Duplication, mutation and recombination of the human orphan gene KIR2DS3 contribute to the diversity of KIR haplotypes

Abstract

The KIR2DS3 gene is an activating homologue of the inhibitory killer-cell immunoglobulin-like receptors (KIR) that recognize HLA-C molecules, enabling NK cells to survey the normal function of endogenous antigen presentation. The genetics of KIR2DS3 is complicated by the existence of alleles with similar coding sequences that map to different regions of the KIR complex in chromosome 19, or whose location in this complex is unknown. Here, by studying the family segregation of the KIR alleles 2DS3*001, *002 and *003N, and the distribution of these in unrelated individuals, we demonstrate the existence of two paralogous KIR2DS3 genes that can be inherited separately or, as it happens frequently in Caucasoids due to linkage disequilibrium, together. Each KIR2DS3 gene is almost invariably associated in its 5 0 end to a different copy of KIR2DL5, a gene previously shown to be duplicated in humans. KIR2DL5 and KIR2DS3 thus form two highly homologous gene clusters situated in the centromeric and the telomeric intervals of KIR haplotypes. Recombination between those clusters is the likely origin of new haplotypes, characterized in this study, which harbour further duplications or deletions of multiple KIR genes. Our results help understand the genetics of KIR2DS3 and the diversity of human KIR genotypes.

Copy number variation leads to considerable diversity for B but not A haplotypes of the human KIR genes encoding NK cell receptors

“…The reason for this is that without determining copy number or defining alleles, ascertainment of the gene arrangements on these haplotypes can be obscured by variation in KIR gene content of the partnering chromosome, even with pedigrees to track gene transmission . Six of the uncommon gene combinations (haplotypes 12, 13, 14, 15, 18, and 33) appeared to match recombinant haplotypes reported previously by us and others (Gomez-Lozano et al 2003, 2005Martin et al 2003;Ordonez et al 2008Ordonez et al , 2011Traherne et al 2010). Using published methods for detecting hybrid genes (e.g., 2DL5/3DP1 [3DP1*004], 2DS2/2DS3 [2DS2*005], and 2DL3/2DP1) and specific alleles associated with these recombinant haplotypes, we were able to Gene copy number varies from zero to three copies on a single haplotype.…”

“…For example, the haplotype motif tA01 may have either form of 2DS4 (2DS4f or 2DS4v), and tB01 may have either variant of 2DS3S5 (2DS3 or 2DS5). T and C suffixes for 2DL5 (2DL5A or 2DL5B) and 2DS3S5 indicate the telomeric and centromeric versions of the genes, respectively (Gomez-Lozano et al 2002;Ordonez et al 2008;Pyo et al 2010). For simplicity, 2DS1 and 2DS4 are shown at the same site because they showed a mutually exclusive relationship.…”

Molecular characterisation of KIR2DS2*005, a fusion gene associated with a shortened KIR haplotype

“…To rule out this possibility and, also, to map KIR2DS2*005 in the unusual haplotype, we studied its arrangement through analysis of the genes flanking KIR2DS2*005. Using a KIR-gene walking approach, 11 we found KIR2DS2*005 downstream of KIR3DL3, the normal arrangement of these two genes. On the contrary, we found that KIR2DS2 was followed not by KIR2DL2 as it happens in most haplotypes, but by the KIR2DP1 pseudogene, from which KIR2DS2 is normally separated by three KIR genes (Figure 1).…”

“…Genetic features of KIR2DS2*005 In a previous study on KIR-B haplotypes, we identified a healthy Caucasoid woman carrying KIR2DS2*005, 11 an uncommon allele with a hybrid primary structure. KIR-gene segregation in her sibling revealed that KIR2DS2*005 was inherited in a KIR haplotype that lacked a KIR2DL2 gene (Figure 1), whereas its central and telomeric regions were characteristic of B haplotypes (KIR 3DP1-2DL4-3DS1-2DL5A*001-2DS5-2DS1-3DL2).…”

“…Generic KIR typing, allelic KIR2DL5 and KIR2DS3 typing, and long-range PCR for initial KIR2DS2*005 identification were done as described. 11,19,20 A new PCR-SSP method for specific detection of KIR2DS2*005 was designed: genomic DNA was amplified using 0.2 U of BioTaq DNA polymerase (Bioline, London, UK), and primers Fi6a þ 3019b (forward, The KIR genes flanking KIR2DS2*005 in donor C180F2 genomic DNA were determined using KIR-gene walking protocols similar to those we have reported previously DNA sequencing. All PCR products were submitted to direct nucleotide sequencing with no cloning step.…”