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 an invivo model, finding that NtrC activation is highly sensitive to the enhancer-promoter (E-P) distance in the 300-6,000bp range. DNA loops formed by Lac repressor were able to strongly regulate enhancer action either positively or negatively, recapitulating promoter targeting and insulation. A single LacI loop combining targeting and insulation produced a strong shift in specificity for enhancer choice between two σ54 promoters. A combined kinetic-thermodynamic model was used to quantify the effect of DNA-looping interactions on promoter activity and revealed that sensitivity to E-P distance and to control by other loops is itself dependent on enhancer and promoter parameters that may be subject to regulation.
Highlights
Enhancers are gene-regulatory elements that bind transcription factors and can activate transcription when located far upstream or downstream of the promoter (Furlong and Levine, 2018; Long et al, 2016; Spitz, 2016; Zabidi and Stark, 2016)
NtrC was supplied from the endogenous locus and was activated by constitutive phosphorylation by NtrB by using the glnL:A129T mutation, which reduces phosphatase activity (Pioszak and Ninfa, 2003)
Stimulation of Enhancer Action by Inside Loop Assistance We previously developed a theoretical framework for loop interactions to analyze interactions between LacI or l CI loops (Hao et al, 2017a; Priest et al, 2014a)
Summary
Enhancers are gene-regulatory elements that bind transcription factors and can activate transcription when located far upstream or downstream of the promoter (Furlong and Levine, 2018; Long et al, 2016; Spitz, 2016; Zabidi and Stark, 2016). Activation requires enhancer-promoter (E-P) contact, and because enhancers act primarily on promoters in cis, DNA loops are formed. Enhancers are ubiquitous and important, far outnumbering genes in eukaryotic genomes (Dunham et al, 2012; Kvon et al, 2014), with enhancer dysfunction increasingly recognized as a cause of genetic diseases (Mumbach et al, 2017; Spitz, 2016). Questions of how promoter activation by enhancers can be efficient and specific and how activation is shared between multiple enhancers and promoters remain to be answered
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