title: Testing the palindromic target site model for DNA transposon insertion using the Drosophila melanogaster P-element.
abstract: 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.
authors.affiliation: Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, UK.
authors.forename: Raquel S
authors.initials: RS
authors.lastname: Linheiro
authors.forename: Casey M
authors.initials: CM
authors.lastname: Bergman
mesh_terms: D000818:Animals; D002874:Chromosome Mapping; D004251:DNA Transposable Elements; D004331:Drosophila melanogaster / Q000235:genetics*; D049750:Genome, Insect; D023281:Genomics; D008957:Models, Genetic; D020079:Terminal Repeat Sequences
chemical_list: D004251:DNA Transposable Elements