Identification of paralogous HERV-K LTRs on human chromosomes 3, 4, 7 and 11 in regions containing clusters of olfactory receptor genes

A locus harboring a human endogenous retroviral LTR (long terminal repeat) was mapped on the short arm of human chromosome 7 (7p22), and its evolution ary history was investigated. Sequences of two human genome fragments that were homologous to the LTR-flanking sequences were found in human genome da tabases: (1) an LTR-containing DNA fragment from region 3p13 of the human g enome, which includes clusters of olfactory receptor genes and pseudogenes; and (2) a fragment of region 21q22.1 lacking LTR sequences. PCR analysis d emonstrated that LTRs with highly homologous flanking sequences could be fo und in the genomes of human, chimp, gorilla, and orangutan, but were absent from the genomes of gibbon and New World monkeys. A PCR assay with a prime r set corresponding to the sequence from human Chr 3 allowed us to detect L TR-containing paralogous sequences on human chromosomes 3, 4, 7, and 11. Th e divergence times for the LTR-flanking sequences on chromosomes 3 and 7, a nd the paralogous sequence on chromosome 21, were evaluated and used to rec onstruct the order of duplication events and retroviral insertions. (1) An initial duplication event that occurred 14-17 Mya - and before LTR insertio n - produced two loci, one corresponding to that located on Chr 21, while t he second was the ancestor of the loci on chromosomes 3 and 7. (2) Insertio n of the LTR (most probably as a provirus) into this ancestral locus took p lace 13 Mya. (3) Duplication of the LTR-containing ancestral locus occurred I I Mya, forming the paralogous modem loci on Chr 3 and 7.