title: Genomic deletions and precise removal of transposable elements mediated by short identical DNA segments in primates.
abstract: Insertion of transposable elements is a major cause of genomic expansion in eukaryotes. Less is understood, however, about mechanisms underlying contraction of genomes. In this study, we show that retroelements can, in rare cases, be precisely deleted from primate genomes, most likely via recombination between 10- to 20-bp target site duplications (TSDs) flanking the retroelement. The deleted loci are indistinguishable from pre-integration sites, effectively reversing the insertion. Through human-chimpanzee-Rhesus monkey genomic comparisons, we estimate that 0.5%-1% of apparent retroelement "insertions" distinguishing humans and chimpanzees actually represent deletions. Furthermore, we demonstrate that 19% of genomic deletions of 200-500 bp that have occurred since the human-chimpanzee divergence are associated with flanking identical repeats of at least 10 bp. A large number of deletions internal to Alu elements were also found flanked by homologies. These results suggest that illegitimate recombination between short direct repeats has played a significant role in human genome evolution. Moreover, this study lends perspective to the view that insertions of retroelements represent unidirectional genetic events.
authors.affiliation: Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada.
authors.forename: Louie N
authors.initials: LN
authors.lastname: van de Lagemaat
authors.forename: Liane
authors.initials: L
authors.lastname: Gagnier
authors.forename: Patrik
authors.initials: P
authors.lastname: Medstrand
authors.forename: Dixie L
authors.initials: DL
authors.lastname: Mager
mesh_terms: D020087:Alu Elements; D000818:Animals; D001483:Base Sequence; D019457:Chromosome Breakage; D004247:DNA / Q000235:genetics*; D004260:DNA Repair; D004251:DNA Transposable Elements / Q000235:genetics*; D017353:Gene Deletion; D015894:Genome, Human; D006801:Humans; D008253:Macaca mulatta / Q000235:genetics; D008969:Molecular Sequence Data; D002679:Pan troglodytes / Q000235:genetics; D011323:Primates / Q000235:genetics*; D011995:Recombination, Genetic; D012689:Sequence Homology, Nucleic Acid; D013045:Species Specificity
chemical_list: D004251:DNA Transposable Elements; D004247:DNA