High levels of sequence polymorphism and linkage disequilibrium at the telomere of 12q: implications for telomere biology and human evolution

Abstract

The human Xp/Yp telomere-junction region exhibits high levels of sequence polymorphism and linkage disequilibrium. To determine whether this is a general feature of human telomeres, we have undertaken sequence analysis at the 12q telomere and have extended the analysis at Xp/Yp. A total of 22 single-nucleotide polymorphisms (SNPs) and one 30-bp duplication were detected in the 1,870 bp adjacent to the 12q telomere. Twenty polymorphic positions were in almost complete linkage disequilibrium, creating three common diverged haplotypes accounting for 80% of 12q telomeres in the white population. A further 6% of 12q telomeres contained a 1,439-bp deletion in the DNA flanking the telomere. The remaining 13% of 12q telomeres did not amplify with the primers used (nulls). The distribution of telomere (TTAGGG) and variant repeats within 12q telomeres was hypervariable, but alleles with similar distribution patterns were associated with the same haplotype in the telomere-adjacent DNA. These data suggest that 12q telomeres, like Xp/Yp telomeres, exhibit low levels of homologous recombination and evolve along haploid lineages. In contrast, high levels of homologous recombination occur in the adjacent proterminal regions of human chromosomes. This suggests that there is a localized telomere-mediated suppression of recombination. In addition, the genetic characteristics of these regions may provide a source of deep lineages for the study of early human evolution, unaffected by both natural selection and recombination. To explain the presence of a few diverged haplotypes adjacent to the Xp/Yp and 12q telomeres, we propose a model that involves the hybridization of two archaic hominoid lineages ultimately giving rise to modern Homo sapiens.

Figure 1

An example of a BsmI RFLP assay. This assay identifies both the −473 SNP (upper two fragments) and the −(659–630) insertion/deletion polymorphism (lower two fragments). Note the association between the polymorphisms observed in DNAs that are either homo- or heterozygous for both.

Figure 2

Diagrammatic representation of the 12q telomere–adjacent DNA. The positions of primers used for PCR analysis are denoted by a horizontal arrow, and polymorphic sites are denoted by a vertical arrow. Polymorphic sites used either in the RFLP analysis or for allele-specific amplification are denoted by their position with respect to the first telomere repeat. Homologies with other subtelomeric sequences are indicated.

Figure 3

DNA sequence of the 12q deletion allele compared with the sequences of haplotypes A and B. a, The sequences of the telomere-repeat arrays from one deletion allele and from haplotype A and B alleles are shown; TTAGGG repeats are indicated by boldface text; TCAGGG repeats, by underlined text; TGAGGG repeats, by italicized text; and other repeats, by plain text. b, Diagram representing the deletion allele and telomere-repeat array. c, Sequence features of the deletion breakpoint include a 19-bp inverted repeat sequence, which is indicated by bold italicized text; note the single sequence difference (indicated by plain text) between the two copies of the inverted repeat. Also shown are the duplication of the proximal 10 bp of the inverted repeat sequence (horizontal arrow), a 4-bp inverted repeat sequence immediately distal to the breakpoint (indicated by underlined text), and sequence differences between the deletion allele and the haplotype A proximal to the breakpoint (indicated by boldface text).

Figure 4

Telomere variant-repeat codes derived from 12q telomeres in the white population. These codes were generated from the −197 polymorphism in individuals who were hetero- or hemizygous for the haplotypes in the 12q telomere–adjacent DNA. For each telomere code, the haplotype in the 12q telomere–adjacent DNA is indicated. Codes were grouped by visual inspection of the patterns, according to coding similarities. Repeat types are represented as follows: dash (-) = TTAGGG; G = TGAGGG; C = TCAGGG; and N = unknown repeat type. The TVR codes from two deletion alleles, Δ, were generated from the deletion-specific primer 12qnull3.

Figure 5

An example of an autoradiograph of the 12q-specific TVR-PCR reactions. Five allele-specific TVR-PCR reactions are shown. Primer 12q-197A was used to amplify haplotype A and A1 alleles specifically; primer 12q-197G, to amplify haplotype B alleles; and 12qdel, to amplify the deletion-associated telomeres. The repeats are numbered from the first repeat in the 12q telomere–repeat array, as shown. The 12q-197G primer is capable of annealing to the 7q telomere–adjacent DNA; consequently, 7q-specific products can be generated with use of this primer. These are observed in the T and C lanes of one HapB telomere (indicated by an asterisk [*]); the bands are bracketed on the right side of the autoradiograph. Repeat types are represented as follows: T = TTAGGG, G = TGAGGG, and C = TCAGGG.

Figure 6

Xp/Yp-telomere codes derived from 22 Africans and from one white individual. Two types of TVR codes were observed. One, which starts with the characteristic repeat motif GNNTCCNNNN…, is common in the African population and is associated with the telomere-adjacent haplotype D in the two individuals (10202 and AF28, who are denoted by an asterisk [*]) analyzed. Individual 10202 is white. The other African TVR codes that are shown start with the NNGGGGGG repeat motif that is characteristic of the Xp/Yp haplotype A–associated TVR codes in white individuals. The different repeat types are represented by the same characters that are used in figure 4.