Abstract
Enhancers are ubiquitous and critical gene regulatory elements. However, quantitative understanding of the role of DNA looping in the regulation of enhancer action and specificity is limited. We used the Escherichia coli NtrC enhancer-σ54 promoter system as a model in vivo system, showing that activation is highly sensitive to the enhancer-promoter (E-P) distance in the 300-6000 bp range, and can be regulated positively or negatively by assisting or insulating loops formed by Lac repressor. Two σ54 promoters controlled by the same enhancer compete weakly, and a single LacI loop can produce a 15-fold shift in promoter choice by the enhancer. A combined kinetic-thermodynamic model quantifies loop interactions and reveals that the response to changes in the E-P tether by insulators and other loops is highly tunable. While the NtrC system is sensitive to E-P distance and looping control, other enhancers and promoters may resist such manipulation.
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