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DNA Repair

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https://www.readbyqxmd.com/read/30409670/deciphering-phenotypic-variance-in-different-models-of-dna-pkcs-deficiency
#1
Jessica A Neal, Katheryn Meek
DNA-PKcs deficiency has been studied in numerous animal models and cell culture systems. In previous studies of kinase inactivating mutations in cell culture systems, ablation of DNA-PK's catalytic activity results in a cell phenotype that is virtually indistinguishable from that ascribed to complete loss of the enzyme. However, a recent compelling study demonstrates a remarkably more severe phenotype in mice harboring a targeted disruption of DNA-PK's ATP binding site as compared to DNA-PKcs deficient mice...
October 30, 2018: DNA Repair
https://www.readbyqxmd.com/read/30413344/werner-syndrome-wrn-dna-helicase-and-base-excision-repair-ber-factors-maintain-endothelial-homeostasis
#2
Kathrin Laarmann, Joana M Kress, Bernd Kaina, Gerhard Fritz
The accelerated ageing disease Werner Syndrome (WRN) is characterized by pronounced atherosclerosis. Here, we investigated the influence of WRN downregulation on the functionality of non-replicating human endothelial cells. RNAi-mediated downregulation of WRN reduces cell motility and enhances the expression of factors regulating adhesion, inflammation, hemostasis and vasomotor tone. Moreover, WRN influences endothelial barrier function and Ca2+ -release, while cell adhesion, Dil-acLDL-uptake and the mRNA expression of NO-synthases (eNOS, iNOS) remained unaffected...
October 28, 2018: DNA Repair
https://www.readbyqxmd.com/read/30391220/the-endonuclease-domain-of-bacillus-subtilis-mutl-is-functionally-asymmetric
#3
Linda Liu, Mary Carmen Ortiz Castro, Javier Rodríguez González, Monica C Pillon, Alba Guarné
DNA mismatch repair is an evolutionarily conserved repair pathway that corrects replication errors. In most prokaryotes and all eukaryotes, the mismatch repair protein MutL is a sequence-unspecific endonuclease that nicks the newly synthesized strand and marks it for repair. Although the sequence of the endonuclease domain of MutL is not conserved, eukaryotic MutLα and prokaryotic MutL share four conserved motifs that define the endonuclease site of the protein. Their endonuclease activity is stimulated by the processivity sliding β-clamp, or its eukaryotic counterpart PCNA, highlighting the functional conservation...
October 24, 2018: DNA Repair
https://www.readbyqxmd.com/read/30348496/inactive-atm-abrogates-dsb-repair-in-mouse-cerebellum-more-than-does-atm-loss-without-causing-a-neurological-phenotype
#4
Efrat Tal, Marina Alfo, Shan Zha, Ari Barzilai, Chris I De Zeeuw, Yael Ziv, Yosef Shiloh
The genome instability syndrome, ataxia-telangiectasia (A-T) is caused by null mutations in the ATM gene, that lead to complete loss or inactivation of the gene's product, the ATM protein kinase. ATM is the primary mobilizer of the cellular response to DNA double-strand breaks (DSBs) - a broad signaling network in which many components are ATM targets. The major clinical feature of A-T is cerebellar atrophy, characterized by relentless loss of Purkinje and granule cells. In Atm-knockout (Atm-KO) mice, complete loss of Atm leads to a very mild neurological phenotype, suggesting that Atm loss is not sufficient to markedly abrogate cerebellar structure and function in this organism...
October 11, 2018: DNA Repair
https://www.readbyqxmd.com/read/30389308/an-rnai-screen-in-human-cell-lines-reveals-conserved-dna-damage-repair-pathways-that-mitigate-formaldehyde-sensitivity
#5
Eleonora Juarez, Nyasha Chambwe, Weiliang Tang, Asia D Mitchell, Nichole Owen, Anuradha Kumari, Raymond J Monnat, Amanda K McCullough
Formaldehyde is a ubiquitous DNA damaging agent, with human exposures occurring from both exogenous and endogenous sources. Formaldehyde exposure can result in multiple types of DNA damage, including DNA-protein crosslinks and thus, is representative of other exposures that induce DNA-protein crosslinks such as cigarette smoke, automobile exhaust, wood smoke, metals, ionizing radiation, and certain chemotherapeutics. Our objective in this study was to identify the genes necessary to mitigate formaldehyde toxicity following chronic exposure in human cells...
October 9, 2018: DNA Repair
https://www.readbyqxmd.com/read/30314738/base-excision-repair-capacity-as-a-determinant-of-prognosis-and-therapy-response-in-colon-cancer-patients
#6
Sona Vodenkova, Katerina Jiraskova, Marketa Urbanova, Michal Kroupa, Jana Slyskova, Michaela Schneiderova, Miroslav Levy, Tomas Buchler, Vaclav Liska, Ludmila Vodickova, Veronika Vymetalkova, Andrew Collins, Alena Opattova, Pavel Vodicka
The DNA-damaging agent 5-fluorouracil represents the most commonly used chemotherapeutic drug for colorectal cancer patients. DNA lesions associated with 5-fluorouracil therapy are primarily repaired by base excision repair (BER) and mismatch repair (MMR) pathways. Published evidence suggests that the individual DNA repair capacity (DRC) may affect a patient's prognosis and response to chemotherapy. With this in mind, we designed a prospective study of which the main aim was to investigate BER-DRC in relation to 5-fluorouracil response as potential predictive and/or prognostic biomarker...
October 1, 2018: DNA Repair
https://www.readbyqxmd.com/read/30292721/involvement-of-transcription-coupled-repair-factor-mfd-and-dna-helicase-uvrd-in-mutational-processes-in-pseudomonas-putida
#7
Kärt Ukkivi, Maia Kivisaar
Stalled RNA polymerases (RNAPs) pose an obstacle for the replicating complexes, which could lead to transcription-replication conflicts and result in genetic instability. Stalled RNAPs and DNA lesions blocking RNAP elongation are removed by transcription-coupled repair (TCR), the process which in bacteria is mediated by TCR factor Mfd and helicase UvrD. Although the mechanism of TCR has been extensively studied, its role in mutagenesis is still obscure. In the current study we have investigated the role of Mfd and UvrD in mutational processes in soil bacterium Pseudomonas putida...
September 26, 2018: DNA Repair
https://www.readbyqxmd.com/read/30314737/cutting-edge-perspectives-in-genomic-maintenance-v
#8
EDITORIAL
Philip C Hanawalt, Samuel H Wilson
No abstract text is available yet for this article.
September 25, 2018: DNA Repair
https://www.readbyqxmd.com/read/30291044/replication-protein-a-as-a-modulator-of-the-poly-adp-ribose-polymerase-1-activity
#9
Ekaterina A Maltseva, Yulia S Krasikova, Maria V Sukhanova, Nadejda I Rechkunova, Olga I Lavrik
Replication protein A contributes to all major pathways of DNA metabolism and is a target for post-translation modifications, including poly(ADP-ribosyl)ation catalyzed by PARP1. Here we demonstrate that the efficiency of RPA poly(ADP-ribosyl)ation strongly depends on the structure of DNA used for PARP1 activation and on the polarity of RPA binding. Moreover, RPA influences PARP1 activity, and this effect also depends on DNA structure: RPA inhibits PAR synthesis catalyzed by PARP1 in the presence of ssDNA and stimulates it in the presence of a DNA duplex, in particular that containing a nick or a gap...
September 24, 2018: DNA Repair
https://www.readbyqxmd.com/read/30274769/regulated-acetylation-and-deacetylation-of-h4-k16-is-essential-for-efficient-ner-in-saccharomyces-cerevisiae
#10
Anagh Ray, Preeti Khan, Ronita Nag Chaudhuri
Acetylation status of H4 K16, a residue in the histone H4 N-terminal tail plays a unique role in regulating chromatin structure and function. Here we show that, during UV-induced nucleotide excision repair H4 K16 gets hyperacetylated following an initial phase of hypoacetylation. Disrupting H4 K16 acetylation-deacetylation by mutating H4 K16 to R (deacetylated state) or Q (acetylated state) leads to compromised chromatin functions. In the silenced mating locus and telomere region H4 K16 mutants show higher recruitment of Sir proteins and spreading beyond the designated boundaries...
September 22, 2018: DNA Repair
https://www.readbyqxmd.com/read/30268365/nucleosomes-and-the-three-glycosylases-high-medium-and-low-levels-of-excision-by-the-uracil-dna-glycosylase-superfamily
#11
Mary E Tarantino, Blaine J Dow, Alexander C Drohat, Sarah Delaney
Human cells express the UDG superfamily of glycosylases, which excise uracil (U) from the genome. The three members of this structural superfamily are uracil DNA glycosylase (UNG/UDG), single-strand selective monofunctional uracil DNA glycosylase (SMUG1), and thymine DNA glycosylase (TDG). We previously reported that UDG is efficient at removing U from DNA packaged into nucleosome core particles (NCP) and is minimally affected by the histone proteins when acting on an outward-facing U in the dyad region. In an effort to determine whether this high activity is a general property of the UDG superfamily of glycosylases, we compare the activity of UDG, SMUG1, and TDG on a U:G wobble base pair using NCP assembled from Xenopus laevis histones and the Widom 601 positioning sequence...
September 20, 2018: DNA Repair
https://www.readbyqxmd.com/read/30254011/rad6-bre1-mediated-histone-h2bub1-protects-uncapped-telomeres-from-exonuclease-exo1-in-saccharomyces-cerevisiae
#12
Zhenfang Wu, Ming-Hong He, Ling-Li Zhang, Jun Liu, Qiong-Di Zhang, Jin-Qiu Zhou
Histone H2B lysine 123 mono-ubiquitination (H2Bub1), catalyzed by Rad6 and Bre1 in Saccharomyces cerevisiae, modulates chromatin structure and affects diverse cellular functions. H2Bub1 plays roles in telomeric silencing and telomere replication. Here, we have explored a novel role of H2Bub1 in telomere protection at uncapped telomeres in yku70Δ and cdc13-1 cells. Deletion of RAD6 or BRE1, or mutation of H2BK123R enhances the temperature sensitivity of both yku70Δ and cdc13-1 telomere capping mutants. Consistently, BRE1 deletion increases accumulation of telomeric single-stranded DNA (ssDNA) in yku70Δ and cdc13-1 cells, and EXO1 deletion improves the growth of yku70Δ bre1Δ and cdc13-1 bre1Δ cells and decreases ssDNA accumulation...
September 17, 2018: DNA Repair
https://www.readbyqxmd.com/read/30268364/fluorescent-fusions-of-the-n-protein-of-phage-mu-label-dna-damage-in-living-cells
#13
Matthew V Kotlajich, Jun Xia, Yin Zhai, Hsin-Yu Lin, Catherine C Bradley, Xi Shen, Qian Mei, Anthony Z Wang, Erica J Lynn, Chandan Shee, Li-Tzu Chen, Lei Li, Kyle M Miller, Christophe Herman, P J Hastings, Susan M Rosenberg
The N protein of phage Mu was indicated from studies in Escherichia coli to hold linear Mu chromosomes in a circular conformation by non-covalent association, and thus suggested potentially to bind DNA double-stranded ends. Because of its role in association with linear Mu DNA, we tested whether fluorescent-protein fusions to N might provide a useful tool for labeling DNA damage including double-strand break (DSB) ends in single cells. We compared N-GFP with a biochemically well documented DSB-end binding protein, the Gam protein of phage Mu, also fused to GFP...
September 14, 2018: DNA Repair
https://www.readbyqxmd.com/read/30266203/regulation-of-the-initiation-of-dna-replication-in-human-cells
#14
REVIEW
Tatiana N Moiseeva, Christopher J Bakkenist
The origin of species would not have been possible without high fidelity DNA replication and complex genomes evolved with mechanisms that control the initiation of DNA replication at multiple origins on multiple chromosomes such that the genome is duplicated once and only once. The mechanisms that control the assembly and activation of the replicative helicase and the initiation of DNA replication in yeast and Xenopus egg extract systems have been identified and reviewed [1,2]. The goal of this review is to organize currently available data on the mechanisms that control the initiation of DNA replication in human cells...
September 12, 2018: DNA Repair
https://www.readbyqxmd.com/read/30262195/the-hsnm1b-apollo-variant-rs11552449-is-associated-with-cellular-sensitivity-towards-mitomycin-c-and-ionizing-radiation
#15
Sarah Herwest, Carolin Albers, Maren Schmiester, Bastian Salewsky, Werner Hopfenmüller, Antje Meyer, Lars Bertram, Ilja Demuth
The polymorphism rs11552449 (c.181C > T, p.His61Tyr) in the hSNM1B/Apollo gene has been repeatedly shown to be associated with an increased risk for breast cancer. The aim of the current study was to investigate the association between rs11552449 and the degree of cellular sensitivity to mitomycin C (MMC) and ionizing radiation (IR). A total of 69 lymphoblastoid cell lines (LCLs) from generally healthy donors were tested for their sensitivity towards MMC and IR in growth inhibition experiments. LCLs heterozygous for rs11552449 were significantly more sensitive to MMC and IR than homozygous cells with the CC genotype (p < 0...
September 12, 2018: DNA Repair
https://www.readbyqxmd.com/read/30249411/phosphorylation-meets-dna-mismatch-repair
#16
REVIEW
Isabel Madeleine Weßbecher, Angela Brieger
DNA mismatch repair (MMR) is a highly conserved process and ensures the removal of mispaired DNA bases and insertion-deletion loops right after replication. For this, a MutSα or MutSβ protein complex recognizes the DNA damage, MutLα nicks the erroneous strand, exonuclease 1 removes the wrong nucleotides, DNA polymerase δ refills the gap and DNA ligase I joins the fragments to seal the nicks and complete the repair process. The failure to accomplish these functions is associated with higher mutation rates and may lead to cancer, which highlights the importance of MMR by the maintenance of genomic stability...
September 11, 2018: DNA Repair
https://www.readbyqxmd.com/read/30309820/impact-of-dna-lesion-repair-replication-and-formation-on-the-mutational-spectra-of-environmental-carcinogens-aflatoxin-b-1-as-a-case-study
#17
Bogdan I Fedeles, John M Essigmann
In a multicellular organism, somatic mutations represent a permanent record of the past chemical and biochemical perturbations experienced by a cell in its local microenvironment. Akin to a perpetual recording device, with every replication, genomic DNA accumulates mutations in patterns that reflect: i) the sequence context-dependent formation of DNA damage, due to environmental or endogenous reactive species, including spontaneous processes; ii) the activity of DNA repair pathways, which, depending on the type of lesion, can erase, ignore or exacerbate the mutagenic consequences of that DNA damage; and iii) the choice of replication machinery that synthesizes the nascent genomic copy...
August 25, 2018: DNA Repair
https://www.readbyqxmd.com/read/30228084/targeting-ber-enzymes-in-cancer-therapy
#18
Torkild Visnes, Maurice Grube, Bishoy Magdy Fekry Hanna, Carlos Benitez-Buelga, Armando Cázares-Körner, Thomas Helleday
Base excision repair (BER) repairs mutagenic or genotoxic DNA base lesions, thought to be important for both the etiology and treatment of cancer. Cancer phenotypic stress induces oxidative lesions, and deamination products are responsible for one of the most prevalent mutational signatures in cancer. Chemotherapeutic agents induce genotoxic DNA base damage that are substrates for BER, while synthetic lethal approaches targeting BER-related factors are making their way into the clinic. Thus, there are three strategies by which BER is envisioned to be relevant in cancer chemotherapy: (i) to maintain cellular growth in the presence of endogenous DNA damage in stressed cancer cells, (ii) to maintain viability after exogenous DNA damage is introduced by therapeutic intervention, or (iii) to confer synthetic lethality in cancer cells that have lost one or more additional DNA repair pathways...
August 25, 2018: DNA Repair
https://www.readbyqxmd.com/read/30220600/preserving-replication-fork-integrity-and-competence-via-the-homologous-recombination-pathway
#19
Anissia Ait Saada, Sarah A E Lambert, Antony M Carr
Flaws in the DNA replication process have emerged as a leading driver of genome instability in human diseases. Alteration to replication fork progression is a defining feature of replication stress and the consequent failure to maintain fork integrity and complete genome duplication within a single round of S-phase compromises genetic integrity. This includes increased mutation rates, small and large scale genomic rearrangement and deleterious consequences for the subsequent mitosis that result in the transmission of additional DNA damage to the daughter cells...
August 25, 2018: DNA Repair
https://www.readbyqxmd.com/read/30190235/r-loop-generation-during-transcription-formation-processing-and-cellular-outcomes
#20
Boris P Belotserkovskii, Silvia Tornaletti, Alicia D D'Souza, Philip C Hanawalt
R-loops are structures consisting of an RNA-DNA duplex and an unpaired DNA strand. They can form during transcription upon nascent RNA "threadback" invasion into the DNA duplex to displace the non-template strand. Although R-loops occur naturally in all kingdoms of life and serve regulatory roles, they are often deleterious and can cause genomic instability. Of particular importance are the disastrous consequences when replication forks or transcription complexes collide with R-loops. The appropriate processing of R-loops is essential to avoid a number of human neurodegenerative and other clinical disorders...
August 25, 2018: DNA Repair
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