The goal of this work is to understand the structure and possible function of highly repeated DNA sequences and to elucidate the mechanisms by which such sequences are amplified either in tandem (satellite DNA) or though transposition to new genomic loci (interspersed repeats). One particular single copy sequence that is conserved in primates and rodents and is joined to species specific satellite DNA in each species analyzed is being characterized. This single copy sequence is located close to the Huntington's disease locus on human chromosome 4p16. Also, the extensive and rapid changes that occur in satellite DNA are being applied to taxonomic and evolutionary problems: in particular, evolutionary relationships in the carnivores are being investigated. To understand the significance of the LINE-1 family of interspersed repeats, the potential for some family members to be functional genes and encode a protein is being investigated. cDNA clones representing polyadenylated, cytoplasmic LINE-1 RNA from human teratocarcinoma cells have been isolated; they define a subset of LINE-1 sequences that appear to be specifically transcribed (or processed) in these cells and must thus be associated with specific transcriptional regulatory sequences. Comparison of the cDNAs indicates an overall structure that contains two open reading frames (ORFs) separated by two in- frame stop codons bracketing 33 bp. Conceptual translation of the 3' ORF (1284 codons) indicates a polypeptide with striking homologies to retroviral and retrotransposon reverse transcriptase. Sequence analysis of a feline LINE-1 allowed us to demonstrate that the reverse transcriptase homology is markedly conserved in LINE-1s from 4 mammalian orders. In vitro translation experiments demonstrate that at least one of the cDNAs can represent a functional mRNA for the 5'-ORF. Overall the data suggest that LINE-1 and retroviruses may share a common ancestor and that reverse transcriptase-encoding sequences have been preserved by selective pressure in mammals.
