Only the promoter region of the constitutively expressed normal and amplified human dihydrofolate reductase gene is DNase I hypersensitive and undermethylated.

The human dihydrofolate reductase (DHFR) gene was found to be undermethylated only in its 5' promoter region; the remaining CCGG residues in the 30-kilobase (kb) DHFR gene were insensitive to digestion by HpaII. Each of 27 CpG residues that were part of an HpaII or HhaI cutting site within a 1.1-kb segment of the DHFR gene promoter region were found to be unmethylated. All 80 copies of the DHFR gene in methotrexate-resistant HeLa cell line exhibited this pattern of undermethylation of only the promoter region. This same region was shown to be DNase I hypersensitive in chromatin from normal cells and from those cells in which the DHFR gene was amplified. Again, all copies of the amplified gene exhibited DNase I hypersensitivity of the promoter region. The remainder of the 30-kb DHFR gene is both completely methylated and insensitive to DNase I digestion. Detailed mapping of the DNase I-hypersensitive region revealed four strong cutting sites within a 500-base pair segment immediately upstream from the DHFR coding sequence and a weak cutting site within intron I. Two of the strong DNase I cutting sites in chromatin were also sensitive to S1 nuclease nicking when this DNA fragment was part of supercoiled plasmid DNA. Promoter undermethylation and DNase I hypersensitivity, features previously shown for specialized and inducible genes, have now been shown to be characteristic of the constitutively expressed DHFR gene. That these features characterize all copies of the amplified DHFR gene in a methotrexate-resistant cell line suggest that all gene copies are transcriptionally active.