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Letter

Genomic deletions and precise removal of transposable elements mediated by short identical DNA segments in primates

¹ Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC, V5Z 1L3, Canada ² Department of Experimental Medical Science, Lund University, BMC B13, 221 84 Lund, Sweden ³ Department of Medical Genetics, University of British Columbia, BC, V6T 1Z3 Canada

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.

[Supplemental material is available online at www.genome.org. The sequence data from this study have been submitted to GenBank under accession nos. of gorilla, gibbon, and chimpanzee sequences: AY953322, AY953323, AY953324, AY953325, and AY953326. The following individuals kindly provided reagents, samples, or unpublished information as indicated in the paper: P. Parham, A.F.A. Smit, and P. Green.]

Article and publication are at http://www.genome.org/cgi/doi/10.1101/gr.3910705.

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