Intraspecific Evolution of Human RCCX Copy Number Variation Traced by Haplotypes of the CYP21A2 Gene

Abstract

The RCCX region is a complex, multiallelic, tandem copy number variation (CNV). Two complete genes, complement component 4 (C4) and steroid 21-hydroxylase (CYP21A2, formerly CYP21B), reside in its variable region. RCCX is prone to nonallelic homologous recombination (NAHR) such as unequal crossover, generating duplications and deletions of RCCX modules, and gene conversion. A series of allele-specific long-range polymerase chain reaction coupled to the whole-gene sequencing of CYP21A2 was developed for molecular haplotyping. By means of the developed techniques, 35 different kinds of CYP21A2 haplotype variant were experimentally determined from 112 unrelated European subjects. The number of the resolved CYP21A2 haplotype variants was increased to 61 by bioinformatic haplotype reconstruction. The CYP21A2 haplotype variants could be assigned to the haplotypic RCCX CNV structures (the copy number of RCCX modules) in most cases. The genealogy network constructed from the CYP21A2 haplotype variants delineated the origin of RCCX structures. The different RCCX structures were located in tight groups. The minority of groups with identical RCCX structure occurred once in the network, implying monophyletic origin, but the majority of groups occurred several times and in different locations, indicating polyphyletic origin. The monophyletic groups were often created by single unequal crossover, whereas recurrent unequal crossover events generated some of the polyphyletic groups. As a result of recurrent NAHR events, more CYP21A2 haplotype variants with different allele patterns belonged to the same RCCX structure. The intraspecific evolution of RCCX CNV described here has provided a reasonable expectation for that of complex, multiallelic, tandem CNVs in humans.

Common Genetic Variants of the Human Steroid 21-Hydroxylase Gene (CYP21A2) Are Related to Differences in Circulating Hormone Levels

“…Both intron 2 haplotype clusters delineate two distinct, well-defined full-length CYP21A2 haplotype clusters [4]; five full-length haplotypes belong to c5, and three are assigned to c8 (Table S1). Therefore, the relationships between hormone levels and CYP21A2 intron 2 haplotypes apply to full-length CYP21A2 haplotypes.…”

“…CYP21A2 is located together with the complement component 4A and 4B genes ( C4A and C4B ) in a multi-allelic, complex and tandem copy number variation (CNV), called RCCX CNV, and, in a wider sense, in the major histocompatibility complex of chromosome 6 [3], [4]. RCCX CNV also comprises the duplicated non-functional pseudogene of steroid 21-hydroxylase ( CYP21A1P ).…”

Fine-tuned characterization of RCCX copy number variants and their relationship with extended MHC haplotypes

“…The fact that even rare RCCX structures occur in different genomic context is in accordance with the relatively frequent observations of de novo nonhomologous recombination events within the RCCX 28,35 and our recent results on the intraspecific genealogy of the RCCX. 14 Both RCCX structural variations and MHC haplotypes have long been studied for their effects on diverse physiological and pathological processes. 6,36,37 The exact relationship between disorder and RCCX is unambiguous when a defective gene is involved; 7,38 most often, however, identification of the real causative factors proves fairly challenging.…”

Szteroid-21-hidroxiláz-deficientia, a congenitalis adrenalis hyperplasia leggyakoribb oka

“…Az így létrejött kiméra CYP21-gén a kicserélődött szakasz hosszától függően kevesebb vagy több, a pszeudogénből származó kóroki mutációt tartalmazhat. A kiméra gének mutációinak pontos meghatározása RCCX-CNV-specifikus molekuláris genetikai metodikák (például allélspecifikus long-range PCR [26]) használa-tát igényli, amelyek nem részei a rutin genetikai diagnosztikának. Szintén RCCX-CNV-specifikus metodikát igényel, és nagyban megnehezíti a 21-OHD genetikai diagnosztikáját, hogy 1 kromoszómán a szokásos 1 CYP21A2-kópia mellett ritkábban még 1 CYP21A2-kó-pia is lehet (2/E ábra).…”