Elsevier

DNA Repair

Volume 100, April 2021, 103035
DNA Repair

Review Article
Kinetics model of DNA double-strand break repair in eukaryotes

https://doi.org/10.1016/j.dnarep.2020.103035Get rights and content

Abstract

This manuscript outlines the kinetics of two main repair pathways of DNA double-strand break (DSB) in eukaryotes: non-homologous end joining (NHEJ) and homologous recombination repair (HRR). In this review, we discuss the precise study of recruitment kinetics of repair proteins based on the latest technologies in the past two decades. Then we simulate the theoretical description of the DNA repair process by mathematical models. In our study, the consecutive reactions chain (CRC) model and continuous-time random walk (CTRW) model have been unified by us, so that we can obtain the function of the number of intermediates with time in the same framework of equations, overcome the incompatibility between the two models. On this basis, we propose a data fitting workflow using these both models. Finally, we give an overview of different real-time quantitative methods and the new mechanism complexity that can be found from the corresponding dynamic models.

Introduction

DNA double-strand breaks (DSBs) represent the most toxic DNA lesion. The existence of a single DSB unrepaired in a vertebrates cell is sufficient to induce lethality [1]. Ionizing radiation and radiomimetic drugs can induce an enormous number of DSBs. DSBs in eukaryotic cells can be well deal with a complex DNA damage response (DDR) network, which is constituted by several intracellular cascade of events including DNA lesion recognition, signaling, regulation of cell cycle progression, and repair events [2]. Finally, they activate specific DNA repair systems to remove these DNA lesions [3]. The reactivity of these systems is quantified by an intuitive method. The histone H2AX in the chromatin regions on both sides of DSB forms γ-H2AX through ATM-mediated phosphorylation of serine 139 (S139). This process is usually completed within minutes after DSBs generation [4], specific fluorescent antibody labeled γ-H2AX "foci" with a volume of about 1μm3 was visualized by laser confocal microscopy [5]. This method lay a fundamental for studying the kinetics of DNA repair by detecting the location and number of DSBs in real time [6].

It is surprising that the elimination of DSB in eukaryotes is not according to the first-order kinetics, but contains at least a biphasic characteristic. The number of DSBs follows a second-order exponential function:DSBt=DSBt0(1-ae-k1t-be-k2t)a,b represents the proportion of two repair methods with a different rate. k1,k2 are their respective rate constants.

Over the same period, studies on DSB repair in prokaryotes and lower eukaryotes demonstrated that homologous recombination repair (HRR) is the major DSB repair pathway, which requires extensive homology between the recombining DNA molecules. But there is another pathway that did not require extensive homology found in eukaryotes, defined as non-homologous end joining (NHEJ) [7]. These two mechanisms are the main DSB repair pathways employed by eukaryotic cells and are agreed with the observed results, they respectively represent the process of slow phase and fast phase of S / G2 phase cells. The components of NHEJ and HRR were gradually identified and resolved to specific biological functions. The function of DNA repair protein often depends on its binding to the end of DNA. Early studies established a preliminary theoretical model by measuring the rough recruitment kinetics of repair protein. In recent years, with the development of high-resolution fluorescence microscopy, single-molecule fluorescence imaging provides the most in-depth visualization method for DSB foci analysis and in-situ analysis. The most representative is Aleksandrov et al. [8] carried out the arduous task in 2018, measuring and mathematically modeling the precise recruitment kinetics of 70 proteins at laser-induced lesion sites. On the other hand, Intermediates in the DSB repair process can be identified by fluorescence resonance energy transfer technique (FRET), like Graham, T. G.et al. [9] identified long-range and short-range bridging intermediates that NHEJ undergoing in 2016.

The comprehensive information obtained by various technologies makes it possible to establish multiple mathematical models that can be connected and clarify the complex DSB repair regulatory network. This paper arranges the basic theory, modeling strategy, and model development of the DSB repair process. On this foundation, we derive a unified intermediate kinetic model of DSB repair.

Section snippets

Basic kinetics theory of DSB repair

We model the kinetics of the DSB repair process as a series of consecutive reactions (Fig. 1). The initial reactant are DSBs and the final product of the reaction are repaired DNA. We assume that the reaction needs to undergo several intermediates thereby the reaction is simplified to finite separable steps, called the consecutive reactions chain (CRC) model [8].

Each circle represents an entity. To simplify the symbol, we use xi to represent the quantity of each entity and ki to represent the

Kinetics model of NHEJ

Previous studies have elucidated the molecular mechanism of the classical NHEJ repair process. First, the Ku70-Ku80 heterodimer (Ku) binds to blunt or short single-stranded DNA ends rapidly to protect them from nucleolytic degradation [13], it recruits DNA-dependent protein kinase catalytic subunit (DNA-PKcs) to generate the DNA-PK holoenzyme. DNA-PKcs regulates subsequent reactions through self-phosphorylation of serine-threonine residues [14]. The assembling of DNA-PK promotes the recruitment

Kinetics model of HRR

HRR can be chronologically divided into three steps: DSB end resection, synthesis of missing sequences by template, and annealing and joining.

DSB end resection is defined by the nucleolytic degradation of the 5’ -terminated strands in DSBs end to form an extended single-strand DNA (ssDNA) region [10]. As we all know, HRR requires available sister chromatids to serve as templates, but the double helix structure of the DNA end could not be complementary with the template chain. Thus, the first

Conclusion

Kinetics has a significant advantage in the study of non-equilibrium systems. It can provide more details of DSB repair mechanism and radiation reaction, and deepen the understanding of the results of complex physical, chemical, and biological interactions. The established DSB repair kinetic model can help us to capture the individual and global behavior of repair proteins [38] to analyze the internal law of the complex system. As McMahon, S. J.et al. [39] reviewed, in contrast to other areas

Declaration of Competing Interest

The authors report no declarations of interest.

Acknowledgments

This work is supported by the National Natural Science Foundation of China, China (Grant No. 81741143 and No. 11705085), the Research Foundation of Education Bureau of Hunan Province, China (Grant No. 17A186) and the Natural Science Foundation of Hunan Province, China (Grant No. 2018JJ3458 and No. 2020JJ6050).

References (39)

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