Simulating the evolution of gene regulatory systems - questions and challenges

An increasing amount of experimental data on global properties of genome organization across various species and phyla is becoming available, suggesting general principles as, e.g., scaling relationships or spatial regularities of gene distribution on DNA. A second level of information is accessible with gene regulatory networks, that control the space-time pattern of gene expression; here, similar (statistical) patterns of conserved regularities are observed. In many models of gene regulatory networks, however, the tight connection between genome architecture and -evolution on one side, and network structure and -dynamics on the other side is ignored, limiting their predictive power. I will introduce and discuss an artificial genome model that allows an integrative approach to model both levels of genome information. In particular, the following questions will be addressed: (1) Which types of network properties could be explained from combinatorial/statistical properties of genomes (random genome model), (2) how do they change in evolving genomes, in particular when (3) selective pressure is present, e.g. stabilizing selection for certain patterns of gene activity (phenotypes). I will also outline how particular questions, e.g. the evolution of a genetic switch for coordinated switching of functional groups of genes, can be addressed in this framework. Last, an outlook will be provided on questions and challenges posed by novel modes of gene regulation present in eukaryotic cells, the complexity of which by far exceeds what is found in Prokaryotes.