Excision repair of topoisomerase DNA-protein crosslinks (TOP-DPC).
Abstract Topoisomerases are essential enzymes solving DNA topological problems such as supercoils, knots and catenanes that arise from replication, transcription, chromatin remodeling and other nucleic acid metabolic processes. They are also the targets of widely used anticancer drugs (e.g. topotecan, irinotecan, enhertu, etoposide, doxorubicin, mitoxantrone) and fluoroquinolone antibiotics (e.g. ciprofloxacin and levofloxacin). Topoisomerases manipulate DNA topology by cleaving one DNA strand (TOP1 and TOP3 enzymes) or both in concert (TOP2 enzymes) through the formation of transient enzyme-DNA cleavage complexes...
Source: DNA Repair - March 7, 2020 Category: Genetics & Stem Cells Authors: Sun Y, Saha S, Wang W, Saha LK, Huang SN, Pommier Y Tags: DNA Repair (Amst) Source Type: research

Chromosomal aberration dynamics through the cell cycle.
Abstract DNA double-strand breaks are the crucial lesions underlying the formation of chromosomal aberrations, their formation and kinetics have been extensively studied, although dynamics of the repair process has not been fully understood. By using a combination of different cytogenetic techniques to analyze cells in G0, G2 and M phase, in the present study we perform a follow up study of the dynamics of different radiation induced chromosomal aberrations. Data here presented show that in G0 phase chromosome fragments lacking telomere signals (incomplete chromosome elements, ICE) show a slow repair, but when rep...
Source: DNA Repair - March 6, 2020 Category: Genetics & Stem Cells Authors: Pujol-Canadell M, Puig R, Armengol G, Barrios L, Barquinero JF Tags: DNA Repair (Amst) Source Type: research

Chromosome breaks generated by low doses of ionizing radiation in G2-phase are processed exclusively by gene conversion.
We reported that during G2-phase, where all pathways are active, GC engages in the processing of almost 50 % of DSBs, at low DSB-loads in the genome, and that this contribution rapidly drops to nearly zero with increasing DSB-loads. At the transition between these two extremes, SSA and alt-EJ compensate, but at extremely high DSB-loads resection-dependent pathways are suppressed and c-NHEJ remains mainly active. We inquired whether in this processing framework all DSBs have similar fates. Here, we analyze in G2-phase the processing of a subset of DSBs defined by their ability to break chromosomes. Our results reveal an abs...
Source: DNA Repair - February 27, 2020 Category: Genetics & Stem Cells Authors: Soni A, Murmann-Konda T, Siemann-Loekes M, Pantelias GE, Iliakis G Tags: DNA Repair (Amst) Source Type: research

Helicobacter pylori severely reduces expression of DNA repair proteins PMS2 and ERCC1 in gastritis and gastric cancer.
Abstract Gastric cancers are the third leading cause of cancer mortality in the world. Helicobacter pylori causes over 60 % of all stomach cancers. Colonization of the gastric mucosa by H. pylori results in increased DNA damage. Repair of DNA damage may also be reduced by H. pylori infection. Reduced DNA repair in combination with increased DNA damage can cause carcinogenic mutations. During progression to gastric cancer, gastric epithelium goes through stages of increasing pathology. Determining the levels of DNA repair enzymes during progression to gastric cancer could illuminate treatment approaches. Our aim is...
Source: DNA Repair - February 26, 2020 Category: Genetics & Stem Cells Authors: Raza Y, Ahmed A, Khan A, Chishti AA, Akhter SS, Mubarak M, Bernstein C, Zaitlin B, Kazmi SU Tags: DNA Repair (Amst) Source Type: research

Two main mutational processes operate in the absence of DNA mismatch repair.
uuml;ts D Abstract The analysis of tumour genome sequences has demonstrated high rates of base substitution mutagenesis upon the inactivation of DNA mismatch repair (MMR), and the resulting somatic mutations in MMR deficient tumours appear to significantly enhance the response to immune therapy. A handful of different algorithmically derived base substitution mutation signatures have been attributed to MMR deficiency in tumour somatic mutation datasets. In contrast, mutation data obtained from whole genome sequences of isogenic wild type and MMR deficient cell lines in this study, as well as from published sources...
Source: DNA Repair - February 25, 2020 Category: Genetics & Stem Cells Authors: Németh E, Lovrics A, Gervai JZ, Seki M, Rospo G, Bardelli A, Szüts D Tags: DNA Repair (Amst) Source Type: research

The importance of Ile716 toward the mutagenicity of 8-Oxo-2'-deoxyguanosine with Bacillus fragment DNA polymerase.
Abstract 8-oxo-2'-deoxyguanosine (OdG) is a prominent DNA lesion that can direct the incorporation of dCTP or dATP during replication. As the latter reaction can lead to mutation, the ratio of dCTP/dATP incorporation can significantly affect the mutagenic potential of OdG. Previous work with the A-family polymerase BF and seven analogues of OdG identified a major groove amino acid, Ile716, which likely influences the dCTP/dATP incorporation ratio opposite OdG. To further probe the importance of this amino acid, dCTP and dATP incorporations opposite the same seven analogues were tested with two BF mutants, I716M an...
Source: DNA Repair - February 20, 2020 Category: Genetics & Stem Cells Authors: Hamm ML, Garcia AA, Gilbert R, Johri M, Ricart M, Sholes SL, Murray-Nerger LA, Wu EY Tags: DNA Repair (Amst) Source Type: research

The "adductome": A limited repertoire of adducted proteins in human cells.
The "adductome": A limited repertoire of adducted proteins in human cells. DNA Repair (Amst). 2020 Feb 19;89:102825 Authors: Kiianitsa K, Maizels N Abstract Proteins form adducts with nucleic acids in a variety of contexts, and these adducts may be cytotoxic if not repaired. Here we apply a proteomic approach to identification of proteins adducted to DNA or RNA in normally proliferating cells. This approach combines RADAR fractionation of proteins covalently bound to nucleic acids with quantitative mass spectrometry (MS). We demonstrate that "RADAR-MS" can quantify induction of TOP...
Source: DNA Repair - February 19, 2020 Category: Genetics & Stem Cells Authors: Kiianitsa K, Maizels N Tags: DNA Repair (Amst) Source Type: research

DNA-protein crosslink formation by endogenous aldehydes and AP sites.
Abstract Covalent binding between proteins and a DNA strand produces DNA-protein crosslinks (DPC). DPC are one of the most deleterious types of DNA damage, leading to the blockage of DNA replication and transcription. Both DNA lesions and endogenous products with carbonyl functional groups can produce DPC in genomic DNA under normal physiological conditions. For example, formaldehyde, the most abundant endogenous human carcinogen, and apurinic/apyrimidinic (AP) sites, the most common type of endogenous DNA lesions, has been shown to crosslink proteins and/or DNA through their carbonyl functional groups. Unfortunat...
Source: DNA Repair - February 10, 2020 Category: Genetics & Stem Cells Authors: Nakamura J, Nakamura M Tags: DNA Repair (Amst) Source Type: research

The dichotomous effects of caffeine on homologous recombination in mammalian cells.
This study was initiated to examine the effects of caffeine on the DNA damage response (DDR) and homologous recombination (HR) in mammalian cells. A 5 mM caffeine treatment caused the cell cycle to stall at G2/M and cells eventually underwent apoptosis. Caffeine exposure also induced a strong DDR along with subsequent activation of wildtype p53 protein. An unexpected observation was the caffeine-induced depletion of Rad51 (and Brca2) proteins. Consequently, caffeine-treated cells were expected to be inefficient in HR. However, a dichotomy in the HR response of cells to caffeine treatment was revealed. Caffeine treatment ...
Source: DNA Repair - February 7, 2020 Category: Genetics & Stem Cells Authors: Magwood AC, Mundia MM, Pladwig SM, Mosser DD, Baker MD Tags: DNA Repair (Amst) Source Type: research

Function and evolution of the DNA-protein crosslink proteases Wss1 and SPRTN.
Abstract Covalent DNA-protein crosslinks (DPCs) are highly toxic DNA adducts, which interfere with faithful DNA replication. The proteases Wss1 and SPRTN degrade DPCs and have emerged as crucially important DNA repair enzymes. Their protective role has been described in various model systems ranging from yeasts, plants, worms and flies to mice and humans. Loss of DPC proteases results in genome instability, cellular arrest, premature ageing and cancer predisposition. Here we discuss recent insights into the function and molecular mechanism of these enzymes. Furthermore, we present an in-depth phylogenetic analysis...
Source: DNA Repair - February 6, 2020 Category: Genetics & Stem Cells Authors: Reinking HK, Hofmann K, Stingele J Tags: DNA Repair (Amst) Source Type: research

Proofreading of single nucleotide insertion/deletion replication errors analyzed by MALDI-TOF mass spectrometry assay.
We examined proofreading of DNAs containing indel errors at various positions of the primer-template junction. We found that indel errors located 1-5-nucleotides (nt) from the primer terminus can be proofread efficiently, while insertion/deletions at 6-nt from the 3' end are partially corrected and extended. Indels located 7-9-nt from the primer terminus escape proofreading and are elongated by polymerase. The possible underlying mechanisms of these observations are discussed in the context of the polymerase and primer-template junction interactions via a structure analysis. PMID: 32036259 [PubMed - as supplied by pub...
Source: DNA Repair - January 30, 2020 Category: Genetics & Stem Cells Authors: Chang HL, Su KY, Goodman SD, Chou NA, Lin KC, Cheng WC, Lin LI, Chang SY, Fang WH Tags: DNA Repair (Amst) Source Type: research

Higher chromosome stability in embryonic neural stem and progenitor cells than in fibroblasts in response to acute or chronic genotoxic stress.
Abstract High fidelity of genetic transmission in neural stem and progenitor cells (NSPCs) has been long time considered to be crucial for brain development and homeostasis. However, recent studies have identified recurrent DSB clusters in dividing NSPCs, which may underlie the diversity of neuronal cell types. This raised the interest in understanding how NSPCs sense and repair DSBs and how this mechanism could be altered by environmental genotoxic stress caused by pollutants or ionizing radiation. Here, we show that embryonic mouse neural stem and progenitor cells (NSPCs) have significantly higher capacity than ...
Source: DNA Repair - January 28, 2020 Category: Genetics & Stem Cells Authors: Mokrani S, Granotier-Beckers C, Etienne O, Kortulewski T, Grisolia C, de Villartay JP, Boussin FD Tags: DNA Repair (Amst) Source Type: research

Cancer type-dependent correlations between TP53 mutations and antitumor immunity.
Abstract Many studies have shown that TP53 mutations play a negative role in antitumor immunity. However, a few studies reported that TP53 mutations could promote antitumor immunity. To explain these contradictory findings, we analyzed five cancer cohorts from The Cancer Genome Atlas (TCGA) project. We found that TP53-mutated cancers had significantly higher levels of antitumor immune signatures than TP53-wildtype cancers in breast invasive carcinoma (BRCA) and lung adenocarcinoma (LUAD). In contrast, TP53-mutated cancers had significantly lower antitumor immune signature levels than TP53-wildtype cancers in stoma...
Source: DNA Repair - January 24, 2020 Category: Genetics & Stem Cells Authors: Li L, Li M, Wang X Tags: DNA Repair (Amst) Source Type: research

Drosophila Xrcc2 regulates DNA double-strand repair in somatic cells.
Abstract Genomic integrity is challenged by endo- and exogenous assaults that are combated by highly conserved DNA repair mechanisms. Repair of DNA double-strand breaks (DSBs) is of particular importance, as DSBs inflict chromosome breaks that are the basis of genomic instability. High fidelity recombination repair of DSBs relies on the Rad51 recombinase, aided by several Rad51 paralogs. Despite their significant contribution to DSB repair, the individual roles for Rad51 paralogs are incompletely understood. Drosophila serves as a metazoan model for DNA damage repair at the organismal level. Yet, only two out of f...
Source: DNA Repair - January 23, 2020 Category: Genetics & Stem Cells Authors: Bayer FE, Deichsel S, Mahl P, Nagel AC Tags: DNA Repair (Amst) Source Type: research

Single-stranded DNA damage: Protecting the single-stranded DNA from chemical attack.
Abstract Cellular processes, such as DNA replication, recombination and transcription, require DNA strands separation and single-stranded DNA is formation. The single-stranded DNA is promptly wrapped by human single-stranded DNA binding proteins, replication protein A (RPA) complex. RPA binding not only prevent nuclease degradation and annealing, but it also coordinates cell-cycle checkpoint activation and DNA repair. However, RPA binding offers little protection against the chemical modification of DNA bases. This review focuses on the type of DNA base damage that occurs in single-stranded DNA and how the damage ...
Source: DNA Repair - January 20, 2020 Category: Genetics & Stem Cells Authors: Anindya R Tags: DNA Repair (Amst) Source Type: research

HPV induction of APOBEC3 enzymes mediate overall survival and response to cisplatin in head and neck cancer.
In this study, the Cancer Genome Atlas (TCGA) HNSC data were used to assess the association between the expression of the seven proteins in the A3 cytidine deaminase family, HPV-status and survival outcomes. Higher A3 G expression in HPV-positive tumors corresponds with better overall survival (OS) (HR 0.33, 95 % CI 0.11-0.93, p = 0.04). FaDu and Scc-25 HNSC cell lines were used to assess alterations in A3, BER and MMR expression in response to cisplatin. We demonstrate that A3, Polβ, and MSH6 knockdown in HNSC cells results in resistance to cisplatin and carboplatin as well as an increase in the rate of ICL removal i...
Source: DNA Repair - January 16, 2020 Category: Genetics & Stem Cells Authors: Conner KL, Shaik AN, Ekinci E, Kim S, Ruterbusch JJ, Cote ML, Patrick SM Tags: DNA Repair (Amst) Source Type: research

Oxidative DNA-protein crosslinks formed in mammalian cells by abasic site lyases involved in DNA repair.
In this report, we surveyed whether additional AP lyases are trapped in oxidative DPC in mammalian cells in culture. Poly(ADP-ribose) polymerase 1 (PARP1), Ku proteins, DNA polymerase λ (Polλ), and the bifunctional 8-oxoguanine DNA glycosylase 1 (OGG1), were all trapped in oxidative DPC in mammalian cells. We also observed significant trapping of Polλ, PARP1, and OGG1 in cells treated with the alkylating agent methylmethane sulfonate (MMS), in addition to dL-inducing agents. Ku proteins, in contrast, followed a pattern of trapping similar to that for Polβ: MMS failed to produce Ku-DPC, while treat...
Source: DNA Repair - January 9, 2020 Category: Genetics & Stem Cells Authors: Quiñones JL, Thapar U, Wilson SH, Ramsden DA, Demple B Tags: DNA Repair (Amst) Source Type: research

The mismatch repair protein MSH6 regulates somatic recombination in Arabidopsis thaliana.
Abstract The mismatch repair (MMR) pathway promotes genome stability by controlling the fidelity of replication and recombination. The first step of the pathway involves recognition of the mismatch by heterodimers composed of MutS homologs (MSH). Although MSH6 has been well characterized in yeasts and humans, the role of the plant protein has not been extensively studied. We first analyzed gene expression in Arabidopsis thaliana. The use of transgenic plants expressing the β-glucuronidase (GUS) reporter gene under the control of approximately 1-kb region upstream of the start codon of the AtMSH6 gene demonstr...
Source: DNA Repair - January 9, 2020 Category: Genetics & Stem Cells Authors: Gonzalez V, Spampinato CP Tags: DNA Repair (Amst) Source Type: research

Repair of DNA-protein crosslinks in plants.
Abstract DNA-protein crosslinks represent a severe kind of DNA damage as they disturb essential processes, such as transcription and DNA replication, due to their bulkiness. To ensure the maintenance of genome integrity, it is necessary for all living organisms to repair these lesions in a timely manner. Over recent years, much knowledge has been obtained regarding the repair of DNA-protein crosslinks (DPC), but it was only recently that the first insights into the mechanisms of DPC repair in plants were obtained. The plant DPC repair network consists of at least three parallel pathways that resolve DPC by distinc...
Source: DNA Repair - January 8, 2020 Category: Genetics & Stem Cells Authors: Hacker L, Dorn A, Puchta H Tags: DNA Repair (Amst) Source Type: research

The activity of the DNA repair enzyme hOGG1 can be directly modulated by ubiquinol.
n J Abstract The DNA of human cells suffers about 1.000-100.000 oxidative lesions per day. One of the most common defects in this category is represented by 7,8-dihydro-8-oxoguanine. There are numerous exogenous effects on DNA that induce the intracellular generation of 7, 8-dihydro-8-oxoguanine. Therefore, a quantitatively sufficient repair of all occurring oxidative damaged guanine bases is often only partially feasible, especially in advanced age. Inadequate removal of these damages can subsequently lead to mutations and thus to serious diseases. All these aspects represent a dangerous situation for an organism...
Source: DNA Repair - January 3, 2020 Category: Genetics & Stem Cells Authors: Schniertshauer D, Gebhard D, van Beek H, Nöth V, Schon J, Bergemann J Tags: DNA Repair (Amst) Source Type: research

Genotoxic effects of topoisomerase poisoning and PARP inhibition on zebrafish embryos.
Abstract Topoisomerase poisons are known to stabilize covalent enzyme-DNA intermediates forming covalent cleavage complexes, which are highly cytotoxic especially for dividing cells and thus, make topoisomerases targets for cancer therapy. Topoisomerases have been extensively studied in mammalian model systems, whereas in other vertebrate models including zebrafish, they still remain less characterized. Here we show similarities in the genotoxic effects of zebrafish and mammalian systems towards topoisomerase I (Top1) poisons and PARP inhibitor - olaparib. On the other hand we observed that topoisomerase II (Top2)...
Source: DNA Repair - December 19, 2019 Category: Genetics & Stem Cells Authors: Karapetian M, Tsikarishvili S, Kulikova N, Kurdadze A, Zaalishvili G Tags: DNA Repair (Amst) Source Type: research

Genetic diversity and functional effect of common polymorphisms in genes involved in the first heterodimeric complex of the Nucleotide Excision Repair pathway.
Abstract Nucleotide excision repair is a multistep process that recognizes and eliminates a spectrum of DNA damages. Five proteins, namely XPC, RAD23, Centrin 2, DDB1 and DDB2 act as a heterodimeric complex at the early steps of the NER pathway and play a crucial role in the removal of DNA lesions. Several exonic mutations on genes coding for these proteins have been identified as associated with Xeroderma-pigmentosum (XP), a rare monogenic disorder. However, the role of regulatory polymorphisms in disease development and inter-ethnic diversity is still not well documented. Due to the high incidence rate of XP in ...
Source: DNA Repair - December 12, 2019 Category: Genetics & Stem Cells Authors: Hamdi Y, Jerbi M, Romdhane L, Ben Rekaya M, El Benna H, Chouchane L, Boubaker MS, Abdelhak S, Yacoub-Youssef H Tags: DNA Repair (Amst) Source Type: research

Macromolecular crowding induces compaction and DNA binding in the disordered N-terminal domain of hUNG2.
Abstract Many human DNA repair proteins have disordered domains at their N- or C-termini with poorly defined biological functions. We recently reported that the partially structured N-terminal domain (NTD) of human uracil DNA glycosylase 2 (hUNG2), functions to enhance DNA translocation in crowded environments and also targets the enzyme to single-stranded/double-stranded DNA junctions. To understand the structural basis for these effects we now report high-resolution heteronuclear NMR studies of the isolated NTD in the presence and absence of an inert macromolecular crowding agent (PEG8K). Compared to dilute buff...
Source: DNA Repair - December 10, 2019 Category: Genetics & Stem Cells Authors: Rodriguez G, Orris B, Majumdar A, Bhat S, Stivers JT Tags: DNA Repair (Amst) Source Type: research

Biochemical reconstitution and genetic characterization of the major oxidative damage base excision DNA repair pathway in Thermococcus kodakarensis.
This study identifies a member of the Ogg-subfamily archaeal GO glycosylase (AGOG) in Thermococcus kodakarensis, an anaerobic, hyperthermophilic archaeon, and delineates its mechanism, kinetics, and substrate specificity. TkoAGOG is the major 8oxoG glycosylase in T. kodakarensis, but is non-essential. In addition to TkoAGOG, the major apurinic/apyrimidinic (AP) endonuclease (TkoEndoIV) required for archaeal base excision repair and cell viability was identified and characterized. Enzymes required for the archaeal oxidative damage base excision repair pathway were identified and the complete pathway was reconstituted. This ...
Source: DNA Repair - December 5, 2019 Category: Genetics & Stem Cells Authors: Gehring AM, Zatopek KM, Burkhart BW, Potapov V, Santangelo TJ, Gardner AF Tags: DNA Repair (Amst) Source Type: research

Computational investigations and molecular dynamics simulations envisioned for potent antioxidant and anticancer drugs using indole-chalcone-triazole hybrids.
Abstract Cancer, also called malignancy, is a disease which is closely related with the oxidative stress instigated by the overproduction of vulnerable oxygen and nitrogen species. Available drugs are relatively painful and toxic and so are trailing their captivation. Keeping this in mind, we have attempted to reach a novel anti-cancer drug by taking a set of nineteen ligands which are hybrids of Indole-chalcone and triazole. These ligands were allowed to interact with the DNA dodecamer 5'(CGCGAATTCGCG)3' one by one using various docking protocols of Glide. Better docked complexes screened through docking scores a...
Source: DNA Repair - December 5, 2019 Category: Genetics & Stem Cells Authors: Yadav SK, Yadav RK, Yadava U Tags: DNA Repair (Amst) Source Type: research

Detection of the small oligonucleotide products of nucleotide excision repair in UVB-irradiated human skin.
Abstract UVB radiation results in the formation of potentially mutagenic photoproducts in the DNA of epidermal skin cells. In vitro approaches have demonstrated that the nucleotide excision repair (NER) machinery removes UV photoproducts from DNA in the form of small (∼30-nt-long), excised, damage-containing DNA oligonucleotides (sedDNAs). Though this process presumably takes place in human skin exposed to UVB radiation, sedDNAs have not previously been detected in human skin. Using surgically discarded human skin, we have optimized the detection of the sedDNA products of NER from small amounts of human epider...
Source: DNA Repair - December 5, 2019 Category: Genetics & Stem Cells Authors: Choi JH, Han S, Kemp MG Tags: DNA Repair (Amst) Source Type: research

A spontaneous mutation in DNA polymerase POL3 during in vitro passaging causes a hypermutator phenotype in Cryptococcus species.
In this study, the molecular basis behind the changes in the lineage of ATCC 24067 was determined by next-generation sequencing of the parent and passaged strain genomes. This analysis resulted in the identification of a point mutation that causes a D270G amino acid substitution within the exonuclease proofreading domain of the DNA polymerase delta subunit encoded by POL3. Complementation with POL3 confirmed that this mutation is responsible for the hypermutator phenotype of this strain. Regeneration of the mutation in C. neoformans, to eliminate the additional mutations present in the ATCC 24067A genetic background, demon...
Source: DNA Repair - November 29, 2019 Category: Genetics & Stem Cells Authors: Boyce KJ, Cao C, Xue C, Idnurm A Tags: DNA Repair (Amst) Source Type: research

Systematic analysis of linker histone PTM hotspots reveals phosphorylation sites that modulate homologous recombination and DSB repair.
Abstract Double strand-breaks (DSBs) of genomic DNA caused by ionizing radiation or mutagenic chemicals are a common source of mutation, recombination, chromosomal aberration, and cell death. Linker histones are DNA packaging proteins with established roles in chromatin compaction, gene transcription, and in homologous recombination (HR)-mediated DNA repair. Using a machine-learning model for functional prioritization of eukaryotic post-translational modifications (PTMs) in combination with genetic and biochemical experiments with the yeast linker histone, Hho1, we discovered that site-specific phosphorylation sit...
Source: DNA Repair - November 29, 2019 Category: Genetics & Stem Cells Authors: Mukherjee K, English N, Meers C, Kim H, Jonke A, Storici F, Torres M Tags: DNA Repair (Amst) Source Type: research

Enhancement of DNA damage repair potential in germ cells of Caenorhabditis elegans by a volatile signal from their irradiated partners.
Abstract Radiation-induced bystander effects have been demonstrated within organisms. Recently, it is found that the organisms can also signal irradiation cues to their co-cultured partners in a waterborne manner. In contrast, there is a limited understanding of radiation-induced airborne signaling between individuals, especially on the aspect of DNA damage responses (DDR). Here, we establish a co-culture experimental system using Caenorhabdis elegans in a top-bottom layout, where communication between "top" and "bottom" worms is airborne. The radiation response of top worms is evaluated using ...
Source: DNA Repair - November 26, 2019 Category: Genetics & Stem Cells Authors: Tang H, Chen L, Dai Z, Zhang W, Wang T, Wu L, Wang G, Bian P Tags: DNA Repair (Amst) Source Type: research

Loss of Setd4 delays radiation-induced thymic lymphoma in mice.
Abstract Radiation-induced lymphomagenesis results from a clonogenic lymphoid cell proliferation due to genetic alterations and immunological dysregulation. Mouse models had been successfully used to identify risk and protective factors for radiation-induced DNA damage and carcinogenesis. The mammalian SETD4 is a poorly understood putative methyl-transferase. Here, we report that conditional Setd4 deletion in adult mice significantly extended the survival of radiation-induced T-lymphoma. However, in Tp53 deficient mice, Setd4 deletion did not delay the radiation-induced lymphomagenesis although it accelerated the ...
Source: DNA Repair - November 25, 2019 Category: Genetics & Stem Cells Authors: Feng X, Lu H, Yue J, Schneider N, Liu J, Denzin LK, Chan CS, De S, Shen Z Tags: DNA Repair (Amst) Source Type: research

Insights into the non-homologous end joining pathway and double strand break end mobility provided by mechanistic in silico modelling.
We describe the construction of a mechanistic model by combination of several hypothesised mechanisms reported in the literature and supported by experiment. Compatibility of these mechanisms was tested by fitting simulation to results reported in the literature. To avoid over-fitting, we used an approach of sequentially testing individual mechanisms within this pathway. We demonstrate that using this approach the model is capable of reproducing published protein kinetics and overall repair trends. This provides evidence supporting the feasibility of the proposed mechanisms and revealed how they interact to produce an over...
Source: DNA Repair - November 20, 2019 Category: Genetics & Stem Cells Authors: Warmenhoven JW, Henthorn NT, Ingram SP, Chadwick AL, Sotiropoulos M, Korabel N, Fedotov S, Mackay RI, Kirkby KJ, Merchant MJ Tags: DNA Repair (Amst) Source Type: research

Absence of XRCC4 and its paralogs in human cells reveal differences in outcomes for DNA repair and V(D)J recombination.
Abstract The repair of DNA double-stranded breaks (DSBs) is an essential function performed by the Classical Non-Homologous End-Joining (C-NHEJ) pathway in higher eukaryotes. C-NHEJ, in fact, does double duty as it is also required for the repair of the intermediates formed during lymphoid B- and T-cell recombination. Consequently, the failure to properly repair DSBs leads to both genomic instability and immunodeficiency. A critical DSB protein required for C-NHEJ is the DNA Ligase IV (LIGIV) accessory factor, X-Ray Cross Complementing 4 (XRCC4). XRCC4 is believed to stabilize LIGIV, participate in LIGIV activatio...
Source: DNA Repair - November 11, 2019 Category: Genetics & Stem Cells Authors: Ruis B, Molan A, Takasugi T, Hendrickson EA Tags: DNA Repair (Amst) Source Type: research

Integration Host Factor IHF facilitates homologous recombination and mutagenic processes in Pseudomonas putida.
Abstract Nucleoid-associated proteins (NAPs) such as IHF, HU, Fis, and H-NS alter the topology of bound DNA and may thereby affect accessibility of DNA to repair and recombination processes. To examine this possibility, we investigated the effect of IHF on the frequency of homologous recombination (HR) and point mutations in soil bacterium Pseudomonas putida by using plasmidial and chromosomal assays. We observed positive effect of IHF on the frequency of HR, whereas this effect varied depending both on the chromosomal location of the HR target and the type of plasmid used in the assay. The occurrence of point mut...
Source: DNA Repair - November 5, 2019 Category: Genetics & Stem Cells Authors: Mikkel K, Tagel M, Ukkivi K, Ilves H, Kivisaar M Tags: DNA Repair (Amst) Source Type: research

RNases H: Multiple roles in maintaining genome integrity.
PMID: 31708455 [PubMed - as supplied by publisher] (Source: DNA Repair)
Source: DNA Repair - October 30, 2019 Category: Genetics & Stem Cells Authors: Cerritelli SM, Crouch RJ Tags: DNA Repair (Amst) Source Type: research

An alternative pathway for repair of deaminated bases in DNA triggered by archaeal NucS endonuclease.
Abstract Recent studies show that NucS endonucleases participate in mismatch repair in several archaea and bacteria. However, the function of archaeal NucS endonucleases has not been completely clarified. Here, we describe a NucS endonuclease from the hyperthermophilic and radioresistant archaeon Thermococcus gammatolerans (Tga NucS) that can cleave uracil (U)- and hypoxanthine (I)-containing dsDNA at 80 °C. Biochemical evidence shows that the cleavage sites of the enzyme are at the second phosphodiester on the 5'- site of U or I, and at the third phosphodiester on the 5'-site of the opposite base of U or I,...
Source: DNA Repair - October 24, 2019 Category: Genetics & Stem Cells Authors: Zhang L, Shi H, Gan Q, Wang Y, Wu M, Yang Z, Oger P, Zheng J Tags: DNA Repair (Amst) Source Type: research

Chromatin remodeling and mismatch repair: Access and excision.
This article reviews studies into the mechanistic and physical interactions between MMR and various chromatin-associated factors, including the histone deposition complex CAF1. Recent Xenopus and Saccharomyces cerevisiae studies describe a physical interaction between Msh2 and chromatin-remodeling ATPase Fun30/SMARCAD1, with potential mechanistic roles for SMARCAD1 in moving histones for both mispair access and excision tract elongation. The RSC complex, another histone remodeling complex, also potentially influences excision tract length. Deletion mutations of RSC2 point to mechanistic interactions with the MMR pathways. ...
Source: DNA Repair - October 17, 2019 Category: Genetics & Stem Cells Authors: Goellner EM Tags: DNA Repair (Amst) Source Type: research

The roles of fission yeast exonuclease 5 in nuclear and mitochondrial genome stability.
Abstract The Exo5 family consists of bi-directional, single-stranded DNA-specific exonucleases that contain an iron-sulfur cluster as a structural motif and have multiple roles in DNA metabolism. S. cerevisiae Exo5 is essential for mitochondrial genome maintenance, while the human ortholog is important for nuclear genome stability and DNA repair. Here, we identify the Exo5 ortholog in Schizosaccharomyes pombe (spExo5). The activity of spExo5 is highly similar to that of the human enzyme. When the single-stranded DNA is coated with single-stranded DNA binding protein RPA, spExo5 become a 5'-specific exonuclease. Ex...
Source: DNA Repair - September 21, 2019 Category: Genetics & Stem Cells Authors: Sparks JL, Gerik KJ, Stith CM, Yoder BL, Burgers PM Tags: DNA Repair (Amst) Source Type: research

Interactions of high mobility group box protein 1 (HMGB1) with nucleic acids: Implications in DNA repair and immune responses.
We report on the roles of HMGB1 in nucleotide excision repair (NER), base excision repair (BER), mismatch repair (MMR) and DNA double-strand break repair (DSBR). We also report on its roles in immune responses via its potential effects on antigen receptor diversity generation [V(D)J recombination] and interactions with foreign and self-nucleic acids. HMGB1 expression is altered in a variety of cancers and immunological disorders. However, due to the diversity and complexity of the biological processes influenced by HMGB1 (and its family members), a detailed understanding of the intracellular and extracellular roles of HMGB...
Source: DNA Repair - September 16, 2019 Category: Genetics & Stem Cells Authors: Mandke P, Vasquez KM Tags: DNA Repair (Amst) Source Type: research

The spectrum of APOBEC3 activity: From anti-viral agents to anti-cancer opportunities.
Abstract The APOBEC3 family of cytosine deaminases are part of the innate immune response to viral infection, but also have the capacity to damage cellular DNA. Detection of mutational signatures consistent with APOBEC3 activity, together with elevated APOBEC3 expression in cancer cells, has raised the possibility that these enzymes contribute to oncogenesis. Genome deamination by APOBEC3 enzymes also elicits DNA damage response signaling and presents therapeutic vulnerabilities for cancer cells. Here, we discuss implications of APOBEC3 activity in cancer and the potential to exploit their mutagenic activity for t...
Source: DNA Repair - September 13, 2019 Category: Genetics & Stem Cells Authors: Green AM, Weitzman MD Tags: DNA Repair (Amst) Source Type: research

Multisystem analyses of two Cockayne syndrome associated proteins CSA and CSB reveal shared and unique functions.
In this study we compared the effects of a CSA or a CSB defect at the levels of the cell and the intact organism. We showed that CSA-deficient zebrafish embryos exhibited modest hypersensitive to UV damage than CSB depletion. We found that loss of CSA can effectively release aggregation of mutant crystallin proteins in vitro. We described the opposite effect of CSA and CSB on neuritogenesis and elucidated the differentiated gene expression pathways regulated by these two proteins. Our data demonstrate convergent and divergent roles for CSA and CSB in DNA repair and transcription regulation and provide potential explanation...
Source: DNA Repair - September 12, 2019 Category: Genetics & Stem Cells Authors: Wu Z, Zhu X, Yu Q, Xu Y, Wang Y Tags: DNA Repair (Amst) Source Type: research

Mechanism of stimulation of DNA binding of the transcription factors by human apurinic/apyrimidinic endonuclease 1, APE1.
In conclusion, we propose that DNA-directed APE1 oligomerization can be regarded as a substitute for diffusion of APE1 along the DNA contour to probe for anisotropic flexibility. APE1 oligomers exacerbate pre-existing distortions in DNA and enable both NIR activity and DNA binding by TFs regardless of their oxidation state. PMID: 31518879 [PubMed - as supplied by publisher] (Source: DNA Repair)
Source: DNA Repair - August 31, 2019 Category: Genetics & Stem Cells Authors: Bazlekowa-Karaban M, Prorok P, Baconnais S, Taipakova S, Akishev Z, Zembrzuska D, Popov AV, Endutkin AV, Groisman R, Ishchenko AA, Matkarimov BT, Bissenbaev A, Le Cam E, Zharkov DO, Tudek B, Saparbaev M Tags: DNA Repair (Amst) Source Type: research

Functional profiling of nucleotide Excision repair in breast cancer.
Abstract Homologous recombination deficiency conferred by alterations in BRCA1 or BRCA2 are common in breast tumors and can drive sensitivity to platinum chemotherapy and PARP inhibitors. Alterations in nucleotide excision repair (NER) activity can also impact sensitivity to DNA damaging agents, but NER activity in breast cancer has been poorly characterized. Here, we apply a novel immunofluorescence-based cellular NER assay to screen a large panel of breast epithelial and cancer cell lines. Although the majority of breast cancer models are NER proficient, we identify an example of a breast cancer cell line with p...
Source: DNA Repair - August 30, 2019 Category: Genetics & Stem Cells Authors: Rajkumar-Calkins AS, Szalat R, Dreze M, Khan I, Frazier Z, Reznichenkov E, Schnorenberg MR, Tsai YF, Nguyen H, Kochupurakkal B, D'Andrea AD, Shapiro GI, Lazaro JB, Mouw KW Tags: DNA Repair (Amst) Source Type: research

A novel DNA repair inhibitor, diallyl disulfide (DADS), impairs DNA resection during DNA double-strand break repair by reducing Sae2 and Exo1 levels.
In this study, we found that diallyl disulfide (DADS), an organosulfur compound, increased the sensitivity of yeast cells to DNA damage and has potential for development as an adjuvant drug for DNA damage-based cancer therapy. We induced HO endonuclease to generate a specific DNA double-strand break (DSB) by adding galactose to yeast and used this system to study how DADS affects DNA repair. In this study, we found that DADS inhibited DNA repair in single-strand annealing (SSA) system and sensitized SSA cells to a single DSB. DADS impaired DNA repair by inhibiting the protein levels of the DNA resection-related proteins Sa...
Source: DNA Repair - August 24, 2019 Category: Genetics & Stem Cells Authors: Kuo CH, Leu YL, Wang TH, Tseng WC, Feng CH, Wang SH, Chen CC Tags: DNA Repair (Amst) Source Type: research

R-loop-dependent replication and genomic instability in bacteria.
Abstract DNA replication, the faithful copying of genetic material, must be tightly regulated to produce daughter cells with intact copies of the chromosome(s). This regulated replication is initiated by binding of specific proteins at replication origins, such as DnaA to oriC in bacteria. However, unregulated replication can sometimes be initiated at other sites, which can threaten genomic stability. One of the first systems of unregulated replication to be described is the one activated in Escherichia coli mutants lacking RNase HI (rnhA). In fact, rnhA mutants can replicate their chromosomes in a DnaA- and oriC-...
Source: DNA Repair - August 21, 2019 Category: Genetics & Stem Cells Authors: Drolet M, Brochu J Tags: DNA Repair (Amst) Source Type: research

Identification of putative G-quadruplex DNA structures in S. pombe genome by quantitative PCR stop assay.
Abstract In order to understand in which biological processes the four-stranded G-quadruplex (G4) DNA structures play a role, it is important to determine which predicted regions can actually adopt a G4 structure. Here, to identify DNA regions in Schizosaccharomyces pombe that fold into G4 structures, we first optimized a quantitative PCR (qPCR) assay using the G4 stabilizer, PhenDC3. We call this method the qPCR stop assay, and used it to screen for G4 structures in genomic DNA. The presence of G4 stabilizers inhibited DNA amplification in 14/15 unexplored genomic regions in S. pombe that encompassed predicted G4...
Source: DNA Repair - August 20, 2019 Category: Genetics & Stem Cells Authors: Jamroskovic J, Obi I, Movahedi A, Chand K, Chorell E, Sabouri N Tags: DNA Repair (Amst) Source Type: research

Vital roles of PCNA K165 modification during C. elegans gametogenesis and embryogenesis.
Abstract In eukaryotes, the DNA damage bypass pathway is promoted by ubiquitylation of PCNA at the conserved lysine 164. Using CRISPR-Cas9 system, we introduced amino acid substitution at K165 of C. elegans PCNA that corresponds to K164 in other characterised organisms and examined the contribution of this residue at a variety of stages during development. In the presence of UV-induced DNA lesions, PCNA-K165 is crucial for not only the early embryonic stages but also during larval development, implicating its functions for a broad time period during animal development. We also show that, without induction of DNA d...
Source: DNA Repair - August 11, 2019 Category: Genetics & Stem Cells Authors: Shao Z, Niwa S, Higashitani A, Daigaku Y Tags: DNA Repair (Amst) Source Type: research

Polyphenols: Major regulators of key components of DNA damage response in cancer.
Abstract DNA fidelity is constantly endangered by various types of intrinsic damages and extrinsic damages. Cells that are affected by DNA damage employ a specific, intricate, and interconnected network of cellular and molecular events (known as DNA damage response (DDR)) in order to maintain genome stability. More importantly, DDR is employed to pass intact genomes on to the next generation. Polyphenols constitute a large group of plant-based secondary metabolites widely present in foods and beverages with plant origins (e.g., fruits, vegetables, grains, spices, soy, essential oils nuts, tea, and wine). Based on ...
Source: DNA Repair - August 8, 2019 Category: Genetics & Stem Cells Authors: Majidinia M, Bishayee A, Yousefi B Tags: DNA Repair (Amst) Source Type: research

Inhibition of APE1-endonuclease activity affects cell metabolism in colon cancer cells via a p53-dependent pathway.
Abstract The pathogenesis of colorectal cancer (CRC) involves different mechanisms, such as genomic and microsatellite instabilities. Recently, a contribution of the base excision repair (BER) pathway in CRC pathology has been emerged. In this context, the involvement of APE1 in the BER pathway and in the transcriptional regulation of genes implicated in tumor progression strongly correlates with chemoresistance in CRC and in more aggressive cancers. In addition, the APE1 interactome is emerging as an important player in tumor progression, as demonstrated by its interaction with Nucleophosmin (NPM1). For these rea...
Source: DNA Repair - August 7, 2019 Category: Genetics & Stem Cells Authors: Codrich M, Comelli M, Malfatti MC, Mio C, Ayyildiz D, Zhang C, Kelley MR, Terrosu G, Pucillo CEM, Tell G Tags: DNA Repair (Amst) Source Type: research

Cutting-edge perspectives in genomic maintenance VI.
PMID: 31427173 [PubMed - as supplied by publisher] (Source: DNA Repair)
Source: DNA Repair - August 5, 2019 Category: Genetics & Stem Cells Authors: Hanawalt PC, Wilson SH Tags: DNA Repair (Amst) Source Type: research

Constitutively active Artemis nuclease recognizes structures containing single-stranded DNA configurations.
Abstract The Artemis nuclease recognizes and endonucleolytically cleaves at single-stranded to double-stranded DNA (ss/dsDNA) boundaries. It is also a key enzyme in the non-homologous end joining (NHEJ) DNA double-strand break repair pathway. Previously, a truncated form, Artemis-413, was developed that is constitutively active both in vitro and in vivo. Here, we use this constitutively active form of Artemis to detect DNA structures with ss/dsDNA boundaries that arise under topological stress. Topoisomerases prevent abnormal levels of torsional stress through modulation of positive and negative supercoiling. We s...
Source: DNA Repair - July 26, 2019 Category: Genetics & Stem Cells Authors: Pannunzio NR, Lieber MR Tags: DNA Repair (Amst) Source Type: research