Image-based modeling reveals dynamic redistribution of DNA damage into nuclear sub-domains.
Image-based modeling reveals dynamic redistribution of DNA damage into nuclear sub-domains.
复制标题
DOI：
10.1371/journal.pcbi.0030155
复制
发表时间：
2007-08
影响因子：
4.3
通讯作者：
Barcellos-Hoff, Mary Helen
中科院分区：
文献类型：
--
作者：
Costes, Sylvain V.;Ponomarev, Artem;Chen, James L.;Nguyen, David;Cucinotta, Francis A.;Barcellos-Hoff, Mary Helen
参与DNA双链断裂（DSB）反应的几种蛋白质在暴露于电离辐射后形成显微镜可见的核结构域或病灶。辐射诱导的病灶（RIF）被认为位于DNA损伤发生的地方。为了验证这一假设，我们分析了53BP1、磷酸化ATM和γ H2AX RIF在高线性能量转移（LET）辐射和低LET辐射照射的细胞中的空间分布。由于能量沿沿着高LET粒子路径随机沉积，因此沿这些路径的RIF沿着也应随机分布。诱导DSB的概率可以从通过脉冲场凝胶电泳实验测量的DNA片段数据导出。我们在蒙特卡洛模拟中使用这种概率来预测由一组完整的人类染色体几何描述的合成细胞核中的DSB位置，同时考虑到来自真实的实验的显微镜光学。正如预期的那样，模拟产生了DNA加权随机（泊松）分布。与此相反，早在5分钟后获得的RIF的分布高LET（1 GeV/amu Fe）是非随机的。这种与预期的DNA加权随机模式的偏差可以进一步通过"相对DNA图像测量"来表征。这种新的成像方法表明，RIF优先位于高和低DNA密度区域之间的界面处，并且在DNA密度较低的区域中比预测的更频繁。同样的优先核位置也测量1戈伊低LET辐射诱导的RIF。对于磷酸化的ATM RIF，这种偏离随机行为仅在照射后5分钟明显，而γ H2AX和53BP1 RIF在照射后30分钟显示出明显的偏离。这些数据表明，DNA损伤诱导的病灶仅限于人类上皮细胞核的某些区域。可能的是，DNA损伤被收集在这些核子域中以进行更有效的修复。DNA损伤是日常细胞事件。如果这些事件在生物体中不受控制，它们可能会导致DNA突变，并可能在很长一段时间内导致癌症。因此，细胞具有非常有效的DNA修复机制。许多研究都集中在修复机制中涉及的不同分子因素，忽略了考虑损伤发生的空间背景。因此，关于核结构在DNA损伤反应中的作用知之甚少。在这项研究中，我们引入了计算机建模和图像分析工具，以便将DNA损伤标记的位置与细胞核的形态学不同区域联系起来。使用这些工具，我们表明，辐射诱导的损伤优先位于非凝聚的DNA区域或凝聚的DNA区域的边界。这些结果与目前的教条相矛盾，即对随机产生的DNA损伤的分子反应与其核位置无关。相反，这表明细胞核中存在修复中心。总的来说，我们的方法表明，细胞核结构在DNA损伤反应中起着重要作用，提醒我们细胞核不仅仅是DNA和蛋白质的汤。
Several proteins involved in the response to DNA double strand breaks (DSB) form microscopically visible nuclear domains, or foci, after exposure to ionizing radiation. Radiation-induced foci (RIF) are believed to be located where DNA damage occurs. To test this assumption, we analyzed the spatial distribution of 53BP1, phosphorylated ATM, and γH2AX RIF in cells irradiated with high linear energy transfer (LET) radiation and low LET. Since energy is randomly deposited along high-LET particle paths, RIF along these paths should also be randomly distributed. The probability to induce DSB can be derived from DNA fragment data measured experimentally by pulsed-field gel electrophoresis. We used this probability in Monte Carlo simulations to predict DSB locations in synthetic nuclei geometrically described by a complete set of human chromosomes, taking into account microscope optics from real experiments. As expected, simulations produced DNA-weighted random (Poisson) distributions. In contrast, the distributions of RIF obtained as early as 5 min after exposure to high LET (1 GeV/amu Fe) were non-random. This deviation from the expected DNA-weighted random pattern can be further characterized by “relative DNA image measurements.” This novel imaging approach shows that RIF were located preferentially at the interface between high and low DNA density regions, and were more frequent than predicted in regions with lower DNA density. The same preferential nuclear location was also measured for RIF induced by 1 Gy of low-LET radiation. This deviation from random behavior was evident only 5 min after irradiation for phosphorylated ATM RIF, while γH2AX and 53BP1 RIF showed pronounced deviations up to 30 min after exposure. These data suggest that DNA damage–induced foci are restricted to certain regions of the nucleus of human epithelial cells. It is possible that DNA lesions are collected in these nuclear sub-domains for more efficient repair. DNA damages are daily cellular events. If such events are left unchecked in an organism, they can lead to DNA mutations and possibly cancer over a long period of time. Consequently, cells have very efficient DNA repair machinery. Many studies have focused on the different molecular factors involved in the repair machinery, neglecting to consider the spatial context where damage occurs. Therefore, little is known about the role the nuclear architecture might have in the DNA damage response. In this study, we introduce computer modeling and image analysis tools in order to relate the position of DNA damage markers to morphologically distinct regions of the nucleus. Using these tools, we show that radiation-induced damages locate preferentially in non-condensed DNA regions or at the boundary of regions with condensed DNA. These results contradict the current dogma that the molecular response to randomly generated DNA damages is independent of their nuclear locations. Instead, this suggests the existence of repair centers in the nucleus. Overall, our approach shows that nuclear architecture plays a role in the DNA damage response, reminding us that the nucleus is not simply a soup of DNA and proteins.
登录
查看更多内容
影响因子：
56.9
作者：
Celeste, A;Petersen, S;Nussenzweig, A
通讯作者：
Nussenzweig, A
DOI：
10.1083/jcb.200510130
发表时间：
2006-04-24
期刊：
The Journal of cell biology
影响因子：
--
作者：
Bekker-Jensen S;Lukas C;Kitagawa R;Melander F;Kastan MB;Bartek J;Lukas J
通讯作者：
Lukas J
影响因子：
3.4
作者：
Costes, SV;Boissière, A;Barcellos-Hoff, MH
通讯作者：
Barcellos-Hoff, MH
影响因子：
9.2
作者：
Paull, TT;Rogakou, EP;Bonner, WM
通讯作者：
Bonner, WM
影响因子：
1.7
作者：
Ponomarev, AL;Brenner, D;Sachs, RK
通讯作者：
Sachs, RK