Human DNA contains many copies of endogenous retroviral sequences. Characterization of molecular clones of these structures reveals the existence of two related families. One family consists of full-length (8.8 kilobases) proviral structures, with typical long terminal repeates (LTR's). The other family consists of structures, which contain only 4.1 kilobases of gag-pol sequences, bounded by a tandem array of imperfect repeats 72 to 76 base pairs in length. Typical LTR sequences that exist as solitary elements in the genome were cloned and characterized.

Novel endogenous human retroviral sequences were cloned by low-stringency hybridization, using the pol gene of endogenous human retrovirus 51-1. One clone, ANP-2, contained gag, pol, env, and long terminal repeat sequences related to the corresponding portions of clone 51-1 and the closely related full-length endogenous human retrovirus 4-1. The sequence of the env gene of NP-2 was 73% homologous to that of 4-1. Genomic Southern blots of male and female DNAs showed that NP-2 is located on the Y chromosome and that the Y chromosome also contains one other sequence closely related to the env and 3' flanking regions of NP-2. Conservation of flanking DNA suggests that the second Y chromosome copy of the NP-2 env sequence arose by gene duplication rather than provirus insertion.Several different endogenous retroviral sequences have been identified in the human genome (1, 3, 4, 11-14, 18, 19, 25). To look for new classes of endogenous human retroviruses, we screened a recombinant bacteriophage human DNA library (9) with a pol probe from the well-characterized human endogenous retroviral sequence 51-1 (18, 19). A pol probe was used because this retroviral gene is highly conserved among different retroviral families (18,19). Recombinant bacteriophage clones were selected which hybridized at low stringency (membranes washed at 550C in 6x SSC [lx SSC is 150 mM NaCl plus 15 mM sodium citrate]) but not at high stringency (membranes washed at 68°C in 0.1 x SSC). At least 5 of 12 clones so selected appeared to have the structure of partial or complete retroviruses, since they also hybridized at low stringency to gag, env, or long terminal repeat (LTR) probes from human retroviral clones 51-1 and 4-1 (18, 25), and the relative positions of restriction fragments hybridizing to these probes were consistent, except for a few instances of apparent deletions, with the gene order LTR-gag-pol-env-LTR. One of these retroviral clones, ANP-2, was analyzed further because preliminary experiments indicated that the human population was highly polymorphic for NP-2-related sequences.A restriction map of the insert in clone XNP-2 is shown in Fig. 1. The position and approximate extent of gag, pol, env, and LTR sequences were determined by low-stringency hybridization with subregion probes from retroviral clones 51-1 and 4-1 (18, 25). To confirm that these crosshybridization reactions were indicative of extensive sequence homology, a 1.1-kilobase (kb) HindIII fragment from the env region of NP-2 (fragment a, Fig. 1) was sequenced. Overall, the sequence of this fragment was 73% homologous to that of the corresponding portion of 4-1 (Fig. 2). A small region of marked divergence (only 45% homology) was noted about one-third of the way into the env coding sequence of 4-1 (coordinates 6930 to 7050, Fig. 2). This region corresponds roughly to regions of hypervariability determining host range in replication-competent murine and avian retroviruses (6,7,15,16). The fact that 4-1 and NP-2 differ more in this region than in other regions of the env ge...

Novel endogenous human retroviral sequences were cloned by low-stringency hybridization, using the pol gene of endogenous human retrovirus 51-1. One clone, lambda NP-2, contained gag, pol, env, and long terminal repeat sequences related to the corresponding portions of clone 51-1 and the closely related full-length endogenous human retrovirus 4-1. The sequence of the env gene of NP-2 was 73% homologous to that of 4-1. Genomic Southern blots of male and female DNAs showed that NP-2 is located on the Y chromosome and that the Y chromosome also contains one other sequence closely related to the env and 3' flanking regions of NP-2. Conservation of flanking DNA suggests that the second Y chromosome copy of the NP-2 env sequence arose by gene duplication rather than provirus insertion.