Transcriptional Regulation by the Numbers 2: Applications

With the increasing amount of experimental data on gene expression and regulation, there is a growing need for quantitative models to describe the data and relate them to the different contexts. The thermodynamic models reviewed in the preceding paper provide a useful framework for the quantitative analysis of bacterial transcription regulation. We review a number of well-characterized bacterial promoters that are regulated by one or two species of transcription factors, and apply the thermodynamic framework to these promoters. We show that the framework allows one to quantify vastly different forms of gene expression using a few parameters. As such, it provides a compact description useful for higher-level studies, e.g., of genetic networks, without the need to invoke the biochemical details of every component. Moreover, it can be used to generate hypotheses on the likely mechanisms of transcriptional control.