Synthesis and analysis of a 640-bp pol region of novel human endogenous retroviral sequences and their evolutionary relationships.

Nucleotide sequence comparisons of the pol gene among 47 retroelements identified two very conserved regions, separated by a span of approximately 640 bp, that have not been previously reported. A set of mixed oligonucleotide primers, 5'-MOP-2 and 3'-MOP-2, homologous to these two conserved pol regions was constructed for use in detection of retroelements. When MOPs-2 were employed in PCR amplification studies, products of about 0.64 kb in size were amplified from human and mouse genomic DNAs and from HIV-1 proviral DNA, but not from negative control plasmid DNAs. The PCR products amplified with MOPs-2 from human LuC-1 teratocarcinoma cell DNA were subcloned and sequenced. Five clones of approximately 0.64 kb in size were identified, and sequence comparisons with all entries in GenBank indicated that these five clones have highest homology, in a range of 64.31 to 98.65%, with the corresponding pol region of HERV-K10 and HM-16 of the human endogenous retrovirus-K (HERV-K) family. Southern hybridizations at high stringency demonstrated that these five clones are present in all human DNAs tested. The evolutionary relationships of these clones with the equivalent pol region of other retroelements were defined by phylogenetic analyses that placed three clones into the HERV-K family and two clones into a new family of human endogenous retroelements. In addition, clone HERV-(K)73 contains the smaller PV1b pol segment that was reported to be selectively expressed in blood leukocytes of patients with polycythemia vera.