Tertiary Level: Location and arrangement of genes

Using a combination of simulation and experiment, we are investigating how spatial distribution and copy number of genes influence gene expression dynamics. Gene regulation is usually portrayed as a bimolecular reaction between DNA and transcription factors; the reaction rate depends on concentrations and diffusion of the reactants. However, the low abundance of transcription factors, one-dimensional diffusion of transcription factors along DNA, and non-uniformly located DNA binding sites make this description rather unrealistic.

Economies of agglomeration: Would the target and walmart stores be better off or worse off by being next to each other? Similarly, what is the effect of the spatial competition among transcription factor binding sites on gene expression?