DNase I preferentially cleaves polyomavirus minichromosomes at two sites in the enhancer, each of which comprises the sequence AAGCAPuPuAAG flanked by short inverted repeats. A tandem duplication of this sequence generates an additional hypersensitive locus. Mutations which alter either the AAGCAPuPuAAG or flanking repeats diminish hypersensitivity. This region must determine the chromatin conformation recognized by DNase I. The chromatin of the 5' flanking regions of many active or potentially active genes is unusually susceptible to nuclease attack (7). This 5' hypersensitivity probably reflects the accessibility of specific sequences in the DNA, but its physical nature and functional significance remain speculative (2,7,17). Polyomavirus is a useful system with which to study sequences conferring DNase I hypersensitivity to chromatin since its DNA can be manipulated and then reintroduced into mouse cells, in which it is packaged into minichromosomes. That region of the viral genome from the origin of replication to the sites of initiation of transcription of late mRNAs is hypersensitive to various nucleases and frequently lacks nucleosome morphology (3,14). These sequences are required both for DNA replication and early mRNA transcription and can serve as a transcriptional enhancer for cis-linked cellular genes (5,6,13,15,16,25,26).We examined the effect of mutations in this region on DNase I hypersensitivity. Our data indicated that altered chromatin structure is determined at the site of DNase I cleavage by the sequence AAGCAPuPuAAG flanked by small inverted repeats.Herbomel et al. (14) previously demonstrated that the enhancer region of the polyomavirus strain A2 contains two regions exhibiting DNase I hypersensitivity, but their analysis did not establish whether cleavage by DNase I was determined by sequences within or outside of the enhancer. To precisely map these DNase I-hypersensitivity sites, we used the technique of indirect end labeling (28) with the BamHI site as reference point (Fig. 1A).Mouse 3T6 cells were infected with polyomavirus strain A3 at 0.5 PFU per cell. After 24 h, the nuclei were isolated and digested with DNase I to produce approximately 1 cut per 10 kilobases. The DNA was purified, digested with BamHI, and fractionated by agarose gel electrophoresis, and then probed with a radiolabeled fragment extending from nucleotide 4659 to 5048. Of the polyomavirus minichromosomes cut with DNase I, most are cleaved in a region 470 to 570 base pairs (bp) from the BamHI site (Fig. 1C). DNase 1 digestion of purified DNA produces an entirely different * Corresponding author. t Present address: Genex Corp., Gaithersburg, MD 20877. pattern ( Fig. 2) and shows that specific cutting between the BamHI site and the site of origin of DNA replication is dependent on chromatin structure. Using densitometric scans, we established the two main locations of cutting to within 5 bp. The two hypersensitive sequences resemble each other in that cleavage occurs within a region containing the sequence AAGCAPuPu...