On the Modeling of Developmental Gene Regulatory Networks

The structural and functional properties of gene regulatory networks (GRNs) can be accessed only by the use of models. In this chapter we consider diverse forms of GRN model, focusing on insights into the biology of developmental GRNs that accrue from the generation of abstract mathematical, logical, or topological models. Topological models provide genome-centered maps of regulatory linkages, and thus graphically represent the architecture of causal interaction networks. We address the significance of network topology in an extensive comparative structure/function analysis of GRN subcircuit architecture. Insights otherwise unattainable accrue from dynamical mathematical treatment of GRN function. We review informative applications of ODE analysis to developmental GRNs of Drosophila and mammalian hematopoietic cells, and consider the regulatory interpretation of morphogen gradients. We turn then to Boolean models which are focused on GRN logic transactions. Several asynchronous models are considered and we end with a summary of the new insights deriving from a comprehensive Boolean logic model of the sea urchin embryo GRN.