A Paradigm Revolution or Just Better Resolution—Will Newly Emerging Superresolution Techniques Identify Chromatin Architecture as a Key Factor in Radiation-Induced DNA Damage and Repair Regulation?

Abstract

DNA double-strand breaks (DSBs) have been recognized as the most serious lesions in irradiated cells. While several biochemical pathways capable of repairing these lesions have been identified, the mechanisms by which cells select a specific pathway for activation at a given DSB site remain poorly understood. Our knowledge of DSB induction and repair has increased dramatically since the discovery of ionizing radiation-induced foci (IRIFs), initiating the possibility of spatiotemporally monitoring the assembly and disassembly of repair complexes in single cells. IRIF exploration revealed that all post-irradiation processes—DSB formation, repair and misrepair—are strongly dependent on the characteristics of DSB damage and the microarchitecture of the whole affected chromatin domain in addition to the cell status. The microscale features of IRIFs, such as their morphology, mobility, spatiotemporal distribution, and persistence kinetics, have been linked to repair mechanisms. However, the influence of various biochemical and structural factors and their specific combinations on IRIF architecture remains unknown, as does the hierarchy of these factors in the decision-making process for a particular repair mechanism at each individual DSB site. New insights into the relationship between the physical properties of the incident radiation, chromatin architecture, IRIF architecture, and DSB repair mechanisms and repair efficiency are expected from recent developments in optical superresolution microscopy (nanoscopy) techniques that have shifted our ability to analyze chromatin and IRIF architectures towards the nanoscale. In the present review, we discuss this relationship, attempt to correlate still rather isolated nanoscale studies with already better-understood aspects of DSB repair at the microscale, and consider whether newly emerging “correlated multiscale structuromics” can revolutionarily enhance our knowledge in this field.

O-GlcNAcylation Affects the Pathway Choice of DNA Double-Strand Break Repair

“…We showed that inhibiting OGT leads to more condensed chromatin, whilst inhibition of OGA induces a global chromatin relaxation. As it was found that, upon DNA damage, chromatin decompaction is stimulated globally [ 28 , 49 ], but also locally [ 27 , 50 , 51 ], and since it is known that within repair of DNA damage the chromatin status is crucial for the repair-pathway choice and the recruitment of DSB repair factors [ 26 , 52 ], we conclude that O-GlcNAcylation may also impact on the DSBs response by regulating chromatin remodeling. This is supported by several findings that OGT and OGA modulate recruitment, stability and activity of key chromatin regulators [ 23 , 24 ].…”

“…The role of O-GlcNAc on chromatin architecture in the context of the DDR has not been studied yet. However, since the chromatin status is crucial for DSB-repair processes [ 26 ], O-GlcNAcylation might impact on DSB repair that way as well. To this end, we made use of a recently established method based on FLIM [ 27 , 28 ] to identify effects of O-GlcNAcylation on the chromatin compaction status after treating the cells with OGT or OGA inhibitors.…”

Super-Resolution Radiation Biology: From Bio-Dosimetry towards Nano-Studies of DNA Repair Mechanisms

“…Among all kinds of ionizing radiation induced biological effects, damages to chromatin especially the DNA molecules in the nucleus of cells are thought to be the most severe with respect to cellular survival and carcinogenesis [2,5,32,33]. DNA base oxidation, single strand breaks (SSBs) and double strand breaks (DSBs) are the most common ionizing radiation induced damages to the DNA molecule, that affect genome integrity and DNA biochemistry [34].…”

“…and biological (e.g., developmental and proliferative state of the affected cell type) factors. As the overall organismal radiation response results from the entirety of all individual radiation responses on the single cell level, deeper understanding of the underlying, complex molecular mechanisms and dynamics of radiation induced DNA damaging and repair on the cellular level is highly relevant for fundamental and applied radiation biology (for review see [1,2,5]).…”

“…Methods based on stochastic reversible photobleaching [9][10][11][12][13][14][15] of single molecules called Single Molecule Localization Microscopy (SMLM) [16] reach effective resolutions down to 10 nm and have become popular among modern super-resolution imaging techniques as their realization is highly practical and straightforward using established specimen preparation methods of standard fluorescence microcopy [17]. As such resolutions allow the detection of single molecules, such as nucleosomes [18], proteins [19,20], receptors and junction proteins [21,22], or even single chromatin loops [23] etc., super-resolution microscopy opens new avenues for the research of radiation induced damaging and repair processes [5,24].…”