110 shown here, at the multiallelic indel rs5889219 (Left) and the microsatellite EPEV-3 (Center). The interpretation in Right shows that the crossovers are clearly demonstrated by EPEV-3 but that rs5889219 is not fully informative; reciprocal crossovers are inherited by 1341-06 (D/C) and 1341-09 (C/D), and corresponding crossovers can be observed on linkage analysis of markers in this region (see Fig. 4 and Table S1).

Fig. 4.

Genetic mapping of β-defensin repeats relative to crossover breakpoints in CEPH pedigrees, shown against genome assembly coordinates. The approximate locations of REPP and REPD are shown, as are the intervals containing the inversion endpoints. The crossovers indicate, at the top, selected unidirectional recombinants mapping the location of all repeat units on a haplotype, identified by family and individual name and parent of origin (e.g., “6607M” is the maternal haplotype of child 07 in family 66). Below are shown selected crossovers that map repeats to the proximal and/or distal sites; the numbers of repeats mapping in each direction are indicated, and the hashed segments indicate uncertainty in the placement of breakpoints because of the lack of informative markers. Based on these data, β-defensin repeats can be mapped to the distal and proximal intervals shown at the bottom.