The evolutionary origin of human subtelomeric homologies--or where the ends begin

Abstract

The subtelomeric regions of human chromosomes are comprised of sequence homologies shared between distinct subsets of chromosomes. In the course of developing a set of unique human telomere clones, we identified many clones containing such shared homologies, characterized by the presence of cross-hybridization signals on one or more telomeres in a fluorescence in situ hybridization (FISH) assay. We studied the evolutionary origin of seven subtelomeric clones by performing comparative FISH analysis on a primate panel that included great apes and Old World monkeys. All clones tested showed a single hybridization site in Old World monkeys that corresponded to one of the orthologous human sites, thus indicating the ancestral origin. The timing of the duplication events varied among the subtelomeric regions, from approximately 5 to approximately 25 million years ago. To examine the origin of and mechanism for one of these subtelomeric duplications, we compared the sequence derived from human 2q13--an ancestral fusion site of two great ape telomeric regions--with its paralogous subtelomeric sequences at 9p and 22q. These paralogous regions share large continuous homologies and contain three genes: RABL2B, forkhead box D4, and COBW-like. Our results provide further evidence for subtelomeric-mediated genomic duplication and demonstrate that these segmental duplications are most likely the result of ancestral unbalanced translocations that have been fixed in the genome during recent primate evolution.

Figure 1

Results of FISH for BAC 136B17 (from human chromosome 4p) on selected members of the primate panel. In human (A), this clone hybridizes to the 4p telomere (large arrows) and to the 1p telomere (small arrows), with the signal intensity being greater on chromosome 4p. Only one hybridization signal (large arrows) is observed for this clone in chimpanzee (B) and macaque (C), both of which correspond to the region orthologous to the human 4p telomere. Similar results were obtained for gorilla, orangutan, and baboon.

Figure 2

Summary of FISH results from seven human genomic clones tested on the primate panel. The evolutionary lineage between the primates tested is depicted above the table; the molecular time scale used is adopted from Kumar and Hedges (1998) and is indicated in millions of years (Myr). For all clones, the chromosomal localization for FISH hybridization is listed by reference to the human ortholog. The hybridization signal was observed at the telomere region of each chromosome, unless otherwise noted. HSA = human; PTR = chimpanzee; GGO = gorilla; PPY = orangutan; OWM = Old World monkeys (macaque and baboon); pericen. = pericentromeric. Clones listed as having “other” hybridization signals indicate that additional hybridization signals were observed that were characterized by number of signals and chromosomal position, as indicated by the following superscripts: 1 = two telomere regions; 2 = one telomere region; 3 = three telomere regions and one interstitial region; and 4 = three telomere regions.

Figure 3

The genomic region of the ancestral telomere fusion site at human 2q13. An idiogram of human chromosome 2 is shown at the top. An expanded physical map is shown below the idiogram, with distance in kilobases from the telomere fusion site (indicated by the “0” point). The BAC contig that covers the region is shown by blackened rectangles under the chromosome. The physical maps of chromosome 22q (from GenBank accession number NT011526; Dunham et al. 1999) and chromosome 9p are shown below the chromosome 2q13 region, for comparison. On the distal side of the fusion site, the subtelomeric region is homologous to the 68-kb subtelomeric region at 22q, as represented by the rectangular pattern in both chromosomes 2 and 22. Two genes, RABL2A and RABL2B, are within these homologous regions on chromosomes 2 and 22, respectively. The “breakpoint” of this homologous region is within the acrosin (ACR) locus on chromosome 22q. The telomeric repeat (TTAGGG)_n is represented by a solid gray box at the end of chromosome 22 and chromosome 9. Chromosomes 2 and 9 share ∼189 kb of homologous subtelomeric sequence (indicated by a checker pattern on both chromosomes). The dashed lines at the telomere of chromosome 9 show a 58-kb region that is not covered by any BAC clones. Two genes, FKHL9 and COBW-like (COBWL), as well as a partial PGM5, are duplicated on chromosomes 2 and 9. Proximal to the ancestral subtelomeric domain on chromosome 2, a 100-kb region (marked by diagonal lines) is duplicated at 2q11.2 (marked by the box with diagonal lines above the clones RPCI11-34G16 and RPCI11-440D17).

Figure 4

Hybridization of BAC CITB-HSP-305J7 to various primate metaphase cells. In human (A), strong hybridization is visible at the 9p telomere (large arrows) and the pericentromeric region (small arrows) of chromosome 9. A weaker hybridization signal is present at 2q13 (arrow heads). In chimpanzee (B), hybridization signals are present at the sites orthologous to the human 9p telomere (large arrows), 9p11 (small arrows), and 2q13 (arrow heads). Additional hybridization signals were observed in chimpanzee, to two telomeric regions. In gorilla (C), orangutan (D), and macaque (E), only a single hybridization signal (large arrows) is observed, at an interstitial site that is orthologous to the human 9p telomere.

Figure 5

Proposed sequence of duplication of the 9p subtelomeric sequence. The sequence of changes is indicated by the arrows, proceeding from the top to the bottom of the figure. A, In gorilla (GGO), the human 9p subtelomeric sequence is within an interstitial region of the orthologous chromosome. A pericentric inversion relocated this sequence to the subtelomeric region, as in human (HSA) and chimpanzee (PTR). This 9p subtelomeric region is partially transposed to the centromere of PTR 11 (HSA 9). In human, the copy at the chromosome 9 centromere is further duplicated around the pericentromeric region. B, Duplication of 9p subtelomeric sequence to PTR 12 through a translocation event between the telomeres. Two great ape chromosomes (PTR 12 and PTR 13) fused to form human chromosome 2, which fixed this subtelomeric sequence at an interstitial position.

Figure 6

A dot plot comparison between the homologous subtelomeric sequences of the 2q13 and 22q regions (A) and the distal subtelomeric domains of 22q and 4p (GenBank accession number Z95704) (B). The subtelomeric 22q sequence contains the acrosin gene (ACR; the last two exons are included), a minisatellite repeat 3′AR, a processed pseudogene U2 snRNP specific polypeptide A (U2snRNP), and the RABL2B gene. All exons are highlighted in yellow, and other sequences are in gray. The degenerative (TTAGGG)_n repeat sequence, which marks the boundary of the proximal and distal subtelomeric domains, is highlighted in pink.

Figure 7

Hybridization of BAC RPCI11-480C16 to a human metaphase cell. Two hybridization signals are observed on human 2q: one at 2q13 (large arrows) and one at 2q11.2 (small arrows). Hybridization signals are also observed in the chromosome 9 pericentromeric region (arrow heads). The inset shows enlargements of the chromosome 2 and 9 homologs; the capture time for the Spectrum Orange signal was increased, to show the hybridization signal at the 9p telomere (yellow arrow).