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https://www.readbyqxmd.com/read/29054115/reversible-mono-adp-ribosylation-of-dna-breaks
#1
Deeksha Munnur, Ivan Ahel
ADP-ribosylation is a chemical modification of macromolecules that plays an important role in regulation of quintessential biological processes such as DNA repair, transcription, chromatin remodelling, stress response, apoptosis, bacterial metabolism and many others. ADP-ribosylation is carried out by ADP-ribosyltransferase proteins, such as poly(ADP-ribose) polymerases (PARPs) that transfer either monomer or polymers of ADP-ribose onto the molecular targets by using nicotinamide adenine dinucleotide (NAD(+) ) as a cofactor...
October 20, 2017: FEBS Journal
https://www.readbyqxmd.com/read/29053826/induction-of-somatic-mutations-by-low-dose-x-rays-the-challenge-in-recognizing-radiation-induced-events
#2
Haruki Nagashima, Kumiko Shiraishi, Saori Ohkawa, Yuki Sakamoto, Kenshi Komatsu, Shinya Matsuura, Akira Tachibana, Hiroshi Tauchi
It is difficult to distinguish radiation-induced events from spontaneous events during induction of stochastic effects, especially in the case of low-dose or low-dose-rate exposures. By using a hypersensitive system for detecting somatic mutations at the HPRT1 locus, we investigated the frequency and spectrum of mutations induced by low-dose X-rays. The mutant frequencies induced by doses of >0.15 Gy were statistically significant when compared with the spontaneous frequency, and a clear dose dependency was also observed for mutant frequencies at doses of >0...
October 19, 2017: Journal of Radiation Research
https://www.readbyqxmd.com/read/29053680/evaluating-in-vitro-dna-damage-using-comet-assay
#3
Yanxin Lu, Yang Liu, Chunzhang Yang
DNA damage is a common phenomenon for each cell during its lifespan, and is defined as an alteration of the chemical structure of genomic DNA. Cancer therapies, such as radio- and chemotherapy, introduce enormous amount of additional DNA damage, leading to cell cycle arrest and apoptosis to limit cancer progression. Quantitative assessment of DNA damage during experimental cancer therapy is a key step to justify the effectiveness of a genotoxic agent. In this study, we focus on a single cell electrophoresis assay, also known as the comet assay, which can quantify single and double-strand DNA breaks in vitro...
October 11, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/29053406/super-resolution-nanoscopy-imaging-applied-to-dna-double-strand-breaks
#4
Sofia D'Abrantes, Sarah Gratton, Pamela Reynolds, Verena Kriechbaumer, Joseph McKenna, Stephen Barnard, Dave Clarke, Stanley W Botchway
Genomic deoxyribonucleic acid (DNA) is continuously being damaged by endogenous processes such as metabolism or by exogenous events such as radiation. The specific phosphorylation of histone H2AX on serine residue 139, described as γ-H2AX, is an excellent indicator or marker of DNA double-strand breaks (DSBs). The yield of γ-H2AX (foci) is shown to have some correlation with the dose of radiation or other DSB-causing agents. However, there is some discrepancy in the DNA DSB foci yield among imaging and other methods such as gel electrophoresis...
October 20, 2017: Radiation Research
https://www.readbyqxmd.com/read/29052759/telomerase-regulation-by-the-pif1-helicase-a-length-dependent-effect
#5
Sonia Stinus, Katrin Paeschke, Michael Chang
Dysfunctional telomere length regulation is detrimental to human health, and both activation and inhibition of telomerase have been proposed in potential therapies to treat human diseases. The Saccharomyces cerevisiae Pif1 protein is an evolutionarily conserved helicase that inhibits telomerase activity at DNA ends. Recent studies have indicated that Pif1 is specifically important for inhibiting telomerase at DNA ends with very little or no telomeric sequence and at long telomeres. At the former, Pif1 prevents the inappropriate addition of a telomere at DNA double-strand breaks...
October 20, 2017: Current Genetics
https://www.readbyqxmd.com/read/29052312/bleomycin-induced-chromosomal-damage-and-shortening-of-telomeres-in-peripheral-blood-lymphocytes-of-incident-cancer-patients
#6
Michal Kroupa, Zdenka Polivkova, Sivaramakrishna Rachakonda, Michaela Schneiderova, Sona Vodenkova, Tomas Buchler, Katerina Jiraskova, Marketa Urbanova, Ludmila Vodickova, Kari Hemminki, Rajiv Kumar, Pavel Vodicka
Disruption of genomic integrity due to deficient DNA repair capacity and telomere shortening constitute hallmarks of malignant diseases. Incomplete or deficient repair of DNA double-strand breaks (DSB) is manifested by chromosomal aberrations (CAs) and their frequency reflects inter-individual differences of response to exposure to mutagenic compounds. In this study, we investigated chromosomal integrity in peripheral blood lymphocytes (PBL) from newly diagnosed cancer patients, including 47 breast (BC) and 44 colorectal cancer (CRC) patients and 90 matched healthy controls...
October 20, 2017: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/29048423/identification-of-cross-talk-between-sumoylation-and-ubiquitylation-using-a-sequential-peptide-immunopurification-approach
#7
Francis P McManus, Frédéric Lamoliatte, Pierre Thibault
Ubiquitin and ubiquitin-like modifiers (UBLs) such as small ubiquitin-like modifier (SUMO) can act as antagonists to one another by competing to occupy similar residues in the proteome. In addition, SUMO and ubiquitin can be coupled to each other at key lysine residues to form highly branched protein networks. The interplay between these modifications governs important biological processes such as double-strand break repair and meiotic recombination. We recently developed an approach that permits the identification of proteins that are modified by both SUMOylation and ubiquitylation...
November 2017: Nature Protocols
https://www.readbyqxmd.com/read/29046436/caenorhabditis-elegans-bub-3-and-san-1-mad3-spindle-assembly-checkpoint-components-are-required-for-genome-stability-in-response-to-treatment-with-ionizing-radiation
#8
Simone Bertolini, Bin Wang, Bettina Meier, Ye Hong, Anton Gartner
Relatively little is known about the crosstalk between the spindle assembly checkpoint and the DNA damage response, especially in multicellular organisms. We performed a Caenorhabditis elegans forward genetic screen to uncover new genes involved in the repair of DNA damage induced by ionizing radiation. We isolated a mutation, gt2000 which confers hypersensitivity to ionizing radiation and showed that gt2000 introduces a premature stop in bub-3 BUB-3 is a key component of the spindle assembly checkpoint. We provide evidence that BUB-3 acts during development and in the germline; irradiated bub-3(gt2000) larvae are developmentally retarded and form abnormal vulvae...
October 18, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/29046123/differential-effects-of-silver-nanoparticles-on-dna-damage-and-dna-repair-gene-expression-in-ogg1-deficient-and-wild-type-mice
#9
Sameera Nallanthighal, Cadia Chan, Thomas M Murray, Aaron P Mosier, Nathaniel C Cady, Ramune Reliene
Due to extensive use in consumer goods, it is important to understand the genotoxicity of silver nanoparticles (AgNPs) and identify susceptible populations. 8-Oxoguanine DNA glycosylase 1 (OGG1) excises 8-oxo-7,8-dihydro-2-deoxyguanine (8-oxoG), a pro-mutagenic lesion induced by oxidative stress. To understand whether defects in OGG1 is a possible genetic factor increasing an individual's susceptibly to AgNPs, we determined DNA damage, genome rearrangements, and expression of DNA repair genes in Ogg1-deficient and wild type mice exposed orally to 4 mg/kg of citrate-coated AgNPs over a period of 7 d...
October 19, 2017: Nanotoxicology
https://www.readbyqxmd.com/read/29045752/genome-size-and-sensitivity-to-dna-damage-by-x-rays-plant-comets-tell-the-story
#10
John Einset, Andrew R Collins
Among several factors affecting radiation sensitivity, genome size has received limited attention during the last 50 years since research at Brookhaven National Laboratory (USA) and other locations demonstrated substantial differences in radiation sensitivities, e.g. between tree species with large (e.g. conifers such as pines) versus small (e.g. dicots such as oaks) genome sizes. Taking advantage of the wide range of genome sizes among species, we investigated radiation sensitivity which we define in this study as DNA damage (break frequency) measured with the alkaline comet assay in isolated nuclei exposed to X-rays...
October 17, 2017: Mutagenesis
https://www.readbyqxmd.com/read/29043647/the-cellclamper-a-convenient-microfluidic-device-for-time-lapse-imaging-of-yeast
#11
Gregor W Schmidt, Olivier Frey, Fabian Rudolf
Time-lapse fluorescence imaging of yeast cells allows the study of multiple fluorescent targets in single cells, but is often hampered by the tedious cultivation using agar pads or glass bottom wells. Here, we describe the fabrication and operation of a microfluidic device for long-term imaging of yeast cells under constant or changing media conditions. The device allows acquisition of high quality images as cells are fixed in a two-dimensional imaging plane. Four yeast strains can be analyzed simultaneously over several days while up to four different media can be flushed through the chip...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29043637/assays-to-study-repair-of-inducible-dna-double-strand-breaks-at-telomeres
#12
Roxanne Oshidari, Karim Mekhail
The ends of linear chromosomes are constituted of repetitive DNA sequences called telomeres. Telomeres, nearby regions called subtelomeres, and their associated factors prevent chromosome erosion over cycles of DNA replication and prevent chromosome ends from being recognized as DNA double-strand breaks (DSBs). This raises the question of how cells repair DSBs that actually occur near chromosome ends. One approach is to edit the genome and engineer cells harboring inducible DSB sites within the subtelomeric region of different chromosome ends...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29043632/single-cell-gel-electrophoresis-for-the-detection-of-genomic-ribonucleotides
#13
Barbara Kind, Christine Wolf, Kerstin Engel, Alexander Rapp, M Cristina Cardoso, Min Ae Lee-Kirsch
Single cell gel electrophoresis or comet assay enables the quantification of DNA damage such as single-strand or double-strand breaks on a single cell level. Here, we describe a variant of this method for the detection of ribonucleotides embedded in genomic DNA. Briefly, cells are embedded in agarose on a microscopic slide, lysed under high salt and alkaline conditions and then subjected to in situ treatment with E. coli RNase HII which nicks 5' to a ribonucleotide within the context of a DNA duplex thereby converting genomic ribonucleotides into strand breaks...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29043625/genome-wide-profiling-of-dna-double-strand-breaks-by-the-bless-and-bliss-methods
#14
Reza Mirzazadeh, Tomasz Kallas, Magda Bienko, Nicola Crosetto
DNA double-strand breaks (DSBs) are major DNA lesions that are constantly formed during physiological processes such as DNA replication, transcription, and recombination, or as a result of exogenous agents such as ionizing radiation, radiomimetic drugs, and genome editing nucleases. Unrepaired DSBs threaten genomic stability by leading to the formation of potentially oncogenic rearrangements such as translocations. In past few years, several methods based on next-generation sequencing (NGS) have been developed to study the genome-wide distribution of DSBs or their conversion to translocation events...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29043624/mapping-dna-breaks-by-next-generation-sequencing
#15
Laura Baranello, Fedor Kouzine, Damian Wojtowicz, Kairong Cui, Keji Zhao, Teresa M Przytycka, Giovanni Capranico, David Levens
Here, we present two approaches to map DNA double-strand breaks (DSBs) and single-strand breaks (SSBs) in the genome of human cells. We named these methods respectively DSB-Seq and SSB-Seq. We tested the DSB and SSB-Seq in HCT1116, human colon cancer cells, and validated the results using the topoisomerase 2 (Top2)-poisoning agent etoposide (ETO). These methods are powerful tools for the direct detection of the physiological and pathological "breakome" of the DNA in human cells.
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29043623/single-molecule-analysis-of-resection-tracks
#16
Pablo Huertas, Andrés Cruz-García
Homologous recombination is initiated by the so-called DNA end resection, the 5'-3' nucleolytic degradation of a single strand of the DNA at each side of the break. The presence of resected DNA is an obligatory step for homologous recombination. Moreover, the amount of resected DNA modulates the prevalence of different recombination pathways. In different model organisms, there are several published ways to visualize and measure with more or less detail the amount of DNA resected. In human cells, however, technical constraints hampered the study of resection at high resolution...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29043622/alkaline-denaturing-southern-blot-analysis-to-monitor-double-strand-break-processing
#17
Chiara Vittoria Colombo, Luca Menin, Michela Clerici
Generation of 3' single-stranded DNA (ssDNA) tails at the ends of a double-strand break (DSB) is essential to repair the break through accurate homology-mediated repair pathways. Several methods have been developed to measure ssDNA accumulation at a DSB in the budding yeast Saccharomyces cerevisiae. Here, we describe one of these assays, which is based on the inability of restriction enzymes to cleave ssDNA. Digestion of genomic DNA prepared at different time points after DSB generation leads to the formation of ssDNA fragments whose length increases as the 5' strand degradation proceeds beyond restriction sites...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29043621/a-qpcr-based-protocol-to-quantify-dsb-resection
#18
Matteo Ferrari, Shyam Twayana, Federica Marini, Achille Pellicioli
The nucleolytic degradation of the 5'-ending strand of a Double-Strand DNA break (DSB) is necessary to initiate homologous recombination to correctly repair the break. This process is called DNA end resection and it is finely regulated to prevent genome rearrangements. Here, we describe a protocol to quantify DSB resection rate by qPCR, which could be applied to every organisms whenever the break site and its flanking region sequences are known.
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29042561/aunip-c1orf135-directs-dna-double-strand-breaks-towards-the-homologous-recombination-repair-pathway
#19
Jiangman Lou, Hongxia Chen, Jinhua Han, Hanqing He, Michael S Y Huen, Xin-Hua Feng, Ting Liu, Jun Huang
DNA double-strand breaks (DSBs) are mainly repaired by either homologous recombination (HR) or non-homologous end-joining (NHEJ). Here, we identify AUNIP/C1orf135, a largely uncharacterized protein, as a key determinant of DSB repair pathway choice. AUNIP physically interacts with CtIP and is required for efficient CtIP accumulation at DSBs. AUNIP possesses intrinsic DNA-binding ability with a strong preference for DNA substrates that mimic structures generated at stalled replication forks. This ability to bind DNA is necessary for the recruitment of AUNIP and its binding partner CtIP to DSBs, which in turn drives CtIP-dependent DNA-end resection and HR repair...
October 17, 2017: Nature Communications
https://www.readbyqxmd.com/read/29042516/across-the-tree-of-life-radiation-resistance-is-governed-by-antioxidant-mn-2-gauged-by-paramagnetic-resonance
#20
Ajay Sharma, Elena K Gaidamakova, Olga Grichenko, Vera Y Matrosova, Veronika Hoeke, Polina Klimenkova, Isabel H Conze, Robert P Volpe, Rok Tkavc, Cene Gostinčar, Nina Gunde-Cimerman, Jocelyne DiRuggiero, Igor Shuryak, Andrew Ozarowski, Brian M Hoffman, Michael J Daly
Despite concerted functional genomic efforts to understand the complex phenotype of ionizing radiation (IR) resistance, a genome sequence cannot predict whether a cell is IR-resistant or not. Instead, we report that absorption-display electron paramagnetic resonance (EPR) spectroscopy of nonirradiated cells is highly diagnostic of IR survival and repair efficiency of DNA double-strand breaks (DSBs) caused by exposure to gamma radiation across archaea, bacteria, and eukaryotes, including fungi and human cells...
October 17, 2017: Proceedings of the National Academy of Sciences of the United States of America
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