Conformation of promoter DNA: fine mapping of S1-hypersensitive sites.

Larsen and Weintraub showed that a feature of active (but not inactive) chromatin is the appearance of S1-nuclease-hypersensitive sites in the 5'-flanking regions of expressing genes. Such sites are also present in supercoiled, but not relaxed, plasmids carrying these gene sequences. We have developed an in vitro approach to map, at the nucleotide level, S1-hypersensitive sites in artificially generated supercoiled circles of naked DNA. In the case of the adult chicken beta-globin gene, our results correlate extremely well with the coarser in vivo mapping. These sites reside in homopurine-homopyrimidine tracts, and, despite their S1 sensitivity, they do not seem to be single-stranded.