DNA transposons and retroviruses are important transgenic tools for genome 
engineering. An important consideration affecting the choice of transgenic 
vector is their insertion site preferences. Previous large-scale analyses of Ds 
transposon integration sites in plants were done on the basis of reporter gene 
expression or germ-line transmission, making it difficult to discern vertebrate 
integration preferences. Here, we compare over 1300 Ds transposon integration 
sites in zebrafish with Tol2 transposon and retroviral integration sites. 
Genome-wide analysis shows that Ds integration sites in the presence or absence 
of marker selection are remarkably similar and distributed throughout the 
genome. No strict motif was found, but a preference for structural features in 
the target DNA associated with DNA flexibility (Twist, Tilt, Rise, Roll, Shift, 
and Slide) was observed. Remarkably, this feature is also found in transposon 
and retroviral integrations in maize and mouse cells. Our findings show that 
structural features influence the integration of heterologous DNA in genomes, 
and have implications for targeted genome engineering.