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Originally published as Genetics Published Articles Ahead of Print on September 12, 2005.
Genetics, Vol. 171, 1183-1194, November 2005, Copyright © 2005
doi:10.1534/genetics.105.043976
Human Endogenous Retroviral Elements as Indicators of Ectopic Recombination Events in the Primate Genome
Jennifer F. Hughes1 and John M. Coffin2
Department of Molecular Microbiology and Program in Genetics, Tufts University School of Medicine, Boston, Massachusetts 02111
2 Corresponding author: Tufts University School of Medicine, 136 Harrison Ave., Boston, MA 02111.
E-mail: john.coffin{at}tufts.edu
HERV elements make up a significant fraction of the human genome and, as interspersed repetitive elements, have the capacity to provide substrates for ectopic recombination and gene conversion events. To understand the extent to which these events occur and gain further insight into the complex evolutionary history of these elements in our genome, we undertook a phylogenetic study of the long terminal repeat sequences of 15 HERV-K(HML-2) elements in various primate species. This family of human endogenous retroviruses first entered the primate genome between 35 and 45 million years ago. Throughout primate evolution, these elements have undergone bursts of amplification. From this analysis, which is the largest-scale study of HERV sequence dynamics during primate evolution to date, we were able to detect intraelement gene conversion and recombination at five HERV-K loci. We also found evidence for replacement of an ancient element by another HERV-K provirus, apparently reflecting an occurrence of retroviral integration by homologous recombination. The high frequency of these events casts doubt on the accuracy of integration time estimates based only on divergence between retroelement LTRs.
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