DISTRIBUTION OF TOPOISOMERASE II-MEDIATED CLEAVAGE SITES AND RELATIONTO STRUCTURAL AND FUNCTIONAL LANDMARKS IN 830 KB OF DROSOPHILA DNA

The pattern of sites for cleavage mediated by topoisomerase II was det ermined in 830 kb of cloned DNA from the Drosophila X chromosome, with the objectives of comparing it with mapped structural and functional landmarks and examining if the correlations with such landmarks report ed in individual loci can be generalized to a region similar to 100 ti mes longer. The relative frequencies of topoisomerase II cleavage site s in 247 restriction fragments from 67 clones were quantified by hybri dization with probes prepared from DNA fragments which abutted all cle avage sites in each clone, selected through the covalently bound topoi somerase II subunit; the specificity and quantitative nature of this m ethod were demonstrated using a plasmid DNA model. The 12 restriction fragments with strong nuclear scaffold attachment (SAR) activity, of w hich seven possess autonomous replication (ARS) activity, show statist ically strong coincidence or contiguity (P less than or equal to 0.11) with regions of high topoisomerase II cleavage site frequency. These regions show no correlation with repetitive sequence or A/T or C/G con tent and some extend over >10 kb; their sensitivity is therefore unlik ely to be due to alternating purine-pyrimidine repeats or regions of Z conformation, which are preferred motifs. The hypothesis that they po ssess intrinsic curvature is consistent with the similarity of their l ength and spacing to regions of predicted curvature in the 315 kb DNA of Saccharomyces cerevisiae chromosome III and with the reported stron g binding preference of topoisomerase II for curved DNA. The topoisome rase II cleavage pattern in this DNA further shows that its relationsh ips to functional properties seen in individual loci, especially to MA R/SAR and ARS activity and to the restricted accessibility of DNA to t opoisomerase II in vivo, can be generalized to much longer regions of the genome.