Measuring cis-regulatory energetics in living cells using allelic manifolds.

ABSTRACT: Gene expression in all organisms is controlled by cooperative interactions between DNA-bound transcription factors (TFs), but quantitatively measuring TF-DNA and TF-TF interactions remains difficult. Here we introduce a strategy for precisely measuring the Gibbs free energy of such interactions in living cells. This strategy centers on the measurement and modeling of 'allelic manifolds', a multidimensional generalization of the classical genetics concept of allelic series. Allelic manifolds are measured using reporter assays performed on strategically designed cis-regulatory sequences. Quantitative biophysical models are then fit to the resulting data. We used this strategy to study regulation by two Escherichia coli TFs, CRP and [Formula: see text] RNA polymerase. Doing so, we consistentl

SUBMITTER: Forcier TL 

PROVIDER: S-EPMC6301791 | biostudies-literature | 2018 Dec

REPOSITORIES: biostudies-literature