Dynamic nature of the proximal AZFc region of the human Y chromosome: multiple independent deletion and duplication events revealed by microsatellite analysis

Abstract

The human Y chromosome shows frequent structural variants, some of which are selectively neutral, while others cause impaired fertility due to the loss of spermatogenic genes. The large-scale use of multiple Y-chromosomal microsatellites in forensic and population genetic studies can reveal such variants, through the absence or duplication of specific markers in haplotypes. We describe Y chromosomes in apparently normal males carrying null and duplicated alleles at the microsatellite DYS448, which lies in the proximal part of the azoospermia factor c (AZFc) region, important in spermatogenesis, and made up of "ampliconic" repeats that act as substrates for nonallelic homologous recombination (NAHR). Physical mapping in 26 DYS448 deletion chromosomes reveals that only three cases belong to a previously described class, representing independent occurrences of an approximately 1.5-Mb deletion mediated by recombination between the b1 and b3 repeat units. The remainder belong to five novel classes; none appears to be mediated through homologous recombination, and all remove some genes, but are likely to be compatible with normal fertility. A combination of deletion analysis with binary-marker and microsatellite haplotyping shows that the 26 deletions represent nine independent events. Nine DYS448 duplication chromosomes can be explained by four independent events. Some lineages have risen to high frequency in particular populations, in particular a deletion within haplogroup (hg) C(*)(xC3a,C3c) found in 18 Asian males. The nonrandom phylogenetic distribution of duplication and deletion events suggests possible structural predisposition to such mutations in hgs C and G.

FIGURE 1

Deletions and duplications of DYS448 caused by rearrangements within the proximal AZFc region. a: Reference sequence organization around DYS448, showing position of the microsatellite on an idiogram of the Y chromosome (with genome position of start of the marker given according to build 36.1 of the reference assembly), and below, a schematic view of the region around DYS448, including large ampliconic repeat units shown as arrows (nomenclature in key after Kuroda-Kawaguchi et al. [2001]). Paralogous repeat copies are indicated by shading or hatching, as indicated in the key to the right. STSs used in mapping are shown below, and the gray curved arrow indicates putative sites of unequal exchange between the b1 and b3 repeat units. The positions of the multi-locus microsatellite DYS464 are also shown. b: Mapping of presence (+) or absence (−) of STSs in DYS448 deletion chromosomes, and proposed extents of deletions in the six different classes. The duplicated nature of sY1161 means that this marker is uninformative in the non-b1/b3 class III deletion (indicated as“−” in parentheses). c: Genes in the region, based on the reference sequence [Skaletsky et al., 2003]. Names above the line are protein-coding genes, and names below are nontranslated genes (in gray). d: Putative b1/b3-mediated arrangement of region in DYS448 duplication chromosomes.

FIGURE 2

Haplogroups andY-STR haplotypes of DYS448 deletion and duplication chromosomes. a: Binary marker phylogeny of the Y chromosome, with haplogroups (hg) [Y Chromosome Consortium, 2002] containing DYS448 deletion (“448del”) and duplication (“448dup”) chromosomes indicated by colored circles. Binary markers (e.g., M175) used to define haplogroups are given above each branch. C3*(xC3a,C3c) is abbreviated as C3*(xa,c). b: Weighted median joining network [Bandelt et al., 1999] representing the molecular relationships between the 19-locusY-STR haplotypes of 27 deletion and nine duplication chromosomes. Circles represent haplotypes, with area proportional to frequency and colored according to haplogroup as in (a). Lines between circles represent microsatellite mutational steps, and asterisks indicate root nodes used for dating purposes.

FIGURE 3

Examples of electropherograms showing variation in the number of alleles of microsatellite DYS464. a–f: different numbers of DYS464 alleles seen in deletion and duplication chromosomes. Note the differences in peak heights, e.g., (c), which could be regarded as a 3:1 ratio. Ratios are not reliable enough to predict relative copy number (see text). Vertical gray bars indicate allele “bins”, defined in GeneMapper (Applied Biosystems). Allele designations, boxed below each peak, are in repeat number. RFU, relative fluorescent units.