The Underlying Molecular and Network Level Mechanisms in the Evolution of Robustness in Gene Regulatory Networks
Figure 2
Schematic representation of the gene-regulatory network model.
(A) Model of development. The expression of each gene is regulated by combinatorial interaction between an explicitly modeled cis-regulatory sequence (black lines) and the gene products (sequence specific transcription factors). Each gene product is represented by a different color. Shapes within the cis-regulatory regions represent sequence determinants of regulatory elements and their colors define the identity of the interacting transcription factor. Within the box, the explicit regulatory sequence representation is illustrated by showing an example of a consensus binding site for a given TF (maximal binding specificity, κmax) and a mutated site (with a lower κ). The extent of gene regulation is a function of the presence and associated binding specificities of each regulatory element (κix, where i is the input gene and x is a regulatory site on gene j), transcription factor abundances (si) and the function of the interacting transcription factors (activator or repressor of transcription, represented as positive and negative si values). (B) Population model. Simulations start with a randomly chosen developmentally stable founder. Variation is introduced in two forms: exchange of promoter regions between two randomly chosen parents (without recombination within promoter regions) and single point mutations at the DNA level. Selective pressure is applied to the offspring on two levels: they must develop a stable expression pattern through time (phenotype) and that phenotype must be similar to that of the founder.