Towards more biological mutation operators in models of gene regulation

James Watson1, Nicholas Geard2, Janet Wiles, University of Queensland;, University of Queensland

Gene regulation is often viewed as a complex system whose properties emerge from interactions between regulatory genes. A primary method for studying the complex dynamics of gene regulation uses directed graphs to explore structure, behaviour and evolvability. Mutation operators in such studies typically involve the insertion and deletion of nodes and links at the network level. Such network-level mutation operators are sufficient to allow the statistical analysis of network structure, but impose limitations on the way the networks are evolved. There are a wide variety of mutations in DNA sequences that are yet to be analysed for their network-level effects. By modelling an artificial genome at the level of a nucleotide sequence and mapping it to a regulatory network, biologically grounded mutations can be mapped to network-level mutations. The method of mapping from nucleotide sequences to regulatory networks is presented, and the effects of three sequence-level mutations (single-point mutation, transposition and duplication) are discussed. In short, it is rarely the case that nodes and links are cleanly added or deleted, with even the simplest nucleotide changes capable of causing a wide variety of network-level modifications. The vast majority of mutations are neutral, resulting in a neutral plateau from which a range of functional behaviours can be reached. This work aims to stimulate more careful consideration of mutation operators in gene regulation models than has previously been given.