Using synthetic bacterial enhancers to reveal a looping-based mechanism for quenching-like repression. Nat. Commun. 7:10407 (2016).
Michal Brunwasser-Meirom, Yaroslav Pollak, Sarah Goldberg, Lior Levy, Orna Atar & Roee Amit
Abstract: We explore a model for quenching repression by studying synthetic bacterial enhancers, each characterized by a different binding site architecture. To do so, we take a three-pronged approach: first, we compute the probability that a protein-bound dsDNA molecule will loop. Second, we use hundreds of synthetic enhancers with varying binding site arrangements to test the model’s predictions in bacteria. Finally, we search for the mechanism bioinformatically in real genomes. Our results show that excluded volume effects generated by DNA-bound proteins can generate substantial quenching. Moreover, the type and extent of the regulatory effect depend strongly on the relative arrangement of the binding sites within the regulatory region. The implications of these results are that enhancers should be tolerant to 10-11 bp INDELs, and intolerant to 5-6 bp INDELs. We tested this prediction on 61 σ54 regulated qrr genes from the Vibrio genus and confirmed the sensitivity of these enhancer’s sequences to the DNA’s helical repeat.