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Human endogenous retroviruses (HERVs) make up a substantial part of the human genome. HERVs and solitary long terminal repeats (solo LTRs) are usually flanked by 4-6 nt short direct repeats through the well-known mechanism of their integration. A number of solo LTRs flanked by unusually long direct repeats were detected in the human genome. These unusual structures might be a product of an alternative virus insertion mechanism.

A chimeric long terminal repeat (LTR) containing the whole LTR of a human endogenous retrovirus-like element of the H family (HERV-H) inserted downstream of the core enhancer region of the 5' LTR of a HERV-K retroelement was detected and sequenced in the human 19p12 locus, known to be enriched with genes encoding zinc finger proteins. Similar chimeras were also detected in human chromosomes 10 and Y in human-hamster hybrid cells containing individual human chromosomes. This finding was interpreted as evidence of transpositions of the chimera in the genome. PCR analyses detected the chimera in the genomes of chimpanzee and gorilla, but not in that of orangutan. These data demonstrate that the chimera appeared in the primate germ cells more than 10 million years ago, before divergence of the human/chimpanzee and the gorilla lineages. The combination of the two LTRs forms a new regulatory system that can be involved in nearby gene expression.