Understanding and Manipulating Chromosomal-Scale DNA Looping in Escherichia coli

One of the fundamental features in eukaryotic gene regulation is the recruitment of transcription factors, bound at sites that are often tens to hundreds of kilobasepairs away from the target promoter. Mutations that disrupt this long-range gene regulation are thought to be a common genetic susceptibility in a wide range of diseases. However, despite the recent advancement in methodologies such as fluorescence in situ hybridization (FISH), genome conformation capture (3C) and Hi-C, studies in multicellular organisms have been hampered by the complexity of these systems, and it is still not understand how correct long distance connections are made and incorrect connections are avoided.

In order to develop a simplified system for studying looping, we have recapitulated in E. coli the very long range DNA looping typical of multicellular organisms using a set of well-defined DNA looping proteins. We show that DNA-looping interactions can be controlled by other DNA loops. Combined with mathematical modeling, our system provides a simple but powerful platform for quantitatively characterizing the efficiency of DNA interactions in vivo. Finally, we have constructed tools which allow very precise manipulation of DNA looping within cells. Understanding the fundamental principles of DNA looping should help unravel the causative links between mutations and diseases and provide opportunities for intervention.