The Underlying Molecular and Network Level Mechanisms in the Evolution of Robustness in Gene Regulatory Networks

Gene regulatory networks show robustness to perturbations. Previous works identified robustness as an emergent property of gene network evolution but the underlying molecular mechanisms are poorly understood. We used a multi-tier modeling approach that integrates molecular sequence and structure information with network architecture and population dynamics. Structural models of transcription factor-DNA complexes are used to estimate relative binding specificities. In this model, mutations in the DNA cause changes on two levels: (a) at the sequence level in individual binding sites (modulating binding specificity), and (b) at the network level (creating and destroying binding sites). We used this model to dissect the underlying mechanisms responsible for the evolution of robustness in gene regulatory networks. Results suggest that in sparse architectures (represented by short promoters), a mixture of local-sequence and network-architecture level changes are exploited. At the local-sequence level, robustness evolves by decreasing the probabilities of both the destruction of existent and generation of new binding sites. Meanwhile, in highly interconnected architectures (represented by long promoters), robustness evolves almost entirely via network level changes, deleting and creating binding sites that modify the network architecture. Development from egg to embryo depends to a large extent on regulatory networks of genes called transcription factors. Previous research has shown these gene regulatory networks to be robust to perturbations at the level of the connections between transcription factors. Here, we investigate the mechanisms underlying the evolution of robustness in gene networks using a modeling approach, which considers three levels: binding of individual transcription factors to DNA, dynamics of gene expression levels, and fitness effects at the population level. In our model the gene regulatory network is determined by transcription factor binding sites within DNA sequences, which undergo mutation. We categorize these mutations in a continuum ranging from silent mutations, which have no effect on regulation and change only the DNA sequence (local-sequence level), to mutations that change connections between genes in the network (network-architecture level). We find that in sparse networks, containing few connections between genes, a balance of local-sequence and network-architecture level mechanisms are responsible for the evolution of robustness, but when the network is densely connected the network-architecture level mechanisms become dominant. We argue that the shift towards the network-architecture level for more densely-connected networks offers a potential explanation for the evolution of increased complexity.