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

2021 ◽  
Author(s):  
Jin-Ho Lee ◽  
Michael Hausmann
Keyword(s):  
Dna Repair ◽  
Ionizing Radiation ◽  
Fluorescence Microscopy ◽  
Spatial Organization ◽  
Super Resolution ◽  
Biological Materials ◽  
Repair Processes ◽  
Repair Protein ◽  
Repair Mechanisms ◽  
Dna Strand

Past efforts in radiobiology, radio-biophysics, epidemiology and clinical research strongly contributed to the current understanding of ionizing radiation effects on biological materials like cells and tissues. It is well accepted that the most dangerous, radiation induced damages of DNA in the cell nucleus are double strand breaks, as their false rearrangements cause dysfunction and tumor cell proliferation. Therefore, cells have developed highly efficient and adapted ways to repair lesions of the DNA double strand. To better understand the mechanisms behind DNA strand repair, a variety of fluorescence microscopy based approaches are routinely used to study radiation responses at the organ, tissue and cellular level. Meanwhile, novel super-resolution fluorescence microscopy techniques have rapidly evolved and become powerful tools to study biological structures and bio-molecular (re-)arrangements at the nano-scale. In fact, recent investigations have increasingly demonstrated how super-resolution microscopy can be applied to the analysis of radiation damage induced chromatin arrangements and DNA repair protein recruitment in order to elucidate how spatial organization of damage sites and repair proteins contribute to the control of repair processes. In this chapter, we would like to start with some fundamental aspects of ionizing radiation, their impact on biological materials, and some standard radiobiology assays. We conclude by introducing the concept behind super-resolution radiobiology using single molecule localization microscopy (SMLM) and present promising results from recent studies that show an organized architecture of damage sites and their environment. Persistent homologies of repair clusters indicate a correlation between repair cluster topology and repair pathway at a given damage locus. This overview over recent investigations may motivate radiobiologists to consider chromatin architecture and spatial repair protein organization for the understanding of DNA repair processes.

scholarly journals Spatial Organization of Transcription in E. Coli using Super-Resolution Fluorescence Microscopy

2017 ◽  
Vol 112 (3) ◽  
pp. 212a
Author(s):  
Xiaoli Weng ◽  
Christopher Bohrer ◽  
Arvin Lagda ◽  
Jie Xiao
Keyword(s):  
Fluorescence Microscopy ◽  
Spatial Organization ◽  
Super Resolution ◽  
E Coli

scholarly journals Roles of the Major, Small, Acid-Soluble Spore Proteins and Spore-Specific and Universal DNA Repair Mechanisms in Resistance of Bacillus subtilis Spores to Ionizing Radiation from X Rays and High-Energy Charged-Particle Bombardment

2007 ◽  
Vol 190 (3) ◽  
pp. 1134-1140 ◽  
Author(s):  
Ralf Moeller ◽  
Peter Setlow ◽  
Gerda Horneck ◽  
Thomas Berger ◽  
Günther Reitz ◽  
...  
Keyword(s):  
Dna Repair ◽  
Bacillus Subtilis ◽  
Ionizing Radiation ◽  
Particle Bombardment ◽  
Strand Break ◽  
High Energy ◽  
X Rays ◽  
Repair Mechanisms ◽  
Spore Proteins ◽  
Genome Protection

ABSTRACT The role of DNA repair by nonhomologous end joining (NHEJ), homologous recombination, spore photoproduct lyase, and DNA polymerase I and genome protection via α/β-type small, acid-soluble spore proteins (SASP) in Bacillus subtilis spore resistance to accelerated heavy ions (high-energy charged [HZE] particles) and X rays has been studied. Spores deficient in NHEJ and α/β-type SASP were significantly more sensitive to HZE particle bombardment and X-ray irradiation than were the recA, polA, and splB mutant and wild-type spores, indicating that NHEJ provides an efficient DNA double-strand break repair pathway during spore germination and that the loss of the α/β-type SASP leads to a significant radiosensitivity to ionizing radiation, suggesting the essential function of these spore proteins as protectants of spore DNA against ionizing radiation.

scholarly journals MKP1 phosphatase is recruited by CXCL12 in glioblastoma cells and plays a role in DNA strand breaks repair

2019 ◽  
Vol 41 (4) ◽  
pp. 417-429
Author(s):  
Matthias Dedobbeleer ◽  
Estelle Willems ◽  
Jeremy Lambert ◽  
Arnaud Lombard ◽  
Marina Digregorio ◽  
...  
Keyword(s):  
Dna Repair ◽  
Map Kinases ◽  
Strand Breaks ◽  
Repair Protein ◽  
Map Kinase Phosphatase ◽  
Dna Repair Protein ◽  
The Central Nervous System ◽  
Subventricular Zones ◽  
Dna Strand ◽  
The Brain

Abstract Glioblastoma (GBM) is the most frequent and aggressive primary tumor in the central nervous system. Previously, the secretion of CXCL12 in the brain subventricular zones has been shown to attract GBM cells and protect against irradiation. However, the exact molecular mechanism behind this radioprotection is still unknown. Here, we demonstrate that CXCL12 modulates the phosphorylation of MAP kinases and their regulator, the nuclear MAP kinase phosphatase 1 (MKP1). We further show that MKP1 is able to decrease GBM cell death and promote DNA repair after irradiation by regulating major apoptotic players, such as Jun-N-terminal kinase, and by stabilizing the DNA repair protein RAD51. Increases in MKP1 levels caused by different corticoid treatments should be reexamined for GBM patients, particularly during their radiotherapy sessions, in order to prevent or to delay the relapses of this tumor.

scholarly journals DNA Damage/Repair Management in Cancers

Cancers ◽  
2020 ◽  
Vol 12 (4) ◽  
pp. 1050 ◽  
Author(s):  
Jehad F. Alhmoud ◽  
John F. Woolley ◽  
Ala-Eddin Al Moustafa ◽  
Mohammed Imad Malki
Keyword(s):  
Dna Damage ◽  
Dna Repair ◽  
Dna Damage Repair ◽  
Critical Factor ◽  
Dna Lesions ◽  
Cancer Development ◽  
Dna Damaging Agents ◽  
Damage Repair ◽  
Repair Mechanisms ◽  
Dna Strand

DNA damage is well recognized as a critical factor in cancer development and progression. DNA lesions create an abnormal nucleotide or nucleotide fragment, causing a break in one or both chains of the DNA strand. When DNA damage occurs, the possibility of generated mutations increases. Genomic instability is one of the most important factors that lead to cancer development. DNA repair pathways perform the essential role of correcting the DNA lesions that occur from DNA damaging agents or carcinogens, thus maintaining genomic stability. Inefficient DNA repair is a critical driving force behind cancer establishment, progression and evolution. A thorough understanding of DNA repair mechanisms in cancer will allow for better therapeutic intervention. In this review we will discuss the relationship between DNA damage/repair mechanisms and cancer, and how we can target these pathways.

scholarly journals Super-resolution imaging of RAD51 and DMC1 in DNA repair foci reveals dynamic distribution patterns in meiotic prophase

2020 ◽  
Author(s):  
Johan A Slotman ◽  
Maarten W Paul ◽  
Fabrizia Carofiglio ◽  
H Martijn de Gruiter ◽  
Tessa Vergroesen ◽  
...  
Keyword(s):  
Dna Repair ◽  
Homologous Recombination ◽  
Meiotic Prophase ◽  
Spatial Organization ◽  
Average Distance ◽  
Super Resolution ◽  
Protein Accumulation ◽  
Dsb Repair ◽  
Depth Analysis ◽  
Super Resolution Microscopy

ABSTRACTThe recombinase RAD51, and its meiosis-specific paralog DMC1 localize at DNA double-strand break (DSB) repair sites in meiotic prophase nuclei. While both proteins are required during meiotic homologous recombination, their spatial organization during meiotic DSB repair is not fully understood. Using super-resolution microscopy on mouse spermatocyte nuclei, we aimed to define their relative position at DSB foci, and how these vary in time. We show that a large fraction of meiotic DSB repair foci (38%) contained a single RAD51 cluster and a single DMC1 cluster (D1R1 configuration) that were partially overlapping (average center-center distance around 70 nm). The majority of the rest of the foci had a similar combination of a major RAD51 and DMC1 cluster, but in combination with additional clusters (D2R1, D1R2, D2R2, or DxRy configuration) at an average distance of around 250 nm. As prophase progressed, less D1R1 and more D2R1 foci were observed, where the RAD51 cluster in the D2R1 foci elongated and gradually oriented towards the distant DMC1 cluster. This correlated with more frequently observed RAD51 bridges between the two DMC1 clusters. D1R2 foci frequency was more constant, and the single DMC1 cluster did not elongate, but was observed more frequently in between the two RAD51 clusters in early stages. D2R2 foci were rare (<10%) and nearest neighbour analyses also did not reveal pair formation between D1R1 foci. In the absence of the transverse filament of the synaptonemal complex (connecting the chromosomal axes of homologs), early configurations were more prominent, and RAD51 elongation occurred only transiently. This in-depth analysis of single cell landscapes of RAD51 and DMC1 accumulation patterns at DSB repair sites at super-resolution thus revealed the variability of foci composition, and defined functional consensus configurations that change over time.AUTHOR SUMMARYMeiosis is a specific type of cell division that is central to sperm and egg formation in sexual reproduction. It forms cells with a single copy of each chromosome, instead of the two copies that are normally present. In meiotic prophase, homologous chromosomes must connect to each other, to be correctly distributed between the daughter cells. This involves the formation and repair of double-strand breaks in the DNA. Here we used super-resolution microscopy to elucidate the localization patterns of two important DNA repair proteins: RAD51 and DMC1. We found that repair sites most often contain a single large cluster of both proteins, with or without one additional smaller cluster of either protein. RAD51 protein clusters displayed lengthening as meiotic prophase progressed. When chromosome pairing was disturbed, we observed changes in the dynamics of protein accumulation patterns, indicating that they actually correspond to certain repair intermediates changing in relative frequency of occurrence. These analyses of single meiotic DNA repair foci reveal the biological variability in protein accumulation patterns, and the localization of RAD51 and DMC1 relative to each other, thereby contributing to our understanding of the molecular basis of meiotic homologous recombination.

Single-molecule live-cell imaging of bacterial DNA repair and damage tolerance

2017 ◽  
Vol 46 (1) ◽  
pp. 23-35 ◽  
Author(s):  
Harshad Ghodke ◽  
Han Ho ◽  
Antoine M. van Oijen
Keyword(s):  
Dna Repair ◽  
Single Molecule ◽  
Live Cell Imaging ◽  
Spatial Organization ◽  
Cell Imaging ◽  
Live Cell ◽  
Live Cells ◽  
Temporal Regulation ◽  
Repair Processes ◽  
Wide Range

Genomic DNA is constantly under threat from intracellular and environmental factors that damage its chemical structure. Uncorrected DNA damage may impede cellular propagation or even result in cell death, making it critical to restore genomic integrity. Decades of research have revealed a wide range of mechanisms through which repair factors recognize damage and co-ordinate repair processes. In recent years, single-molecule live-cell imaging methods have further enriched our understanding of how repair factors operate in the crowded intracellular environment. The ability to follow individual biochemical events, as they occur in live cells, makes single-molecule techniques tremendously powerful to uncover the spatial organization and temporal regulation of repair factors during DNA–repair reactions. In this review, we will cover practical aspects of single-molecule live-cell imaging and highlight recent advances accomplished by the application of these experimental approaches to the study of DNA–repair processes in prokaryotes.

scholarly journals Tools for Decoding Ubiquitin Signaling in DNA Repair

2021 ◽  
Vol 9 ◽  
Author(s):  
Benjamin Foster ◽  
Martin Attwood ◽  
Ian Gibbs-Seymour
Keyword(s):  
Dna Repair ◽  
Mammalian Cells ◽  
Genome Stability ◽  
Dna Lesions ◽  
Post Translational Modifications ◽  
Dna Repair Mechanisms ◽  
Repair Processes ◽  
Repair Mechanisms ◽  
Mechanistic Basis ◽  
Cellular Dna

The maintenance of genome stability requires dedicated DNA repair processes and pathways that are essential for the faithful duplication and propagation of chromosomes. These DNA repair mechanisms counteract the potentially deleterious impact of the frequent genotoxic challenges faced by cells from both exogenous and endogenous agents. Intrinsic to these mechanisms, cells have an arsenal of protein factors that can be utilised to promote repair processes in response to DNA lesions. Orchestration of the protein factors within the various cellular DNA repair pathways is performed, in part, by post-translational modifications, such as phosphorylation, ubiquitin, SUMO and other ubiquitin-like modifiers (UBLs). In this review, we firstly explore recent advances in the tools for identifying factors involved in both DNA repair and ubiquitin signaling pathways. We then expand on this by evaluating the growing repertoire of proteomic, biochemical and structural techniques available to further understand the mechanistic basis by which these complex modifications regulate DNA repair. Together, we provide a snapshot of the range of methods now available to investigate and decode how ubiquitin signaling can promote DNA repair and maintain genome stability in mammalian cells.

scholarly journals Quantification of DNA damage induced γH2AX focus formation via super-resolution dSTORM localization microscopy

2019 ◽  
Author(s):  
Dániel Varga ◽  
Hajnalka Majoros ◽  
Zsuzsanna Újfaludi ◽  
Miklós Erdélyi ◽  
Tibor Pankotai
Keyword(s):  
Dna Damage ◽  
Chromatin Structure ◽  
Spatial Organization ◽  
Super Resolution ◽  
Quantitative Information ◽  
Dna Double Strand Breaks ◽  
Focus Formation ◽  
Break Site ◽  
Nucleosome Density ◽  
Repair Mechanisms

SUMMARYIn eukaryotic cells, each process, in which DNA is involved, should take place in the context of chromatin structure. DNA double-strand breaks (DSBs) are one of the most deleterious damages often leading to chromosomal rearrangement. In response to environmental stresses, cells have developed repair mechanisms to eliminate the DSBs. Upon DSB induction, several factors play roles in chromatin relaxation by catalysing the appropriate histone posttranslational modification (PTM) steps, therefore promoting the access of the repair factors to the DSBs. Among these PTMs, the phosphorylation of the histone variant H2AX at its Ser139 residue (also known as γH2AX) could be observed at the break sites. The structure of γH2AX focus has to be organized during the repair as it contributes to accessibility of specific repair proteins to the damaged site. Our aim was to develop a quantitative approach to analyse the morphology of individual repair foci by super-resolution dSTORM microscopy to gain insight into genome organization in DNA repair. We have established a specific dSTORM measurement process by developing a new analytical algorithm for gaining quantitative information about chromatin morphology and repair foci topology at individual γH2AX enriched repair focus. By this method we quantified unique repair foci to show the average distribution of γH2AX clusters. By monitoring γH2AX signal, we could reach 20 nm spatial resolution and resolve a single DNA damage spot, which allow us to identify different chromatin sub-clusters around the break site. Additionally, based on our new analysis method, we were able to show the number of nucleosomes in each sub-cluster that could allow us to define the possible chromatin structure and the nucleosome density around the break sites. This method is the first demonstration of a single-cell based quantitative measurement of a discrete repair focus, which could provide new opportunities to categorize spatial organization of dot patterns by parametric determination of topological similarity.

scholarly journals In Situ Imaging of Spatial Organization of Accessible Chromatin at the Nanoscale with ATAC-see and Single-Molecule Super-Resolution Fluorescence Microscopy

2018 ◽  
Vol 114 (3) ◽  
pp. 539a
Author(s):  
Maurice Y. Lee ◽  
Xingqi Chen ◽  
Anna-Karin Gustavsson ◽  
Howard Y. Chang ◽  
W.E. Moerner
Keyword(s):  
Fluorescence Microscopy ◽  
Single Molecule ◽  
Spatial Organization ◽  
Super Resolution ◽  
Accessible Chromatin ◽  
In Situ Imaging
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