GENOMIC CIS-REGULATORY LOGIC - EXPERIMENTAL AND COMPUTATIONAL ANALYSIS OF A SEA-URCHIN GENE

The genomic regulatory network that controls gene expression ultimatel y determines form and function in each species. The operational nature of the regulatory programming specified in cis-regulatory DNA sequenc e was determined from a detailed functional analysis of a sea urchin c ontrol element that directs the expression of a gene in the endoderm d uring development. Spatial expression and repression, and the changing rate of transcription of this gene, are mediated by a complex and ext ended cis-regulatory system. The system may be typical of developmenta l cis-regulatory apparatus. All of its activities are integrated in th e proximal element, which contains seven target sites for DNA binding proteins. A quantitative computational model of this regulatory elemen t was constructed that explicitly reveals the logical Interrelations h ard-wired into the DNA.