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

Abstract

␤-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 Ϸ5 Mb apart on chromosome band 8p23.1, contradicting the most recent genome assembly. We also demonstrate that the predominant mechanism of change in ␤-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 Ϸ0.7% per gamete. This places it among the fastest-changing copy number variants currently known.

Interchromosomal core duplicons drive both evolutionary instability and disease susceptibility of the Chromosome 8p23.1 region

“…Paired-end sequence analysis does not confirm the organization of the corresponding region in H1 but does support the organization of H2 (Supplemental Section 1). Due to the proximity of the distal gap and previous experimental data indicating that the distal beta-defensin cluster 2 should in fact be located at the REPP cluster (Bakar et al 2009), we conclude that inversion 3 represents an assembly artifact. To this end, we reconstructed the tiling path of RP11 clones underlying the H1 reference assembly and found that clone overlaps within the inversion 3 region in H1 were shorter on average (<20-kbp overlaps) and corresponded to high-identity regions where there is evidence that a hybrid assembly between H1/H2 occurred within the REPP gap region (Supplemental Section 2;Supplemental Figs.…”

“…6A). We surmise that the existence of large-scale, alternate structural configurations and copy number polymorphic loci resulted in misassignment of paralogous betadefensin copies in the H1 organization (Bakar et al 2009), confounding complete assembly of the Chromosome 8p23.1 locus. Figure 6.…”

“…The beta defensins vary substantially in copy number, and this common variation has been associated with multiple immune-related phenotypes, including psoriasis and Crohn's disease (Cantsilieris and White 2013). Despite the importance of the Chromosome 8p23.1 locus in human health and disease, the existence of large alternative structural haplotypes, combined with a complex organization of SDs, has led to inconsistencies in the current human reference assembly that have not yet been resolved (Bakar et al 2009). Moreover, such genomic complexity represents a significant challenge that has impeded studies of genetic association, including susceptibility to disease (Hollox 2012).…”

Human gene copy number variation and infectious disease

“…Studies of complex multiallelic CNVs have shown that the mutation 95 rate is high, several orders of magnitude higher than for single nucleotide polymorphisms, usually 96 because of recurrent NAHR (Abu Bakar et al 2009;Fu et al 2010;Lam and Jeffreys 2006). This has 97 two consequences: firstly CNVs can accumulate variation under mutation-drift balance resulting in a 98 particular DNA sequence having a high level of standing variation and therefore a substrate for 99 subsequent selection.…”

Low α-defensin gene copy number increases the risk for IgA nephropathy and renal dysfunction

“…We measured the copy numbers of DEFA1, DEFA3 and DEFA1A3 (DEFA1+DEFA3) as well as the copy numbers of three bi-allelic polymorphisms, 5bp indel (129bp vs. 124bp), 7bp duplication (282bp vs. 275bp) and the 4bp deletion (211bp vs. 215bp) using well-established paralogue ratio test (PRT)-based methods (16,24) (Fig.S1). The PRTbased methods have been shown to have much greater accuracy for measuring the copy numbers of multi-allelic CNVs than real-time PCR analysis (25,26) and have been successfully applied to studies of genes encoding chemokines (CCL3L1/CCL4L1) (27), immunoglobulin-receptor (FCGR3) (28), and beta-defensins (DEFB) (25,29).…”