Isolation and phylogeny of new endogenous retroviral sequences belonging to the HERV-F family

Abstract

A new human endogenous retroviral family (HERV-F) has been identified from human chromosome 7q31.1-q31.3 that was identical to the XA34 cDNA clone isolated from a human glioma cDNA library with an ERV-9 env probe. We investigated pol gene sequences of the HERV-F family from a human monochromosomal DNA panel and analyzed these with HERV-F. The pol gene sequences of the HERV-F family were detected on chromosomes 3, 6, 7, 10, 11, 14, 19, 20, X, and Y as examined by PCR. Thirty-six pol gene sequences identified from the human chromosomes have a high degree of sequence similarity (80-99%) with that of the HERV-F. Phylogenetic analysis of pol gene sequences distinctively showed four groups, indicating that the HERV-F family could be amplified at least four times after the original integration into the human genome or represent integration events separately during hominid evolution. One clone (HFY-3) on chromosome Y shared 100% sequence identity with a clone (HF19-2) on chromosome 19, and a clone (HF20-6) on chromosome 20 suggests either a recent retrotransposition or a chromosomal translocation. The history of endogenous retroviral sequences may contribute to an understanding of evolutionary change in human genomes.