Image-based modeling reveals dynamic redistribution of DNA damage into nuclear sub-domains

• Published in: PLoS computational biology Vol. 3; no. 8; p. e155
• Main Authors: Costes, Sylvain V, Ponomarev, Artem, Chen, James L, Nguyen, David, Cucinotta, Francis A, Barcellos-Hoff, Mary Helen
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 01.08.2007; Public Library of Science (PLoS)
• Subjects: Analysis; BASIC BIOLOGICAL SCIENCES; biochemical simulations; Biological models; Biophysics; Cell Nucleus - metabolism; Cell Nucleus - radiation effects; Cell Nucleus - ultrastructure; chromatin; Computer Simulation; DNA; DNA - chemistry; DNA - physiology; DNA - radiation effects; DNA - ultrastructure; DNA damage; DNA Damage - physiology; DNA repair; DNA Repair - physiology; DNA Repair - radiation effects; Epithelial Cells - physiology; Epithelial Cells - radiation effects; gamma radiation; Homo (Human); Humans; Image Interpretation, Computer-Assisted - methods; ionizing radiation; MATHEMATICS AND COMPUTING; Models, Biological; Monte Carlo method; probability density; Properties; Proteins; Studies; United States; Models, Biological; Computer Simulation; DNA; DNA Repair; Humans; Image Interpretation, Computer-Assisted; Epithelial Cells; DNA Damage; Cell Nucleus
• ISSN: 1553-7358; 1553-734X; 1553-7358
• DOI: 10.1371/journal.pcbi.0030155

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 gammaH2AX 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 gammaH2AX 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.