Extensive Normal Copy Number Variation of a β-Defensin Antimicrobial-Gene Cluster

Abstract

Using a combination of multiplex amplifiable probe hybridization and semiquantitative fluorescence in situ hybridization (SQ-FISH), we analyzed DNA copy number variation across chromosome band 8p23.1, a region that is frequently involved in chromosomal rearrangements. We show that a cluster of at least three antimicrobial beta-defensin genes (DEFB4, DEFB103, and DEFB104) at 8p23.1 are polymorphic in copy number, with a repeat unit >/=240 kb long. Individuals have 2-12 copies of this repeat per diploid genome. By segregation, microsatellite dosage, and SQ-FISH chromosomal signal intensity ratio analyses, we deduce that individual chromosomes can have one to eight copies of this repeat unit. Chromosomes with seven or eight copies of this repeat unit are identifiable by cytogenetic analysis as a previously described 8p23.1 euchromatic variant. Analysis of RNA from different individuals by semiquantitative reverse-transcriptase polymerase chain reaction shows a significant correlation between genomic copy number of DEFB4 and levels of its messenger RNA (mRNA) transcript. The peptides encoded by these genes are potent antimicrobial agents, especially effective against clinically important pathogens, such as Pseudomonas aeruginosa and Staphylococcus aureus, and DEFB4 has been shown to act as a cytokine linking the innate and adaptive immune responses. Therefore, a copy number polymorphism involving these genes, which is reflected in mRNA expression levels, is likely to have important consequences for immune system function.

Expansion of a 12-kb VNTR containing the REXO1L1 gene cluster underlies the microscopically visible euchromatic variant of 8q21.2

“…39 Interestingly, a diploid REXO1L2P median copy number of 172, almost identical to the 173 in our controls, was found using sequencing in 159 ethnically diverse subjects from the 1000 Genomes Project, 32 and the Database of Genomic Structural Variation records 272 copies, within the EV range, of a 7-kb segment including the REXO1L1 gene in a Southern Kalahari hunter-gatherer (KB1). 40 RP11-96G1 at 8q21.2 is the third most common benign CNV identified by Whitby et al 34 using BAC array CGH and, like the second most common (RP11-122N11 at 8p23.1), becomes microscopically visible at high copy number, 31 contains tandemly repeated DNA families, 27 predisposes to polymorphic inversions 41 and has been associated with neocentromere formation. 42 The 8q21.2 VNTR is one of the nine autosomal tandem arrays 42 kb that contain a single gene and show CNV.…”

Genomic variations within DEFB1 are associated with the susceptibility to and the fatal outcome of severe sepsis in Chinese Han population

“…5 Meanwhile, in vivo study showed a protective role of overexpressed bdefensin 2 against sepsis via anti-inflammation activity. 31 Studies have shown that DEFB4 and DEFB103 as well as DEFB104 were polymorphic in copy number variation, [20][21][22] and the genomic copy number of DEFB4 correlated with the level of its transcript. 20 Copy number polymorphism of defensin may have a crucial role in inflammatory disease, which has been demonstrated in Crohn's disease.…”

“…31 Studies have shown that DEFB4 and DEFB103 as well as DEFB104 were polymorphic in copy number variation, [20][21][22] and the genomic copy number of DEFB4 correlated with the level of its transcript. 20 Copy number polymorphism of defensin may have a crucial role in inflammatory disease, which has been demonstrated in Crohn's disease. 32 Therefore, the functional SNP À44C/ G and the related haplotypes within the DEFB1 gene in this study, as in any genetic association study, may not be causative but may be in strong linkage disequilibrium with separate causative polymorphisms such as copy number polymorphisms in other defensin genes.…”

“…19 Recent studies found that the genes coding a-defensins 1 (DEFA1) and 3 (DEFA3) as well as b-defensins 2 (DEFB4), 3 (DEFB103) and 4 (DEFB104) exhibit copy number polymorphisms, while the DEFB1 gene was a single copy gene containing several SNPs. [20][21][22][23] The SNPs in DEFB1 have been associated with the pathogenesis of asthma and chronic obstructive pulmonary disease (COPD) as well as infectious disease. [24][25][26][27][28] However, the genetic predisposition of individuals carrying these SNPs to sepsis remains unknown.…”

Expresión diferencial en placenta de beta-defensinas humanas y detección de variantes alélicas en el gen DEFB1 de madres positivas para VIH-1

“…DEFB4 and DEFB103 genes exhibit normal copy number variation (68) and most likely their allelic distribution is in accordance with the HardyWeinberg equilibrium (69,70). However, the DEFB1 gene does not exhibit this phenomenon (69) and thereby becomes an excellent target for the search of SNPs associated with degree of susceptibility.…”