title: The influence of assortativity on the robustness of signal-integration logic in gene regulatory networks.
abstract: Gene regulatory networks (GRNs) drive the cellular processes that sustain life. To do so reliably, GRNs must be robust to perturbations, such as gene deletion and the addition or removal of regulatory interactions. GRNs must also be robust to genetic changes in regulatory regions that define the logic of signal-integration, as these changes can affect how specific combinations of regulatory signals are mapped to particular gene expression states. Previous theoretical analyses have demonstrated that the robustness of a GRN is influenced by its underlying topological properties, such as degree distribution and modularity. Another important topological property is assortativity, which measures the propensity with which nodes of similar connectivity are connected to one another. How assortativity influences the robustness of the signal-integration logic of GRNs remains an open question. Here, we use computational models of GRNs to investigate this relationship. We separately consider each of the three dynamical regimes of this model for a variety of degree distributions. We find that in the chaotic regime, robustness exhibits a pronounced increase as assortativity becomes more positive, while in the critical and ordered regimes, robustness is generally less sensitive to changes in assortativity. We attribute the increased robustness to a decrease in the duration of the gene expression pattern, which is caused by a reduction in the average size of a GRN's in-components. This study provides the first direct evidence that assortativity influences the robustness of the signal-integration logic of computational models of GRNs, illuminates a mechanistic explanation for this influence, and furthers our understanding of the relationship between topology and robustness in complex biological systems.
authors.affiliation: Computational Genetics Laboratory, Dartmouth College, Hanover, NH 03755, USA. dov.pechenick@dartmouth.edu
authors.forename: Dov A
authors.initials: DA
authors.lastname: Pechenick
authors.forename: Joshua L
authors.initials: JL
authors.lastname: Payne
authors.forename: Jason H
authors.initials: JH
authors.lastname: Moore
mesh_terms: D000818:Animals; D003198:Computer Simulation; D053263:Gene Regulatory Networks / Q000502:physiology*; D005838:Genotype; D008957:Models, Genetic; D010641:Phenotype; D015398:Signal Transduction / Q000235:genetics