Interrogation of systems level mechanisms controlling DNA repair processes

描述（由申请人提供）：一个完整的生物系统的综合模型将能够预测面对新的遗传和环境扰动的表型结果。细胞系统的这种预测能力，如DMA修复，将对遗传性疾病的早期检测和诊断产生巨大影响，并最终设计预防和/或治愈性治疗。然而，由于其巨大的复杂性，对真核DNA修复系统的充分理解提出了一个艰巨的挑战，特别是考虑到系统方法还不够成熟，无法对这种复杂的过程进行数学建模。在分子水平上，真核生物的遗传信息处理以一种简化的方式反映在它们的进化祖先古细菌上。在盐杆菌NRC-1中，我们有一个简单而强大的约2400个基因的模型系统，其中可以描绘系统方法的基本一般原理。这种嗜盐古菌通常会减轻高盐度，紫外线辐射和干燥-再水化循环的损害。我们将使用这个模型系统来解决的假设，即决策过程中的细胞命运后，暴露于DMA损伤事件，如紫外线照射是介导的强大的基因调控网络，同时处理信息的光谱特征的撞击辐射，性质和程度的DMA损伤和潜在的准备作用的细胞夹带昼夜周期。这一假设的动机是两个主要的观察：a。在UV响应的系统分析中，尽管非常耐受，但并非该微生物中所有预期的修复基因都对辐照或损伤作出响应; B.然而，这些损伤无反应修复基因中的许多确实对昼夜夹带有反应。在基本水平上，这表明细胞在照射时的驻留状态可能会影响引起的反应类型。一个系统的方法是理想的适合于delinate网络的基础上，这一决策过程。具体而言，我们将测量动态的全局变化（损伤程度，mRNA /蛋白质水平，蛋白质-蛋白质和蛋白质-DNA相互作用）在野生型和突变株（传感器，信号转导，调节和修复蛋白缺陷）受到组合的入射辐射，损伤类型和辐射时细胞的驻留状态的变化。通过对这些不同系统水平数据的综合分析，我们将从统计学上了解扰动诱导的基因调控网络的重新布线，该网络将环境扰动（输入）处理为表型（输出），即用于修复的调控机制的预测模型。这个基本模型将作为一个模板，设计系统的方法来模拟更复杂的真核修复过程。

DESCRIPTION (provided by applicant): A comprehensive model of a complete biological system will enable prediction of phenotypic outcomes in face of novel genetic and environmental perturbations. Such predictive power for cellular systems, such as DMA repair, will have tremendous impacts on early detection and diagnosis of genetic disorders and, ultimately in designing preventive and/or curative treatments. However, the full understanding of eukaryotic DMA repair systems presents a daunting challenge due to their enormous complexity, especially given that systems approaches are not yet sufficiently mature to mathematically model such complex processes. At a molecular level, eukaryotic genetic information processing is mirrored in a simplified manner by their evolutionary ancestors, the archaea. In Halobacterium NRC-1 we have a simple yet powerful model system of -2400 genes in which the underlying generalized principles of a systems approach can be delineated. This halophilic archaeon routinely mitigates damage from high salinity, UV radiation and desiccation-rehydration cycles. We will use this model system to address the hypothesis that the decision making process governing cell fate after exposure to DMA damaging events such as UV irradiation is mediated by robust gene regulatory networks that simultaneously process information on spectral characteristics of the impinging radiation, the nature and extent of DMA damage and the potential preparative role of cellular entrainment to diurnal cycles. This hypothesis is motivated by two main observations: a. in systems analysis of UV response, although extraordinarily resistant, not all expected repair genes in this microbe responded to irradiation or damage; b. many of these damage-unresponsive repair genes did, however, respond to day-night entrainment. At a fundamental level this suggested that the resident state of the cell at time of irradiation may influence the type of response elicited. A systems approach is ideally suited to delinate the networks underlying this decision making process. Specifically, we will measure dynamic global changes (degree of damage, mRNA /protein levels, protein-protein and protein-DNA interactions) in wild type and mutant strains (defective in sensors, signal transducers, regulators and repair proteins) subjected to combinatorial changes in incident radiation, type of damage inflicted and resident state of the cell at the time of radiation. Through an integrated analysis of these diverse systems level data we will statistically learn perturbation-induced rewiring of a gene regulatory network that processes environmental perturbations (input) into phenotype (output), i.e. a predictive model for regulatory mechanisms for repair. This basic model will serve as a template for designing systems approaches to model higher complexities of eukaryotic repair processes.