The function of architecture and logic in developmental gene regulatory networks

Abstract

An important contribution of systems biology is the insight that biological systems depend on the function of molecular interactions and not just on individual molecules. System level mechanisms are particularly important in the development of animals and plants which depends not just on transcription factors and signaling molecules, but also on regulatory circuits and gene regulatory networks (GRNs). However, since GRNs consist of transcription factors, it can be challenging to assess the function of regulatory circuits independently of the function of regulatory factors. The comparison of different GRNs offers a way to do so and leads to several observations. First, similar regulatory circuits operate in various developmental contexts and in different species, and frequently, these circuits are associated with similar developmental functions. Second, given regulatory circuits are often used at particular positions within the GRN hierarchy. Third, in some GRNs, regulatory circuits are organized in a particular order in respect to each other. And fourth, the evolution of GRNs occurs not just by co-option of regulatory genes but also by rewiring of regulatory linkages between conserved regulatory genes, indicating that the organization of interactions is important. Thus, even though in most instances the function of regulatory circuits remains to be discovered, it becomes evident that the architecture and logic of GRNs are functionally important for the control of genome activity and for the specification of the body plan.

Keywords: Feedback circuit; Feedforward circuit; Gene regulatory networks; Network topology; Regulatory logic; Subcircuit.