Integration specificity of the hobo element of Drosophila melanogaster is dependent on sequences flanking the integration site

We analyzed the integration specificity of the hobo transposable element of Drosophila melanogaster. Our results indicate that hobo is similar to othe r transposable elements in that it can integrate into a large number of sit es, but that some sites are preferred over others, with a few sites acting as integration hot spots. A comparison of DNA sequences from 112 hobo integ ration sites identified a consensus sequence of NTNNNNAC, but this consensu s was insufficient to account for the observed integration specificity. To begin to define the parameters affecting hobo integration preferences, we a nalyzed sequences flanking a donor hobo element, as well as sequences flank ing a hobo integration hot spot for their relative influence on hobo integr ation specificity. We demonstrate experimentally that sequences flanking a hobo donor element do not influence subsequent integration site preference, whereas, sequences contained within 31 base pairs flanking an integration hot spot have a significant effect on the frequency of integration into tha t site. However, sequence analysis of the DNA flanking several hot spots fa iled to identify any common sequence motif shared by these sites. This lack of primary sequence information suggests that higher order DNA structural characteristics of the DNA and/or chromatin may influence integration site selection by the hobo element.