Stability depends on positive autoregulation in Boolean gene regulatory networks.
Network motifs have been identified as building blocks of regulatory networks, including gene regulatory networks (GRNs). The most basic motif, autoregulation, has been associated with bistability (when positive) and with homeostasis and robustness to noise (when negative), but its general importance in network behavior is poorly understood. Moreover, how specific autoregulatory motifs are selected during evolution and how this relates to robustness is largely unknown. Here, we used a class of GRN models, Boolean networks, to investigate the relationship between autoregulation and network stability and robustness under various conditions. We ran evolutionary simulation experiments for different models of selection, including mutation and recombination. Each generation simulated the development of a population of organisms modeled by GRNs. We found that stability and robustness positively correlate with autoregulation; in all investigated scenarios, stable networks had mostly positive autoregulation. Assuming biological networks correspond to stable networks, these results suggest that biological networks should often be dominated by positive autoregulatory loops. This seems to be the case for most studied eukaryotic transcription factor networks, including those in yeast, flies and mammals.
Department of Biology, Stanford University, Stanford, California, United States of America; PhD Program in Computational Biology, Instituto Gulbenkian de Ciência, Oeiras, Portugal.
Ricardo
R
Pinho
Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland.
Victor
V
Garcia
EMBL/CRG Research Unit in Systems Biology, Centre for Genomic Regulation (CRG), Barcelona, Spain.
Manuel
M
Irimia
Department of Biology, Stanford University, Stanford, California, United States of America.
Marcus W
MW
Feldman
D000818:Animals; D019295:Computational Biology; D004175:Diptera; D053263:Gene Regulatory Networks; D006706:Homeostasis / Q000235:genetics*; D008322:Mammals; D008954:Models, Biological; D010641:Phenotype; D015003:Yeasts