Exceptional Chromosome Regions II



Integration of Telomere Sequences with the Draft Human Genome Sequence

Robert K. Moyzis
University of California, Irvine

PowerPoint Presentation

Human telomeres end with a stretch of the conserved simple repeat sequence (TTAGGG)n. To capture single-copy human DNA regions linked to telomeres, large telomere-terminal fragments of human chromosomes were cloned using specialized yeast artificial chromosome (YAC) vectors. By contrast, bacterial artificial chromosome (BAC) libraries are not expected to contain sequences extending to the telomere, owing to the absence of restriction sites in (TTAGGG)n, the effects of length associated with the construction of size-selected DNA recombinant clones, and the genomic instability of these regions. By DNA end-sequencing of cosmid subclones derived from telomere YACs, connection to the working draft human sequence has now been accomplished (Riethman et. al., Nature 409, 948-951, 2001; www.genome.uci.edu ). Integration with the working draft sequence was confirmed for 32 telomeres (out of the 46 distinct ends), with framework sequence extending to within 250kb-50kb of the physical end of these chromosomes. The remaining 14 telomere ends have not been connected, due to 1) inability to obtain YAC clones (5p and 20q), 2) the lack of extension of the working draft sequence into telomeric regions, and/or ambiguous identification due to repetitive sequences (2q,7p,17p,17q,19p,19q,and Xp/Yp), and 3) cloning instability/repeats in the ribosomal gene containing acrocentric chromosomes (13p,14p,15p,21p, and 22p). Subtelomeric sequence structure appears to vary widely, mainly as a result of large differences in subtelomeric repeat sequence abundance and organization at individual telomeres. Many subtelomeric regions appear to be gene-rich, matching both known and unknown expressed genes.

The successes and problems encountered with human telomeric regions suggest a number of directions that future research on ECRs might take:

  1. A focused effort to confirm current assemblies and close remaining gaps will be critical. These are difficult regions, and must be attacked by a variety of methods. RARE cleavage analysis (to determine gap length/assembly consistency) and TAR cloning (to target gaps), have great potential.
  2. The great variability in subtelomeric (and other ECR) regions between individuals has potential biological significance. Finishing a "single" sequence in these regions has little meaning, without extensive population/species sampling. A number of ECRs should be targeted for "high-depth" reanalysis/resequencing/haplotyping.

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