Robustness of DNA Repair through Collective Rate Control

Abstract

DNA repair and other chromatin-associated processes are carried out by enzymatic macromolecular complexes that assemble at specific sites on the chromatin fiber. How the rate of these molecular machineries is regulated by their constituent parts is poorly understood. Here we quantify nucleotide-excision DNA repair in mammalian cells and find that, despite the pathways' molecular complexity, repair effectively obeys slow first-order kinetics. Theoretical analysis and data-based modeling indicate that these kinetics are not due to a singular rate-limiting step. Rather, first-order kinetics emerge from the interplay of rapidly and reversibly assembling repair proteins, stochastically distributing DNA lesion repair over a broad time period. Based on this mechanism, the model predicts that the repair proteins collectively control the repair rate. Exploiting natural cell-to-cell variability, we corroborate this prediction for the lesion-recognition factor XPC and the downstream factor XPA. Our findings provide a rationale for the emergence of slow time scales in chromatin-associated processes from fast molecular steps and suggest that collective rate control might be a widespread mode of robust regulation in DNA repair and transcription.

Subnuclear localization, rates and effectiveness of UVC-induced unscheduled DNA synthesis visualized by fluorescence widefield, confocal and super-resolution microscopy

“…This time course of the repair is in agreement with observations described in other reports. [32][33][34] We have previously noticed significant increase of the nuclear volume following DNA damage (dsDNA breaks) induced by topotecan. 35 This increase may be caused by global chromatin decondensation observed during DNA repair.…”

Frequency Modulation of Transcriptional Bursting Enables Sensitive and Rapid Gene Regulation

“…Stimulated by these experimental observations, a new class of ''non-equilibrium'' models of gene regulation has begun to be developed (Ahsendorf et al, 2014;Estrada et al, 2016;Scholes et al, 2017). The defining feature of these models is the presence of dynamic transitions between gene states, characterized both by TF binding and chromatin configuration; similar concepts have been developed for DNA repair (Luijsterburg et al, 2010;Verbruggen et al, 2014). Estrada et al (2016) proposed a model that shows with considerable generality that gene regulation out of equilibrium may breach a regulatory ''barrier'' for the shape of the gene-regulation function inherent in equilibrium-binding models.…”

Gene expression noise randomizes the adaptive response to DNA alkylation damage in E. coli

“…The role of noise in the fidelity of DNA repair has been investigated in eukaryotes, where nucleotide excision repair involves stochastic and reversible assembly of repair factors into large complexes (52, 53). Collective rate control renders the overall repair pathway robust to variation in the abundances of the individual components (34). The situation is opposite for damage signalling by Ada, which acts alone in the regulation of the adaptive response and feedback amplification results in extreme sensitivity to gene expression noise.…”

“…These surprising observations call for a quantitative model to pinpoint the noise source responsible for heterogeneity in the adaptive response. Quantitative models have been key to our current understanding of gene expression noise and its important functions in diverse biological processes (13, 27–30), including DNA damage signalling and repair (16, 31–34). Here, I capitalized on time-lapse microscopy data for the adaptive response that were recorded for a large range of damage conditions in hundreds of single E. coli cells (18).…”