Mechanistic modelling and Bayesian inference elucidates the variable dynamics of double-strand break repair

Abstract

DNA double-strand breaks are lesions that form during metabolism, DNA replication and exposure to mutagens. When a double-strand break occurs one of a number of repair mechanisms is recruited, all of which have differing propensities for mutational events. Despite DNA repair being of crucial importance, the relative contribution of these mechanisms and their regulatory interactions remain to be fully elucidated. Understanding these mutational processes will have a profound impact on our knowledge of genomic instability, with implications across health, disease and evolution. Here we present a new method to model the combined activation of non-homologous end joining, single strand annealing and alternative end joining, following exposure to ionising radiation. We use Bayesian statistics to integrate eight biological data sets of double-strand break repair curves under varying genetic knockouts and confirm that our model is predictive by re-simulating and comparing to additional data. Analysis of the model suggests that there are at least three disjoint modes of repair, which we assign as fast, slow and intermediate. Our results show that when multiple data sets are combined, the rate for intermediate repair is variable amongst genetic knockouts. Further analysis suggests that the ratio between slow and intermediate repair depends on the presence or absence of DNA-PKcs and Ku70, which implies that non-homologous end joining and alternative end joining are not independent. Finally, we consider the proportion of double-strand breaks within each mechanism as a time series and predict activity as a function of repair rate. We outline how our insights can be directly tested using imaging and sequencing techniques and conclude that there is evidence of variable dynamics in alternative repair pathways. Our approach is an important step towards providing a unifying theoretical framework for the dynamics of DNA repair processes. Author SummaryDNA double-strand breaks occur during metabolism, DNA replication and by exposure to exogenous sources such as ionising radiation. When the genome is inflicted with this type of damage, DNA repair machinery is promoted to restore genome structure. The efficient interplay between DNA damage and repair is crucial to genome stability because the choice of repair mechanism directly affects the probability of mutation. Multiple mechanisms of DNA repair are known to exist, however, the subtleties of how they are activated and their interactions are yet to be fully determined. We hypothesise that a combination of Bayesian statistics and mathematical modeling is essential to elucidate the network dynamics. Studies in the literature have presented time series data of double-strand break repair in wild type and mutant cells. By combining existing time series data, our modeling approach can quantify the differences in activation amongst mutants and in addition identify a number of novel insights into the dynamics of the competing mechanisms. We conclude that alternative mechanisms of rep...