In cancer therapy, the application of (fractionated) harsh radiation treatment is state of the art for many types of tumors. However, ionizing radiation is a "double-edged sword"-it can kill the tumor but can also promote the selection of radioresistant tumor cell clones or even initiate carcinogenesis in the normal irradiated tissue. Individualized radiotherapy would reduce these risks and boost the treatment, but its development requires a deep understanding of DNA damage and repair processes and the corresponding control mechanisms. DNA double strand breaks (DSBs) and their repair play a critical role in the cellular response to radiation. In previous years, it has become apparent that, beyond genetic and epigenetic determinants, the structural aspects of damaged chromatin (i.e., not only of DSBs themselves but also of the whole damage-surrounding chromatin domains) form another layer of complex DSB regulation. In the present article, we summarize the application of super-resolution single molecule localization microscopy (SMLM) for investigations of these structural aspects with emphasis on the relationship between the nano-architecture of radiation-induced repair foci (IRIFs), represented here by γH2AX foci, and their chromatin environment. Using irradiated HeLa cell cultures as an example, we show repair-dependent rearrangements of damaged chromatin and analyze the architecture of γH2AX repair clusters according to topological similarities. Although HeLa cells are known to have highly aberrant genomes, the topological similarity of γH2AX was high, indicating a functional, presumptively genome type-independent relevance of structural aspects in DSB repair. Remarkably, nano-scaled chromatin rearrangements during repair depended both on the chromatin domain type and the treatment. Based on these results, we demonstrate how the nano-architecture and topology of IRIFs and chromatin can be determined, point to the methodological relevance of SMLM, and discuss the consequences of the observed phenomena for the DSB repair network regulation or, for instance, radiation treatment outcomes.

Institute for Theoretical Physics Heidelberg University 69120 Heidelberg Germany

Institute of Biophysics Czech Academy of Sciences 612 65 Brno Czech Republic

Kirchhoff Institute for Physics Heidelberg University 69120 Heidelberg Germany

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Lukášová E., Kozubek S., Falk M., Kozubek M., Žaloudík J., Vagunda V., Pavlovský Z. Topography of Genetic Loci in the Nuclei of Cells of Colorectal Carcinoma and Adjacent Tissue of Colonic Epithelium. Chromosoma. 2004;112:221–230. doi: 10.1007/s00412-003-0263-3. PubMed DOI

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Falk M., Lukasova E., Gabrielova B., Ondrej V., Kozubek S. Chromatin Dynamics during DSB Repair. Biochim. Biophys. Acta. 2007;1773:1534–1545. doi: 10.1016/j.bbamcr.2007.07.002. PubMed DOI

Condensed Matter Systems Exposed to Radiation: Multiscale Theory, Simulations, and Experiment

Advanced image-free analysis of the nano-organization of chromatin and other biomolecules by Single Molecule Localization Microscopy (SMLM)

Spatial-Temporal Genome Regulation in Stress-Response and Cell-Fate Change

Incorporation of Low Concentrations of Gold Nanoparticles: Complex Effects on Radiation Response and Fate of Cancer Cells

Topological Analysis of γH2AX and MRE11 Clusters Detected by Localization Microscopy during X-ray-Induced DNA Double-Strand Break Repair