A System of Repressor Gradients Spatially Organizes the Boundaries of Bicoid-Dependent Target Genes

The homeodomain (HD) protein Bicoid (Bcd) is thought to function as a gradient morphogen that positions boundaries of target genes via threshold-dependent activation mechanisms. Here, we analyze 66 Bcd-dependent regulatory elements and show that their boundaries are positioned primarily by repressive gradients that antagonize Bcd-mediated activation. A major repressor is the pair-rule protein Runt (Run), which is expressed in an opposing gradient and is necessary and sufficient for limiting Bcd-dependent activation. Evidence is presented that Run functions with the maternal repressor Capicua and the gap protein Kruppel as the principal components of a repression system that correctly orders boundaries throughout the anterior half of the embryo. These results put conceptual limits on the Bcd morphogen hypothesis and demonstrate how the Bcd gradient functions within the gene network that patterns the embryo. [Display omitted] ▸ A Runt protein gradient represses Bicoid-dependent activation in Drosophila embryos ▸ Runt and two other repressors spatially position Bicoid target gene boundaries ▸ At least one repressor binds directly to all 66 known Bicoid-dependent enhancers ▸ The repression system puts conceptual limits on the Bicoid morphogen hypothesis The Bicoid morphogen gradient cannot by itself specify all of the gene expression boundaries of its targets in developing fly embryos. At least three repressors, which bind Bicoid enhancers to antagonize Bicoid target genes, are also required for the formation of well-separated boundaries.