Modeling Damage Complexity-Dependent Non-Homologous End-Joining Repair Pathway

Abstract

Non-homologous end joining (NHEJ) is the dominant DNA double strand break (DSB) repair pathway and involves several repair proteins such as Ku, DNA-PKcs, and XRCC4. It has been experimentally shown that the choice of NHEJ proteins is determined by the complexity of DSB. In this paper, we built a mathematical model, based on published data, to study how NHEJ depends on the damage complexity. Under an appropriate set of parameters obtained by minimization technique, we can simulate the kinetics of foci track formation in fluorescently tagged mammalian cells, Ku80-EGFP and DNA-PKcs-YFP for simple and complex DSB repair, respectively, in good agreement with the published experimental data, supporting the notion that simple DSB undergo fast repair in a Ku-dependent, DNA-PKcs-independent manner, while complex DSB repair requires additional DNA-PKcs for end processing, resulting in its slow repair, additionally resulting in slower release rate of Ku and the joining rate of complex DNA ends. Based on the numerous experimental descriptions, we investigated several models to describe the kinetics for complex DSB repair. An important prediction of our model is that the rejoining of complex DSBs is through a process of synapsis formation, similar to a second order reaction between ends, rather than first order break filling/joining. The synapsis formation (SF) model allows for diffusion of ends before the synapsis formation, which is precluded in the first order model by the rapid coupling of ends. Therefore, the SF model also predicts the higher number of chromosomal aberrations observed with high linear energy transfer (LET) radiation due to the higher proportion of complex DSBs compared to low LET radiation, and an increased probability of misrejoin following diffusion before the synapsis is formed, while the first order model does not provide a mechanism for the increased effectiveness in chromosomal aberrations observed.

Organization and dynamics of the nonhomologous end-joining machinery during DNA double-strand break repair

“…4B). The observation of large foci mediated by DNAPKcs is in agreement with recent studies showing that DNAPKcs facilitates the aggregated joining of multiple DNA breaks, playing a role in the repair of clustered DSBs rather than simple DSBs (23,47,48). Thus, these findings specifically identify Ku/ LX/XLF as the core complex required to mediate synapsis and productive end-joining.…”

Genome-based, mechanism-driven computational modeling of risks of ionizing radiation: The next frontier in genetic risk estimation?

“…In a follow-up of this work, Li et al [114] formulated a mechanistic mathematical model and examined whether it could simulate the kinetics of formation of foci reported by Reynolds et al The question was answered in the affirmative (i.e., the model supported the experimental findings that simple DSBs undergo fast repair in a Ku-dependent and DNA-PK cs -independent manner, whereas complex DSBs also require DNA-PK cs for end processing, resulting in its slow repair). An important prediction of their model is that the rejoining of the complex DSBs is through a process of synapsis formation, similar to a second order reaction between ends, rather than first order break filling/joining.…”

“…The solutions of the equations provide individual protein activity kinetics and overall repair kinetics, and these can be compared with experimental measurements (usually rate of repair of DSBs, post-irradiation, using PFGE in the dose range of 40-100 Gy). While most of the models dealt with the NHEJ pathway (e.g., [41,42,44,49,63,64,[111][112][113][114], some have also considered single-strand annealing (SSA) [115]; microhomology-mediated end-joining (MMEJ) [48]; application to high LET radiations [48]; and base-excision-repair (BER) [46].…”

“…Another potentially useful idea in the above context comes from the paper of Li et al [114] on the modeling of the DNAcomplexity-dependent NHEJ repair pathway discussed earlier.…”

DSB repair model for mammalian cells in early S and G1 phases of the cell cycle: Application to damage induced by ionizing radiation of different quality

“…For damage induced by photons and electrons, we and others have proposed independent models of NHEJ that predict the DSB repair kinetics fairly accurately [19][20][21]45]. In other studies, the PARTRAC Monte Carlo track structure simulation code was used to calculate the repair kinetics of nitrogen ions [46,47].…”