A single-primer PCR-based retroviral-related DNA polymorphism shared by two distinct human populations

Almost 10% of the human genome consists of DNA sequences that share homology with retroviruses. These sequences, which represent a stable component of the human genome (although some may retain the ability to transpose), remain poorly understood. We used degenerate primers specific 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 amplified represent numerous sites of retroviral integration in the human genome. In both populations studied, one of the two primers yielded a polymorphic band, present in approximately 30% of the samples, that has probably been present in the human genome since before the divergence of the two populations approximately 10,000 years ago. It was established that this polymorphism was due to priming-site differences and not to deletions. Further, this priming site is duplicated at two genomic sites (representing 341- and 343-bp fragments) with at least two alleles each. Such novel polymorphisms should provide useful markers and permit assessment of evolutionary mechanisms associated with retroviral-related genomic evolution.