Structure–function relations are subtle in genetic regulatory networks

Recent studies have yielded insights into structure–function relations in genetic regulatory networks. Models of feed-forward loops show that the input–output behavior depends critically on the input signal as well as transcription interactions. Models of induction of the lac operon in Escherichia coli reveal the importance of metabolism in determining genetic regulatory network behavior. Combined experimental and computational studies of activation by MarA in E. coli show how mechanisms of transcription regulation, hidden at the level of genetic regulatory networks, can influence behavior. Together these studies illustrate that gene regulation is critically influenced by factors beyond the topology of genetic regulatory interactions. Prediction of the specific information processing roles of gene circuits is more difficult than we would like, but it is still possible. Thinking about evolution of proteins and networks might make it easier.