Fig. 8. Potential mechanisms to account for differential response of genes to graded Shh signaling. (A) Graded Shh signaling establishes a ventral-to-dorsal gradient of Gli activity (Gli activator, yellow; Gli repressor, purple) in the neural tube. In addition, uniformly expressed activators (blue) and repressors (red) are hypothesized to be expressed in neural progenitors. Three mechanisms could explain the differential sensitivity of genes to the level of Shh signaling: (B) The number or affinity of Gli binding sites (GBSs) in a regulatory module might explain differential gene expression. Genes with several high affinity GBSs (yellow gene C) would respond to low concentrations of Shh, resulting in a broad expression domain, with a dorsal boundary far from the ventral midline. Genes with fewer high affinity GBSs (orange gene B) or low affinity GBSs (green gene A) would require higher levels of Gli activity and therefore would be expressed in correspondingly more restricted regions of the neural tube. (C) Gli activity may act in conjunction with other repressor and activator signals. In this case, the presence of other transcription factors influences the response of individual genes to Shh signaling. For example, in yellow C and orange gene B, the presence of binding sites for transcription factors acting as activators (TF+) sensitizes the response of these genes, facilitating induction at lower levels of signaling. By contrast, the red gene A, which contains binding sites for a transcriptional inhibitor (TF-), requires higher levels Gli activity and, consequently, higher levels of signaling to overcome the repressive activity. (D) The addition of cross-regulation between Shh-dependent genes (see Fig. 7) is likely to refine specific domains of expression in the ventral neural tube. Adding an inhibitory input between two genes from the network in panel C restricts the expression of gene C to a specific domain of progenitors. Such a mechanism could account for the regulation of genes such as Nkx2.2 and Olig2. RF, roof plate; FP, floor plate; Gli, Gli transcription factor; TF, transcription factor.