CHARACTERIZATION OF ALU REPEATS THAT ARE ASSOCIATED WITH TRINUCLEOTIDE AND TETRANUCLEOTIDE REPEAT MICROSATELLITES

The association of subclasses of Alu repetitive elements with various classes of trinucleotide and tetranucleotide microsatellites was chara cterized as a first step toward advancing our understanding of the evo lution of microsatellite repeats. In addition, information regarding t he association of specific classes of microsatellites with families of Alu elements was used to facilitate the development of genetic marker s. Sequences containing Alu repeats were eliminated because unique pri mers could not be designed. Various classes of microsatellites are ass ociated with different classes of Alu repeats. Very abundant and poly( A)-rich microsatellite classes (ATA, AATA) are frequently associated w ith an evolutionarily older subclass of Alu repeats, AluSx, whereas mo st of GATA and CA microsatellites are associated with a recent Alu sub family, AluY. Our observations support all three possible mechanisms f or the association of Alu repeats to microsatellites. Primers designed using a set of sequences from a particular microsatellite class showe d higher homology with more sequences of that class than probes design ed for other classes. We developed an efficient method of prescreening GGAA and ATA microsatellite clones for Alu repeats with probes design ed in this study. We also showed that Alu probes labeled in a single r eaction (multiplex labeling) could be used efficiently for prescreenin g of GGAA clones. Sequencing of these prescreened GGAA microsatellites revealed only 5% Alu repeats. Prescreening with primers designed for ATA microsatellite class resulted in the reduction of the loss of mark ers from similar to 50% to 10%. The new Alu probes that were designed have also proved to be useful in Alu-Alu fingerprinting.