Recent evolutionary expansion of a subfamily of RTVL-H human endogenous retrovirus-like elements

The RTVL-H family is a medium repetitive family endogenous retrovirus-like sequences found in the genomes of humans and other primates. Different subfamilies of RTVL-H elements can be identified based on sequence differences clustered within the U3 region of their long terminal repeats (LTRs). These subfamilies have been designated Type I, Type Ia, and Type II. Examination of the U3 repeat structure of the LTR suggests that the Type Ia LTR is a recombinant between Types I and II. Northern analysis of cell lines indicates that expression of RTVL-H elements with Type Ia LTRs is less restricted than the other two LTR types. We have examined the evolutionary history of these subfamilies within the primate lineage through Southern blot analyses and library screening procedures to determine copy numbers and through polymerase chain reaction (PCR) analyses to determine integration times of individual elements at orthologous loci in different primate species. Our findings suggest that the Type I and Type II subfamilies arose early in primate evolution and had undergone their most significant expansions before the divergence of apes and Old World monkeys 30 MYr ago. In contrast, the Type Ia subfamily has expanded more recently, being found in significant numbers only in hominoids.