BACKGROUND: Axial pattern formation in vertebrate embryos depends on signals from the node and, later, from the notochord and floor plate. Previous studies have shown that HNF-3 beta, a member of the winged-helix transcription factor family, plays key roles in the development of all three organizing centres. RESULTS: Enhancer analysis of HNF-3 beta has therefore been performed using lacZ reporter gene constructs in transgenic mouse embryos. This has led to the identification of independent node/notochord and floor plate enhancers, at positions far upstream (-15 to -14 kb) and downstream (+6 to +11 kb) of the transcription star site, respectively. The node/notochord enhancer activity has been localized to a 520 bp fragment. Floor plate gene expression requires a combination of two separate fragments of the enhancer. Deletion analysis of one of these fragments (400 bp) has identified subregions required for the initiation and the maintenance of floor plate expression, and for the suppression of ectopic expression within the neural tube. CONCLUSION: We conclude that HNF-3 beta gene expression in the node/notochord and in the floor plate are controlled through different enhancers, which consist of positive and negative elements.

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