Gene regulatory network (GRN) theory defines the principal structural and functional properties of genomic control programs in animals. Here we provide an introductory overview, specifying the components of GRNs, and focusing on higher level design features such as hierarchy, modular organization, and the unidirectionality of these encoded regulatory systems. We consider two major aspects of GRN output, the generation of regulatory states that in turn determine all downstream genetic functions, and the Boolean nature of spatial gene expression that underlies developmental process. The genomic regulatory transactions linked together in GRNs are executed by cis-regulatory modules, and their combinatorial information processing function deeply affect GRN organization. This chapter further includes a first principles quantitative treatment of network dynamics, which rationalizes the measurable kinetics of accumulation of transcriptional products and permits computational assessment of the outputs of regulatory gene cascades. Current GRN theory devolves from multiple earlier roots which we very briefly trace.
Common Design 