The anatomy of supercoiled loops in the Drosophila 7F locus

The genome in eucaryotes is organized into a series of supercoiled loops, topologically anchored at their bases by components of the nuclear matrix. Previous studies have shown that active genes are associated with the nuclear matrix. We wished to know whether loops in general were solely organized by active genes. We therefore examined a locus of the Drosophila X-chromosome comprising 163,000 bp of continuous DNA sequences and devoid of known active genes. Of the 52 EcoRI restriction fragments comprising this region, we found 5 anchored fragments which non-randomly organized this region into 4 DNA loops. Each of the 5 anchored fragments contained a transcribed sequence. These results strongly suggest that supercoiled loops are organized in a specific fashion with respect to DNA sequence, with the anchorage points exclusively demarcated by transcriptionally active genes.