The spatial organization of cell fates in developing tissues often involves the control of transcriptional networks by morphogen gradients. A well-studied example of this is the Sonic-hedgehog (Shh) controlled pattern of neuronal subtype differentiation in the vertebrate neural tube. Here we discuss recent studies involving genome wide analyses, functional experiments and theoretical models that have begun to characterise the molecular logic by which neural cells interpret Shh signalling. The view that emerges from this work is that cell identity results from the combined input of Shh signalling, uniformly expressed neural factors and the cross-regulatory network of downstream Shh target genes. A similar logic is also likely to underpin the patterning of many developing tissues.
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