DNA loop domains in a 1.4-Mb region around the human hprt gene mapped by cleavage mediated by nuclear matrix-associated topoisomerase II

We have mapped the positions in a similar to 1.4-Mb region of genomic DNA a round the human hprt gene which are accessible in vivo to cleavage by topoi somerase II associated with the nuclear matrix. These positions, which are interpreted as the boundaries of DNA loop domains, were mapped in K562 cell s by examining the truncation of rare-cutter restriction fragments separate d by pulsed field gel electrophoresis after topoisomerase II-mediated cleav age, using seven linked markers mapped in this region as probes for indirec t end-labeling. Eleven cleavage positions were detected and were interprete d as defining ten loop domains of lengths between 70 and 210 kb (average si milar to 135 kb); the hprt gene resides in a 150-kb loop domain. Loop domai n boundaries coincided with three of the fifteen deletion breakpoints mappe d in a 600-kb sector of this region in human lymphocytes, within the limits of resolution of pulsed field gel electrophoresis; this correlation was no t statistically significant.