Mechanistic Modelling and Bayesian Inference Elucidates the Variable Dynamics of Double-Strand Break Repair
Mechanistic Modelling and Bayesian Inference Elucidates the Variable Dynamics of Double-Strand Break Repair
复制标题
DOI：
10.1371/journal.pcbi.1005131
复制
发表时间：
2016-10-01
影响因子：
4.3
通讯作者：
Barnes, Chris P.
中科院分区：
文献类型：
--
作者：
Woods, Mae L.;Barnes, Chris P.
DNA双链断裂是在新陈代谢、DNA复制和暴露于诱变剂期间形成的损伤。当双链断裂发生时，许多修复机制中的一种被招募，所有这些机制都有不同的突变事件倾向。尽管DNA修复是至关重要的，但这些机制及其调控相互作用的相对贡献仍有待充分阐明。了解这些突变过程将对我们对基因组不稳定的知识产生深远影响，并涉及健康、疾病和进化。在这里，我们提出了一种新的方法来模拟非同源末端连接、单链退火和交替末端连接在电离辐射下的联合激活。我们使用贝叶斯统计方法对不同基因敲除情况下的双链断裂修复曲线的8个生物数据集进行整合，并通过重新模拟和与额外数据的比较来确认我们的模型是可预测的。对模型的分析表明，至少存在三种不相交的修复模式，我们将其归类为快速、缓慢和中等。我们的结果表明，当组合多个数据集时，不同基因敲除的中间修复率是不同的。进一步的分析表明，缓慢修复和中期修复的比例取决于DNA-PKcs和Ku70的存在与否，这意味着非同源末端连接和替代末端连接不是独立的。最后，我们将每个机制中双链断裂的比例视为一个时间序列，并作为修复率的函数来预测活动。我们概述了如何使用成像和测序技术直接测试我们的洞察力，并得出结论，在替代修复途径中存在可变动力学的证据。我们的方法是朝着为DNA修复过程的动力学提供统一的理论框架迈出的重要一步。
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.