Nucleic Acids Research Advance Access published online on October 1, 2008
Nucleic Acids Research, doi:10.1093/nar/gkn563
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OA - Genomics |
Testing the palindromic target site model for DNA transposon insertion using the Drosophila melanogaster P-element
Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, UK
*To whom correspondence should be addressed. Tel: +44 0 161 275 1713; Fax: +44 0 161 275 5980; Email: casey.bergman{at}manchester.ac.uk
Received July 8, 2008. Revised August 18, 2008. Accepted August 19, 2008.
Understanding the molecular mechanisms that influence transposable element target site preferences is a fundamental challenge in functional and evolutionary genomics. Large-scale transposon insertion projects provide excellent material to study target site preferences in the absence of confounding effects of post-insertion evolutionary change. Growing evidence from a wide variety of prokaryotes and eukaryotes indicates that DNA transposons recognize staggered-cut palindromic target site motifs (TSMs). Here, we use over 10 000 accurately mapped P-element insertions in the Drosophila melanogaster genome to test predictions of the staggered-cut palindromic target site model for DNA transposon insertion. We provide evidence that the P-element targets a 14-bp palindromic motif that can be identified at the primary sequence level, which predicts the local spacing, hotspots and strand orientation of P-element insertions. Intriguingly, we find that the although P-element destroys the complete 14-bp target site upon insertion, the terminal three nucleotides of the P-element inverted repeats complement and restore the original TSM, suggesting a mechanistic link between transposon target sites and their terminal inverted repeats. Finally, we discuss how the staggered-cut palindromic target site model can be used to assess the accuracy of genome mappings for annotated P-element insertions.