Regulatory asymmetry in the negative single-input module network motif: Role of network size, growth rate and binding affinity

The single-input module (SIM) is a regulatory motif capable of coordinating gene expression across functionally related genes. We explore the relationship between regulation of the central autoregulated TF in a negatively regulated SIM and the target genes using a synthetic biology approach paired with stochastic simulations. Surprisingly, we find a fundamental asymmetry in the level of regulation experienced by the TF gene and its targets, even if they have identical regulatory DNA; the TF gene experiences stronger repression than its targets. This asymmetry is not predicted from deterministic modeling of the system but is revealed from corresponding stochastic simulations. The magnitude of asymmetry depends on factors such as the number of targets in the SIM, TF degradation rate (or growth rate) and TF binding affinity. Beyond implications for SIM motifs, the influence of network connectivity on regulatory levels highlights an interesting challenge for predictive models of gene regulation.