Full-sized HERV-K (HML-2) human endogenous retroviral LTR sequences on human chromosome 21: map locations and evolutionary history

One of the evolutionary mechanisms for acquisition of novel functional sequ ences can be domestication of exogenous retroviruses, that have been integr ated into the germ line. The whole genome mapping of such elements in vario us species could reveal differences in positions of the retroviral integrat ion and suggest possible roles of these differences in speciation. Here. we describe the number, locations and sequence features of the human endogeno us retrovirus HERV-K (HML-2) long terminal repeat (LTR) sequences on human chromosome 21. We show that their distribution along the chromosome is not only non-random but also roughly correlated with the gene density. Amplific ation of orthologous LTR sites from a number of primate genomes produced pa tterns of presence and absence for each LTR sequence and allowed determinat ion of the phylogenetic ages and evolutionary order of appearance of indivi dual LTRs. The identity level and phylogenetic age of the LTRs did not corr elate with their map locations. Thus, despite the non-random distribution o f LTRs, they have apparently been inserted randomly into the chromosome rel ative to each other. As evidenced in previous studies of chromosomes 19 and 22, this is a characteristic of HERV-K integration. (C) 2001 Published by Elsevier Science B.V. All rights reserved.