Assessing regulatory information in developmental gene regulatory networks

Abstract

Gene regulatory networks (GRNs) provide a transformation function between the static genomic sequence and the primary spatial specification processes operating development. The regulatory information encompassed in developmental GRNs thus goes far beyond the control of individual genes. We here address regulatory information at different levels of network organization, from single node to subcircuit to large-scale GRNs and discuss how regulatory design features such as network architecture, hierarchical organization, and cisregulatory logic contribute to the developmental function of network circuits. Using specific subcircuits from the sea urchin endomesoderm GRN, for which both circuit design and biological function have been described, we evaluate by Boolean modeling and in silico perturbations the import of given circuit features on developmental function. The examples include subcircuits encoding positive feedback, mutual repression, and coherent feedforward, as well as signaling interaction circuitry. Within the hierarchy of the endomesoderm GRN, these subcircuits are organized in an intertwined and overlapping manner. Thus, we begin to see how regulatory information encoded at individual nodes is integrated at all levels of network organization to control developmental process.developmental GRN | network topology | circuit function | network hierarchy | Boolean modeling D evelopmental process is controlled by gene regulatory networks (GRNs), the regulatory interactions between genes encoding transcription factors and signaling interactions that determine developmental gene expression throughout the genome (1-3). At the level of a single node, the information captured in GRNs is intuitively accessible. However, the information encompassed in GRNs is not just to regulate individual genes. During development, GRNs control the differential specification of cell fates and determine the organization of body parts, organs, and cell types within the animal body plan. As more and more GRNs become experimentally solved, the question arises as to how network features can be recognized that carry information for more complex developmental transactions.Comparison of different regulatory networks shows that particular constellations of regulatory interactions among a few genes, so-called subcircuits, are recurrently deployed in very different biological contexts (1, 4, 5). These subcircuits are composed of different regulatory genes, but nevertheless encode similar regulatory functions. Specific subcircuit topologies include, for example, positive feedback circuitry, leading to stabilization of gene expression, or mutual-repression circuits that lead to the exclusion of regulatory states (6-9). Several types of network subcircuits have been identified so far, each associated with specific regulatory functions (1, 4, 5). It appears, furthermore, that given types of subcircuits are often found at given positions within the GRN hierarchy, although the number of experimentally solved largescale networks is so far still sma...

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