We have identified two allelic genomic cosmids from human chromosome 2, c8.1 and c29B, each containing two inverted arrays of the vertebrate telomeric repeat in a head-to-head arrangement, 5'(TTAGGG),,-(CCCTAA),,3'. Sequences fln g this telomeric repeat are characteristic of present-day human pretelomeres. BAL-31 nuclease experiments with yeast artificial chromosome clones of human telomeres and fluorescence in situ hybridization reveal that sequences flanking these inverted repeats hybridize both to band 2q13 and to different, but overlapping, subsets of human chromosome ends. We conclude that the locus cloned in cosmids c8.1 and c29B is the relic of an ancient telomeretelomere fusion and marks the point at which two ancestral ape chromosomes fused to give rise to human chromosome 2.Similarities in chromosome banding patterns and hybridization homologies between ape and human chromosomes suggest that human chromosome 2 arose out of the fusion of two ancestral ape chromosomes (1-3). Molecular data show evidence that this event must have occurred only a few million years ago (refs. 4 and 5 and the references therein). Although the precise nature of this putative fusion is unknown, cytogenetic data point to either a centromeric or telomeric fusion in the vicinity of region 2ql (1, 2, and 6). The observation that telomeric DNA is present in chromosomal band q13 suggests that telomeres, the extreme ends of chromosomes, may have been involved in this fusion (7,8). Normally, telomeres form a dynamic buffer against loss of internal sequence and prevent chromosomes from fusing (for review, see ref. 9). By contrast, nontelomeric DNA ends are subject to degradation by nucleases and to fusion by ligation (10,11).The termini of human chromosomes consist of head-to-tail tandem arrays ofTTAGGG, running 5'--3' toward the end of the chromosome, with average lengths of 5-10 kilobases (kb) in somatic cells (7,12,13). The proximal ends of these arrays contain degenerate forms of this repeat, such as (TTGGGG), and (TGAGGG)J, (14). Sequences adjacent to these simple repeats have been characterized in a number of human chromosomes and shown to consist of repetitive elements, each shared by a subset of all chromosomes (13,(15)(16)(17). In addition, stretches of telomeric repeats are present at interstitial sites, usually in subtelomeric regions but also at a distinct internal site within band 2q13 (8). We describe here the architecture of the sequence at this internal locus at 2q13, which represents a relic of the fusion of two ancestral ape chromosomes in the evolution ofhuman chromosome 2. 11 MATERIALS AND METHODS Library Screening. Approximately 1.4 x 106 colonies from a human genomic cosmid library containing Mbo I partial digestion fragments of 35-41 kb in vector pWE15, propagated in host NM554 (Stratagene), were screened with pSC4, a human genomic 300-base-pair (bp) Alu I fragment present at the subtelomeric regions offive different chromosomes, as well as at a single nonterminal locus at 2q13, described elsewhere (8). ...