CHARACTERIZATION OF A NOVEL CLASS OF INTERSPERSED LTR ELEMENTS IN PRIMATE GENOMES - STRUCTURE, GENOMIC DISTRIBUTION, AND EVOLUTION

Retrovirus-like sequences and their solitary (solo) long terminal repe ats (LTRs) are common repetitive elements in eukaryotic genomes. We re ported previously that the tandemly arrayed genes encoding U2 snRNA (t he RNU2 locus) in humans and apes contain a solo LTR (U2-LTR) which wa s presumably generated by homologous recombination between the two LTR s of an ancestral provirus that is retained in the orthologous baboon RNU2 locus. We have now sequenced the orthologous U2-LTRs in human, ch impanzee, gorilla, orangutan, and baboon and examined numerous homolog s of the U2-LTR that are dispersed throughout the human genome. Althou gh these U2-LTR homologs have been collectively referred to as LTR13 i n the literature, they do not display sequence similarity to any known retroviral LTRs; however, the structure of LTR13 closely resembles th at of other retroviral LTRs with a putative promoter, polyadenylation signal, and a tandemly repeated 53-bp enhancer-like element. Genomic b lotting indicates that LTR13 is primate-specific; based on sequence an alysis, we estimate there are about 2,500 LTR13 elements in the human genome. Comparison of the primate U2-LTR sequences suggests that the h omologous recombination event that gave rise to the solo U2-LTR occurr ed soon after insertion of the ancestral provirus into the ancestral U 2 tandem array. Phylogenetic analysis of the LTR13 family confirms tha t it is diverse, but the orthologous U2-LTRs form a coherent group in which chimpanzee is closest to the humans; orangutan is a clear outgro up of human, chimpanzee, and gorilla; and baboon is a distant relative of human, chimpanzee, gorilla, and orangutan. We compare the LTR13 fa mily with other known LTRs and consider whether these LTRs might play a role in concerted evolution of the primate RNU2 locus.