A SINGLE-PRIMER PCR-BASED RETROVIRAL-RELATED DNA POLYMORPHISM SHARED BY 2 DISTINCT HUMAN-POPULATIONS

Almost 10% of the human genome consists of DNA sequences that share ho mology with retroviruses. These sequences, which represent a stable co mponent of the human genome (although some may retain the ability to t ranspose), remain poorly understood. We used degenerate primers specif ic to the two conserved regions (boxes 4 and 5) of the retroviral pol gene, common to all retroviruses, and PCR-amplified related sequences from individuals representing two distinct populations: Caucasians and Dogrib Indians. The large number of sequences that are reproducibly a mplified represent numerous sites of retroviral integration in the hum an genome. In both populations studied, one of the two primers yielded a polymorphic band, present in similar to 30% of the samples, that ha s probably been present in the human genome since before the divergenc e of the two populations similar to 10000 years ago. It was establishe d that this polymorphism was due to priming-site differences and not t o deletions. Further, this priming site is duplicated at two genomic s ites (representing 341- and 343-bp fragments) with at least two allele s each. Such novel polymorphisms should provide useful markers and per mit assessment of evolutionary mechanisms associated with retroviral-r elated genomic evolution.