HERV-F, a new group of human endogenous retrovirus sequences

Using primers from a conserved region of the XA34 human endogenous retrovir us (HERV) family, four pol fragments originating from new members of the fa mily were amplified from human genomic DNA, Southern blot analysis demonstr ated similar hybridization patterns in human, chimpanzee and orangutan and distinct hybridization to macaque DNA, The probes also exhibited weaker hyb ridization to squirrel monkey DNA, Using large genomic clones, two full-len gth XA34-related HERVs have been identified. One of the HERVs is located do wnstream of a human Kruppel-related zinc finger protein gene, ZNF195, Both of the newly identified long terminal repeats have potential TATA boxes, po ly(A) signals and transcription factor-binding sites but they differ to a h igh degree, especially in the U-3 region, The primer-binding sites were fou nd to be homologous to tRNA(Phe) (TTC), and therefore these new HERVs have been given the name HERV-F, The closest relatives to the HERV-Fs are the RT VLH-RGH family. Phylogenetic analyses of the Gag, Pol and Env regions are d iscussed. Both of the newly identified HERV-Fs were shown to contain protea se, reverse transcriptase, integrase and env regions and had characteristic deletions in the integrase and env regions. In addition, the capsid protei n gene of gag and two conserved zinc-binding motifs that are characteristic of a potential nucleic acid-binding protein were also identified. Apart fr om an ORF spanning the protease of one HERV-F, no other longer ORFs were fo und.