Modeling non-homologous end joining

Li, Yongfeng; Cucinotta, Francis A.

doi:10.1016/j.jtbi.2011.05.015

Cited by 17 publications

(12 citation statements)

References 33 publications

(5 reference statements)

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“…Although classically described as a pathway, growing evidence argues that NHEJ is not a strictly sequential process (6–8, 40, 41). So, whereas a sequential pathway or sequential assembly can provide useful insights, it falls short of integrating all existing data.…”

Section: Discussionmentioning

confidence: 99%

An Intrinsically Disordered APLF Links Ku, DNA-PKcs, and XRCC4-DNA Ligase IV in an Extended Flexible Non-homologous End Joining Complex

Hammel

Radhakrishnan

et al. 2016

Journal of Biological Chemistry

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DNA double-strand break (DSB) repair by non-homologous end joining (NHEJ) in human cells is initiated by Ku heterodimer binding to a DSB, followed by recruitment of core NHEJ factors including DNA-dependent protein kinase catalytic subunit (DNA-PKcs), XRCC4-like factor (XLF), and XRCC4 (X4)-DNA ligase IV (L4). Ku also interacts with accessory factors such as aprataxin and polynucleotide kinase/phosphatase-like factor (APLF). Yet, how these factors interact to tether, process, and ligate DSB ends while allowing regulation and chromatin interactions remains enigmatic. Here, small angle X-ray scattering (SAXS) and mutational analyses show APLF is largely an intrinsically disordered protein that binds Ku, Ku/DNA-PKcs (DNA-PK), and X4L4 within an extended flexible NHEJ core complex. X4L4 assembles with Ku heterodimers linked to DNA-PKcs via flexible Ku80 C-terminal regions (Ku80CTR) in a complex stabilized through APLF interactions with Ku, DNA-PK, and X4L4. Collective results unveil the solution architecture of the six-protein complex and suggest cooperative assembly of an extended flexible NHEJ core complex that supports APLF accessibility while possibly providing flexible attachment of the core complex to chromatin. The resulting dynamic tethering furthermore, provides geometric access of L4 catalytic domains to the DNA ends during ligation and of DNA-PKcs for targeted phosphorylation of other NHEJ proteins as well as trans-phosphorylation of DNA-PKcs on the opposing DSB without disrupting the core ligation complex. Overall the results shed light on evolutionary conservation of Ku, X4, and L4 activities, while explaining the observation that Ku80CTR and DNA-PKcs only occur in a subset of higher eukaryotes.

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Section: Discussionmentioning

confidence: 99%

An Intrinsically Disordered APLF Links Ku, DNA-PKcs, and XRCC4-DNA Ligase IV in an Extended Flexible Non-homologous End Joining Complex

Hammel

Radhakrishnan

et al. 2016

Journal of Biological Chemistry

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“…These models are based on the rate of repair of DSBs post irradiation, as measured by PFGE (generally in the dose range of 40–100 Gy), where the rate determining step essentially defines the rate of DSB rejoining, generally ligation of the majority of DSB for low LET radiation. Li and Cucinotta [28] used mathematical analysis to study the importance of the sequence of recruitment of several repair proteins in NHEJ. More recently, Taleei and Nikjoo [34], [35] have modeled NHEJ repair kinetics from biochemical data in repair proficient and deficient cells following high IR doses (10–80 Gy).…”

Section: Introductionmentioning

confidence: 99%

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

Reynolds

O’Neill

et al. 2014

PLoS ONE

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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.

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“…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].…”

Section: Published Computational Modeling Studies Of Dsb Repairmentioning

confidence: 99%