Drosophila P elements preferentially transpose to replication origins

Abstract

The P transposable element recently invaded wild Drosophila melanogaster strains worldwide. A single introduced copy can multiply and spread throughout the fly genome in just a few generations, even though its cut-and-paste transposition mechanism does not inherently increase copy number. P element insertions preferentially target the promoters of a subset of genes, but why these sites are hotspots remains unknown. We show that P elements selectively target sites that in tissue-culture cells bind origin recognition complex proteins and function as replication origins. The association of origin recognition complex-binding sites with selected promoters and their absence near clustered differentiation genes may dictate P element site specificity. Inserting at unfired replication origins during S phase may allow P elements to be both repaired and reduplicated, thereby increasing element copy number. The advantage transposons gain by moving from replicated to unreplicated genomic regions may contribute to the association of heterochromatin with late-replicating genomic regions. genome evolution | cell cycle | DNA replication | pre-replication complex

Methods to study Drosophila immunity

“…While mapping EMS mutations can be time-consuming, novel sequencing-based methods have greatly improved efficiency of mapping [70,71]. Transposon mutagenesis, albeit suffering from insertion bias [72], allows for easy retrieval of positional information, and forms the basis for a downstream toolkit of genetic applications including imprecise excision knock-out, Gal4-UAS overexpression of flanking genes, or element replacement by targeting vectors, to name but a few [73][74][75][76][77]. Extensive libraries of P-element-based transposon insertions are available through stock centers, along with deletion and duplication lines [78][79][80][81].…”

The recent invasion of natural Drosophila simulans populations by the P-element

“…RNA was extracted from whole adults of D. simulans females from Florida that were kept in the laboratory for two generations at 15°C. Insertion bias of P-elements was measured using publicly available data of 18,214 independent P-element insertions (37) and ORC binding sites (38), and regions 500 bp within transcription start sites were used as putative promotor sequences (annotation of D. melanogaster v5.57; flybase.org/). The programming language R (53) was used for all statistical analyses.…”

“…An increase in copy numbers is achieved by postreplication repair of double-strand breaks resulting from P-element excisions using the sister chromatid as a template, thus preserving the insertion at the excision site (41). Copy numbers may be further increased by preferential insertion of P-elements into unreplicated regions, which could be mediated by a bias for insertion into ORC binding sites (38). Consistent with results for D. melanogaster, we find the strongest insertion site bias is for ORCs (Table 1); assuming conservation of ORC sites, we find a 34-fold enrichment of D. simulans P-element insertions in ORC binding sites (χ 2 = 9,703; df = 1; P < 2.2e-16; Table 1).…”

“…Further, P-element insertions typically occur at low frequency; it is implausible that the shared insertions would have segregated at low frequencies without being lost by genetic drift since the split of the two species. Instead, the presence of insertions at similar sites is likely due to insertion biases: De novo P-element insertions tend to occur in a few hotspots, with 30-40% of all P-element insertions occurring in just 2-3% of the genome (37,38). To investigate whether the same insertion bias occurs in D. simulans, we identified 1-kb windows that contained at least two independent insertions generated in the course of the Drosophila Gene Disruption Project (18,214 insertions) (37).…”

“…In D. melanogaster, the P-element shows a strong preference for insertion into the promotor regions of genes (37) and a further bias for origin recognition complex (ORC) binding sites (38). We found that a substantial fraction of P-element insertions were at similar positions (±1,000 bp) in both D. melanogaster and D. simulans (428 of 1,466 insertions in D. melanogaster, where 15 are expected due to chance; χ 2 = 11,488; df = 1; P < 2.2e-16; Fig.…”