The maize Adh1 promoter: structures in supercoiled DNA

We have examined the alcohol dehydrogenase-1 promoter for supercoil-induced structural anomalies that would indicate regions of possible interaction with regulatory molecules. We have found and mapped with nucleotide level precision S1 nuclease hypersensitive sites that correspond to similar sites in many animal genes. The first site maps to position -65, the heart of a region of DNA characterized by drastic purine/pyrimidine asymmetry. The top strand of the region from -52 to -72 is almost exclusively pyrimidines (20 of 21 bases). Similar regions of homopurine/homopyrimidine asymmetry have been noted and shown to be sensitive to S1 while in the supercoiled state in many animal promoters, from chicken collagen to rabbit globin to some viral promoters, but have not yet been noted in plant promoters. This type of S1 hypersensitive structure has been implicated in the recognition and binding of regulatory and/or transcriptional proteins. For example, recently purified transcription factors involved in the histone gene system of Drosophila footprint to an area of DNA that is S1 hypersensitive in vitro (Parker and Topol, Cell 36:357, 1984).

We have determined that a second S1 hypersensitive "site" maps to the borders of a region of alternating pyrimidines and purines, a region theoretically capable of assuming the Z-DNA conformation. In fact, nucleotide level analysis showed that the region from -316 to -331 has the S1 nuclease "signature" of Z-DNA. We have very recently used chemical probes to further support the fact that this region exists as Z-DNA while in the supercoiled state.

Robert J. Ferl, Harry S. Nick and Beth J. Laughner

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