Exceptional Chromosome Regions II



Status Report on Gap Closure of the Human Chromosome 5 BAC Map

Steve Lowry, Joel Martin, Duncan Scott, and Jan-Fang Cheng
Lawrence Berkeley National Laboratory, Joint Genome Institute

The human chromosome 5 BAC contig map is being assembled by restriction fragment overlaps and sequence overlaps. Other information used to confirm the map include BAC end sequence matches, FISH data, UniSTS matches, and FPC data. The current chr5 map consists of 95 gaps with bridging clones (from the FPC map) and 33 gaps with no bridging clones. We compared the flanking sequences of the 33 unbridged gaps with Celera assembled sequence and found that 11 are located within a scaffold, suggesting that these gaps are clonable by E coli vectors. The reminding 22 gaps include the 5p telomeric region and a gap surrounding the centromere. For the 5q telomeric region, the work of Dr. Harold Riethman's group has identified a half-YAC telomeric clone spanning the 120kb gap between the telomeric end of RP11-324K20 (the most distal BAC on 5q) and the molecular telomere. A cosmid contig is being constructed for sequencing. The most distal BAC on 5p, RP11-811I15, whose physical distance from the molecular telomere is not known, contains characteristic subtelomeric repeats. For the pericentromeric regions, 6 YACs were identified to span 1.9 Mb and 2.7 Mb of the p and q arms, respectively. The alphoid repeat subsets were found in the YACs flanking the centromere. Restriction maps from digests with 5 rare cutters have been determined for the 6 YACs and can be used to estimate the size of the gaps between BAC contigs surrounding the centromere. We are in the process of screening additional human BAC libraries to fill the remaining physical gaps.

Other regions requiring careful scrutiny are those containing conflicting map and sequence data. For instance, we have found 24 BAC sequences containing UniSTSs from more than one chromosome even though they all mapped to chr5 by FISH. In 7 BACs, the sequences containing multi-chromosomal UniSTSs were assembled into a single sequence contig. Possible explanations are chimeric clones, interchromosomal duplications, or misassembly. The other 17 dubious sequences may contain mixed projects since the UniSTSs hit different sequence contigs. We also have 23 BACs that were mapped to chr5 by FISH but contain UniSTSs from other chromosomes. This apparent discrepancy may be the result of interchromosomal duplications or clone/sequence mistracking. There are three large intrachromosomal duplicated segments on chr5, one on the p arm and two on the q arm. The BACs spanning these regions can be identified in FISH hybridization.

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