In vivo footprinting reveals unique cis-elements and different modes of hypoxic induction in maize Adh1 and Adh2

The transcriptional activation of maize alcohol dehydrogenase-1 (Adh1) and alcohol dehydrogenase-2 (Adh2) is accompanied by changes in the chromatin structure within the 5'-flanking region of each gene. The positions of DNA-binding factors bound to the 5'-flanking regions were determined by in vivo dimethyl sulfate footprinting of maize suspension cultures over 8 hours of hypoxic induction. In Adh1 there are two types of DNA-binding factors associated with the promoter region. One set of factors is constitutively associated with the cis-regulatory anaerobic response element, whereas two additional factors bind only after Adh1 has been induced by hypoxic stress. Returning hypoxically stressed cells to an aerobic environment restores the dimethyl sulfate footprint observed for the uninduced Adh1 gene. In contrast, all of the factors bound to the 5'-flanking region of Adh2 are constitutively present and unchanged by hypoxia. There is one footprint site common to both Adh1 and Adh2, but it is not an anaerobic response-like element.