Segmental polymorphisms in the proterminal regions of a subset of human chromosomes

Abstract

The subtelomeric domains of chromosomes are probably the most rapidly evolving structures of the human genome. The highly variable distribution of large duplicated subtelomeric segments has indicated that frequent exchanges between nonhomologous chromosomes may have been taking place during recent genome evolution. We have studied the extent and variability of such duplications using in situ hybridization techniques and a set of well-defined subtelomeric cosmid probes that identify discrete regions within the subtelomeric domain. In addition to reciprocal translocation and illegitimate recombination events that could explain the observed mosaic pattern of subtelomeric regions, it is likely that homology-based recombination mechanisms have also contributed to the spread of distal subtelomeric sequences among particular groups of nonhomologous chromosome arms. The frequency and distribution of large-scale subtelomeric polymorphisms may have direct implications for the design of chromosome-specific probes that are aimed at the identification of cryptic subtelomeric deletions. Furthermore, our results indicate that the relevance of some of the telomere closures proposed within the present Human Genome Sequence draft are restricted to specific allelic variants of unknown frequencies.

Figure 1

(A) Cartography of the subtelomeric domain common to Chromosome arms 1p/q, 5q, 6q, and 17q (Monfouilloux et al. 1998). The arrows indicate the limit between the subtelomeric domain and chromosome-specific sequences for three of the chromosomes. This limit has not been found for 1p/qter. The limits between regions have been previously defined (Monfouilloux et al. 1998; Vergnaud 1999), and their relative positions are indicated here. The length of the lines approximately corresponds to the size of the cosmid probes used in this study. Extremities of the same color indicate actual overlapping among clones. (B) Colocalization of probes by two-color FISH. (Left) Cohybridization obtained using region 1 probes (red and green). Chromosomes are counterstained with DAPI. Chromosome arms bearing presence/absence polymorphisms are indicated. All other locations are homozygous in this individual. (Right) Cohybridization using probes specific to regions 1 (green) and 3 (red). Arrows indicate colocalization. The 5C4 probe also hybridizes to interstitial locations (indicated with an asterisk) on Chromosomes 1, 4, 7, and 10. The results presented in Table 1 and Figure 2 only take into account signals that are distinct and consistently detected (i.e., are present in all metaphases analyzed from an individual).

Figure 2

Cartography by FISH of the subtelomeric domains observed in 18 nonrelated individuals (36 haploid genomes). Colored boxes indicate that a consistent fluorescent signal was observed with the corresponding cosmid probe (color code for probes is as in Fig. 1), whereas their absence indicates no fluorescent signal obtained. The cohybridization of probes allowed, in all cases showing presence/absence of polymorphisms, the distinction between homologous chromosomes and the reconstitution of subtelomeric domains for individual chromosome arms. For a given combination, certain regions showed differences in fluorescence intensity between chromosome arms (not noted here), which may reflect additional size or sequence heterogeneity. The variants A to P were first arranged according to their complexity within the more proximal half of the subtelomeric domain, and then, within each group, according to the complexity of the more distal half. Variant Z corresponds to the absence of signal for all probes used (null allele). Homologous recombination events implicating the more proximal half of subtelomeric domains may have contributed to the shuffling of more distal sequences among the chromosome arms contained within the solid-line rectangles. The dotted rectangles outline invariable loci. (*) 34 observations, the remaining two correspond to f7501/DNF92 colocalizations in which a subtelomeric structure of type J/K was detected. (**) Out of 10 male individuals.

Figure 3

(Left) Schematic representation of the segmental organization of large genomic fragments. The colored boxes (drawn to scale) represent the different subtelomeric segments according to the code in Figure 2. All sequences are identified by their accession numbers (only finished, not draft, sequences were analyzed). The proposed chromosome location is also indicated. AC004842 is assigned to 7p22 in the GenBank; however, a 6p location was found using the Genebridge4 hybrid panel (Y.-M. Borde, unpubl.). Similarly, AC004908 (no chromosomal location indicated by NCBI) has been assigned to Chromosome 8p using the Genebridge4 hybrid panel (Y.-M. Borde, unpubl.). AL627309 (previously named AC073186) has been successively assigned to Chromosomes 7, 21, and, more recently, 1, illustrating the difficulties of assigning subtelomeric genomic fragments with no obvious connection to chromosome-specific sequences. The black box represents a novel region not included in our FISH studies. (Right) Proposed illegitimate recombination events leading to the incorporation of an intervening subtelomeric region. The color code is as above with lighter colors representing the boundaries of the corresponding regions. Boxes are not drawn to scale. The sequence AC005627 carries the ancestral configuration, and AC004908 represents one of the final products after a double recombination event, implicating sequences similar to the ones found in AC005604 and AC055861. Although not found in the sequence database, the reciprocal product may correspond to the E variant observed by FISH in the population.