Head-specific gene expression in Hydra:: Complexity of DNA-protein interactions at the promoter of ks1 is inversely correlated to the head activation potential

To gain insight into the molecular mechanisms that direct position-dependent gene expression in the simple and evolutionarily old metazoan Hydra, we have examined DNA-protein interactions in the 1.5-kb cis regulatory region of the head-specific gene ks1. In vitro footprinting and gel-retardation techniques have been used to map the location of all protein-binding sites. To our surprise, we found substantially more proteins binding to ks1 promoter elements in nuclear extract from basal (gastric) than from apical (head-and tentacle-formation zone) cells. One of these proteins is the homeobox protein Cnox-2, In the head regeneration-deficient mutant reg-16, an increased level of nuclear protein binds to ks1 promoter elements. Treatment of polyps with the ks1-inducing phorbol ester 12-O-tetradecanoylphorbol W-acetate (TPA) resulted in reduced binding of nuclear proteins to the ks1 cis regulatory region. As activation of ks1 transcription is correlated with the absence of nuclear proteins binding to the ks1 promoter, we propose that the majority of these proteins act as transcriptional repressors. In this view, the gradient of head activation along the Hydra body axis is caused by a decreasing amount of inhibitory factors, rather than an increasing amount of activators, toward the head. Thus, inhibitory mechanisms might have played a crucial role in regulating position-dependent gene activation during early metazoan evolution.