A simple method for rapid isolation of microsatellites from yeast artificial chromosomes

Microsatellites are widely recognised as providing a rich source of polymorphic markers for genetic mapping. Consequently, highly polymorphic CA repeats tightly linked to a disease locus are invaluable tools in linkage studies. We have developed an efficient technique for cloning microsatellite repeats from a region of interest contained within a yeast artificial chromosome (YAC). The YAC material is digested with a frequent cutting restriction endonuclease and ligated to polymerase chain reaction (PCR) amplifiable catch-linkers. A 5' biotinylated (CA)11 oligonucleotide is then used to select fragments containing a complementary repeat by binding to streptavidin-coated magnetic beads. The catch-linkers enable these fragments to be PCR amplified, cloned and sequenced. Primers are then designed to amplify the repeat locus and to confirm its genomic localization and heterozygosity. We have successfully used this technique to clone a new (CA)18 microsatellite from a 360-kb YAC. The YAC contains the CYBB locus in Xp21.1 and is thought to contain at least part of the RP3 gene responsible for X-linked retinitis pigmentosa. This new CA repeat is highly polymorphic with nine alleles identified so far and a heterozygosity of 0.75.