Towards a complete cosmid contig map of the short arm pseudoautosomal region

This thesis describes the building of a cosmid contig map across the short arm pseudoautosomal region (PAR1) of the sex chromosomes. The purpose being to prepare the region in a sequence ready format. Sequence Tagged Sites (STS) from this region were used to screen two Y Chromosome specific cosmid libraries. All clones hybridising to an STS were identified and fingerprinted. By digesting the cosmid with Hin f1 and end labelling, the fragments were then radio labelled and separated by polyacrylamide gel electrophoresis. A digitised image of this band pattern was used to deduce overlap between cosmids. Those clones that hybridised to the STS probes and also clones which by fingerprinting were deduced to be in the same contig were then amplified by PCR with the STS primers. This confirmed the presence of the STS in clones and provided regional localisation of the STS within the contig. The libraries were screened with probes generated from 57 loci of which 50 were STSs, 7 were single copy probes. Of the 57 loci used 52 are within PAR1, four are within the Y specific sequence just proximal to the pseudoautosomal boundary and the gene CD24 is on Yq. These probes have selected 646 cosmids. Of the 48 STSs which localise to PAR1, 42 have been localised to at least one cosmid. All non PCR generated probes have been localised. Between 60% and 80% of the 2.6 Mb of this region has been covered in cosmids.