The Xp/Yp telomere and its adjacent DNA : structure, sequence organisation and mutation

My research has focused on developing an understanding of processes operating in and around the Xp/Yp telomere, combined with detailed analysis of the unusual properties seen immediately adjacent to it. To this end, 7 kb of telomere adjacent-sequence was analysed, revealing a SNP density, pi, of 1.73 x 10-3 across the first 3 kb, 2-fold above average genome level. Furthermore, the sequence analysis revealed a 1.9 kb tandem duplication in 86% of chromosomes. This included the minisatellite DXYS14, and both copies were found to be hypervariable, with pedigree analysis revealing mutation rates of 0.94% and 0.62% for DXYS14a and DXYS14b respectively, with double mutations often occurring.;Haplotype analysis revealed strong SNP associations across the entire 7 kb region. High-resolution crossover analysis was carried out using allele-specific PCR methods to selectively amplify recombinant sperm molecules, which indicated that the Xp/Yp telomere-adjacent DNA is recombinationally inert, with a rate of 2.4 x 10-6 cM Mb-1 calculated from 1.250,000 amplifiable molecules.;It was thought secondary structure may be implicated in both the high SNP density and low recombination rate seen, so analysis of t-loops and nucleosome phasing was carried out at the Xp/Yp telomere. While the efficiency of t-loop visualisation prevented specific targeting of the Xp/Yp telomere, preliminary nucleosome data suggest that nucleosomes are present, but not phased in this region.;Finally, analysis was conducted on the presence of the CTAGGG variant repeat at the Xp/Yp telomere. This variant repeat is presented at ∼7% of Xp/Yp telomeres, and in CEPH families, two telomeres containing arrays of CTAGGG were shown to display a ∼46% germline mutation rate, higher than the 0.6% rate estimated in telomeres not harbouring this repeat. It is possible that secondary structure may be responsible for the instability associated with this repeat type.