Repetitive DNA sequences in the horse genome

Mammalian genomes, are composed of several different classes of DNA sequence including coding genes, regulatory elements, satellite repetitive elements, and interspersed repetitive elements. DNA satellite sequence and interspersed repetitive sequence within the genome of Equus caballus (domestic horse) were investigated and their distribution in the genomes of other equid species explored.;A 22 base long satellite was cloned from the horse genome and characterized for sequence variation and chromosomal distribution. The satellite was physically mapped to chromosomes of several species in the genus Equus by Fluorescent In Situ Hybridization (FISH). FISH signal was observed near the centromeres of 15/18 acrocentric horse chromosomes and 2/13 metacentric; horse chromosomes. For other equid species, FISH signal was observed at either centromeres or telomeres in a pattern consistent with phylogenetic relationships. These data provided insights into the comparative morphology of chromosomes of species in the genus Equus.;Two families of Short Interspersed Nucleotide Elements (SINEs) were identified that were associated with (AC)n microsatellite markers. These two families, ERE-1 and ERE-2, were 220 and 160 bases long respectively and were homologous over a 60 base long region. In addition, there were instances when either ERE-1 or ERE-2 were present in the promoter region, intron, or coding region of horse genes. FISH data indicated that ERE-1 and ERE-2 were interspersed across the chromosome arms of the horse genome. Analysis of base content of horse microsatellite markers indicated that there was a tendency for ERE-1 and ERE-2 to be present in GC-rich portions of the genome.;Clones for 16 cDNAs were identified that had sequence homologous to ERE-1 or ERE-2. Of these 16 clones 13 possessed ERE in a positive orientation immediately adjacent to the polyA tail. For 7 of the clones it was possible to identify homology to human transcribed sequence. In addition, 3 horse cDNA sequences from genbank were identified that possessed ERE-2. These data indicated that ERE-1 and ERE-2 can be associated with transcribed sequence in the horse genome and may have the capacity to influence polyadenylation of transcripts.