Negative DNA supercoiling makes protein-mediated looping deterministic and ergodic within the bacterial doubling time

Abstract

Protein-mediated DNA looping is fundamental to gene regulation and such loops occur stochastically in purified systems. Additional proteins increase the probability of looping, but these probabilities maintain a broad distribution. For example, the probability of lac repressor-mediated looping in individual molecules ranged 0–100%, and individual molecules exhibited representative behavior only in observations lasting an hour or more. Titrating with HU protein progressively compacted the DNA without narrowing the 0–100% distribution. Increased negative supercoiling produced an ensemble of molecules in which all individual molecules more closely resembled the average. Furthermore, in only 12 min of observation, well within the doubling time of the bacterium, most molecules exhibited the looping probability of the ensemble. DNA supercoiling, an inherent feature of all genomes, appears to impose time-constrained, emergent behavior on otherwise random molecular activity.

DNA fluctuations reveal the size and dynamics of topological domains

“…Proteins that interact via two DNA sites (e.g., recombinases, transcription factors, architectural proteins, or many restriction enzymes) can bridge across plectonemic segments and thereby introduce DNA topological domains ( 12 , 14 , 56 , 57 ) ( Fig. S5 ).…”

Structural interplay between DNA-shape protein recognition and supercoiling: The case of IHF

“…The observation of this bridge in the most supercoiled minicircle suggests some relationship between bridge formation and supercoiling, which we explain as the result of the proximity of distal DNA sites that are far apart in torsionally relaxed DNA [40] , [76] , [77] . In this regard, DNA bridges involving secondary nonspecific recognition sites have also been identified for other bacterial proteins like Topoisomerase IB [34] and ParB [78] in supercoiled DNA.…”

Women’s contribution in understanding how topoisomerases, supercoiling, and transcription control genome organization

“…In fact, the incorporation of relaxed chromatin inside the supercoiled loop temporarily drops down its energy, towards a more energetically favorable state (Rusková and Račko, 2021). Indeed, in vitro studies agree with this model, since they show how the accumulation of supercoiling decreases the variation in looping probability, shifting the equilibrium completely to the looped state (Yan et al, 2021).…”