scholarly journals Genomic landscape of oxidative DNA damage and repair reveals regioselective protection from mutagenesis

2017 ◽  
Author(s):  
Anna R Poetsch ◽  
Simon J Boulton ◽  
Nicholas M Luscombe
Keyword(s):  
Dna Damage ◽  
Oxidative Damage ◽  
Oxidative Dna Damage ◽  
Molecular Mechanisms ◽  
Accumulation Rate ◽  
Repetitive Sequences ◽  
Open Chromatin ◽  
Regulatory Sequences ◽  
Dna Damage And Repair ◽  
A Genome

AbstractDNA is subject to constant chemical modification and damage, which eventually results in variable mutation rates throughout the genome. Although detailed molecular mechanisms of DNA damage and repair are well-understood, damage impact and execution of repair across a genome remains poorly defined. To bridge the gap between our understanding of DNA repair and mutation distributions we developed a novel method, AP-seq, capable of mapping apurinic sitesand 8-oxo-7,8-dihydroguanine bases at ∼300bp resolution on a genome-wide scale. We directly demonstrate that the accumulation rate of oxidative damage varies widely across the genome, with hot spots acquiring many times more damage than cold spots. Unlike SNVs in cancers, damage burden correlates with marks for open chromatin notably H3K9ac and H3K4me2. Oxidative damage is also highly enriched in transposable elements and other repetitive sequences. In contrast, we observe decreased damage at promoters, exons and termination sites, but not introns, in a seemingly transcription-independent manner. Leveraging cancer genomic data, we also find locally reduced SNV rates in promoters, genes and other functional elements. Taken together, our study reveals that oxidative DNA damage accumulation and repair differ strongly across the genome, but culminate in a previously unappreciated mechanism that safe-guards the regulatory sequences and the coding regions of genes from mutations.

scholarly journals Genome wide mapping of DNA lesions by Repair Assisted Damage Detection sequencing – RADD-Seq

2021 ◽  
Author(s):  
Noa Gilat ◽  
Dena Fridman ◽  
Hila Sharim ◽  
Sapir Margalit ◽  
Natalie R. Gassman ◽  
...  
Keyword(s):  
Dna Damage ◽  
Damage Detection ◽  
Oxidative Dna Damage ◽  
Dna Lesions ◽  
Open Chromatin ◽  
Dna Damage And Repair ◽  
Genome Wide ◽  
A Genome ◽  
Wide Range ◽  
Before And After

AbstractMapping DNA damage and its repair has immense potential in understanding environmental exposures, their genotoxicity, and their impact on human health. Monitoring changes in genomic stability also aids in the diagnosis of numerous DNA-related diseases, like cancer, and assists in monitoring their progression and prognosis. However, genome-wide maps of DNA damage distribution are challenging to produce. Here we describe the localization of DNA damage and repair loci by Repair Assisted Damage Detection sequencing – RADD-Seq. Based on the enrichment of damage lesions coupled with a pull-down assay and followed by next generation sequencing, this method is easy to perform and can produce compelling results with minimal coverage. RADD-seq enables the localization of both DNA damage and repair sites for a wide range of single-strand damage types. Using this technique, we created a genome-wide map of oxidative DNA damage loci before and after repair. Oxidative lesions were heterogeneously distributed along the human genome, with less damage occurring in tight chromatin regions. Furthermore, we showed repair is prioritized for highly expressed, essential genes and in open chromatin regions. RADD-seq sheds light on cellular repair mechanisms and capable of identifying genomic hotspots prone to mutation.

scholarly journals Beta-carotene enhances the recovery of lymphocytes from oxidative DNA damage.

1998 ◽  
Vol 45 (1) ◽  
pp. 183-190 ◽  
Author(s):  
L Fillion ◽  
A Collins ◽  
S Southon
Keyword(s):  
Dna Damage ◽  
Oxidative Damage ◽  
Oxidative Dna Damage ◽  
Enhanced Recovery ◽  
Beta Carotene ◽  
Epidemiological Studies ◽  
Dietary Factors ◽  
Causal Mechanism ◽  
Strand Breaks

Epidemiological studies have revealed a strong correlation between high intake of fruit and vegetables and low incidence of certain cancers. Micronutrients present in these foods are thought to decrease free radical attack on DNA and hence protect against mutations that cause cancer, but the fine details of the causal mechanism have still to be elucidated. Whether dietary factors can modulate DNA repair--a crucial element in the avoidance of carcinogenesis--is an intriguing question that has not yet been satisfactorily answered. In order to investigate the effects of beta-carotene on oxidative damage and its repair, volunteers were given a single 45 mg dose and lymphocytes taken before and after the supplement were treated in vitro with H2O2. DNA strand breaks and oxidised pyrimidines were measured at intervals, to monitor the removal of oxidative DNA damage. We found inter-individual variations in response. In cases where the baseline plasma beta-carotene concentration was high, or where supplementation increased the plasma concentration, recovery from oxidative damage (i.e. removal of both oxidised pyrimidines and strand breaks) was relatively rapid. However, what seems to be an enhancement of repair might in fact represent an amelioration of the continuing oxidative stress encountered by the lymphocytes under in vitro culture conditions. We found that culture in a 5% oxygen atmosphere enhanced recovery of lymphocytes from H2O2 damage.

scholarly journals Molecular Mechanisms of Zinc Oxide Nanoparticle-Induced Genotoxicity

Materials ◽  
2017 ◽  
Vol 10 (12) ◽  
pp. 1427 ◽  
Author(s):  
Agmal Scherzad ◽  
Till Meyer ◽  
Norbert Kleinsasser ◽  
Stephan Hackenberg
Keyword(s):  
Dna Damage ◽  
Zinc Oxide ◽  
Mammalian Cells ◽  
Oxidative Dna Damage ◽  
Molecular Mechanisms ◽  
Consumer Products ◽  
Zno Nps ◽  
Cytotoxic Effects

Background: Zinc oxide nanoparticles (ZnO NPs) are among the most frequently applied nanomaterials in consumer products. Evidence exists regarding the cytotoxic effects of ZnO NPs in mammalian cells; however, knowledge about the potential genotoxicity of ZnO NPs is rare, and results presented in the current literature are inconsistent. Objectives: The aim of this review is to summarize the existing data regarding the DNA damage that ZnO NPs induce, and focus on the possible molecular mechanisms underlying genotoxic events. Methods: Electronic literature databases were systematically searched for studies that report on the genotoxicity of ZnO NPs. Results: Several methods and different endpoints demonstrate the genotoxic potential of ZnO NPs. Most publications describe in vitro assessments of the oxidative DNA damage triggered by dissoluted Zn2+ ions. Most genotoxicological investigations of ZnO NPs address acute exposure situations. Conclusion: Existing evidence indicates that ZnO NPs possibly have the potential to damage DNA. However, there is a lack of long-term exposure experiments that clarify the intracellular bioaccumulation of ZnO NPs and the possible mechanisms of DNA repair and cell survival.

Paternal impacts on development: identification of genomic regions vulnerable to oxidative DNA damage in human spermatozoa

2019 ◽  
Vol 34 (10) ◽  
pp. 1876-1890 ◽  
Author(s):  
M J Xavier ◽  
B Nixon ◽  
S D Roman ◽  
R J Scott ◽  
J R Drevet ◽  
...  
Keyword(s):  
Oxidative Stress ◽  
Dna Damage ◽  
Male Infertility ◽  
Oxidative Damage ◽  
Oxidative Dna Damage ◽  
Human Spermatozoa ◽  
Research Centre ◽  
Environmental Toxicants ◽  
Next Generation ◽  
Genomic Regions

Abstract STUDY QUESTION Do all regions of the paternal genome within the gamete display equivalent vulnerability to oxidative DNA damage? SUMMARY ANSWER Oxidative DNA damage is not randomly distributed in mature human spermatozoa but is instead targeted, with particular chromosomes being especially vulnerable to oxidative stress. WHAT IS KNOWN ALREADY Oxidative DNA damage is frequently encountered in the spermatozoa of male infertility patients. Such lesions can influence the incidence of de novo mutations in children, yet it remains to be established whether all regions of the sperm genome display equivalent susceptibility to attack by reactive oxygen species. STUDY DESIGN, SIZE, DURATION Human spermatozoa obtained from normozoospermic males (n = 8) were split into equivalent samples and subjected to either hydrogen peroxide (H2O2) treatment or vehicle controls before extraction of oxidized DNA using a modified DNA immunoprecipitation (MoDIP) protocol. Specific regions of the genome susceptible to oxidative damage were identified by next-generation sequencing and validated in the spermatozoa of normozoospermic males (n = 18) and in patients undergoing infertility evaluation (n = 14). PARTICIPANTS/MATERIALS, SETTING, METHODS Human spermatozoa were obtained from normozoospermic males and divided into two identical samples prior to being incubated with either H2O2 (5 mm, 1 h) to elicit oxidative stress or an equal volume of vehicle (untreated controls). Alternatively, spermatozoa were obtained from fertility patients assessed as having high basal levels of oxidative stress within their spermatozoa. All semen samples were subjected to MoDIP to selectively isolate oxidized DNA, prior to sequencing of the resultant DNA fragments using a next-generation whole-genomic sequencing platform. Bioinformatic analysis was then employed to identify genomic regions vulnerable to oxidative damage, several of which were selected for real-time quantitative PCR (qPCR) validation. MAIN RESULTS AND THE ROLE OF CHANCE Approximately 9000 genomic regions, 150–1000 bp in size, were identified as highly vulnerable to oxidative damage in human spermatozoa. Specific chromosomes showed differential susceptibility to damage, with chromosome 15 being particularly sensitive to oxidative attack while the sex chromosomes were protected. Susceptible regions generally lay outside protamine- and histone-packaged domains. Furthermore, we confirmed that these susceptible genomic sites experienced a dramatic (2–15-fold) increase in their burden of oxidative DNA damage in patients undergoing infertility evaluation compared to normal healthy donors. LIMITATIONS, REASONS FOR CAUTION The limited number of samples analysed in this study warrants external validation, as do the implications of our findings. Selection of male fertility patients was based on high basal levels of oxidative stress within their spermatozoa as opposed to specific sub-classes of male factor infertility. WIDER IMPLICATIONS OF THE FINDINGS The identification of genomic regions susceptible to oxidation in the male germ line will be of value in focusing future analyses into the mutational load carried by children in response to paternal factors such as age, the treatment of male infertility using ART and paternal exposure to environmental toxicants. STUDY FUNDING/COMPETING INTEREST(S) Project support was provided by the University of Newcastle’s (UoN) Priority Research Centre for Reproductive Science. M.J.X. was a recipient of a UoN International Postgraduate Research Scholarship. B.N. is the recipient of a National Health and Medical Research Council of Australia Senior Research Fellowship. Authors declare no conflict of interest.

Molecular Mechanisms of DNA Damage and Repair

2014 ◽  
pp. 201-209
Author(s):  
David S. Chang ◽  
Foster D. Lasley ◽  
Indra J. Das ◽  
Marc S. Mendonca ◽  
Joseph R. Dynlacht
Keyword(s):  
Dna Damage ◽  
Molecular Mechanisms ◽  
Dna Damage And Repair

scholarly journals Characteristics of mutational signatures of unknown etiology

NAR Cancer ◽  
2020 ◽  
Vol 2 (3) ◽  
Author(s):  
Xiaoju Hu ◽  
Zhuxuan Xu ◽  
Subhajyoti De
Keyword(s):  
Dna Damage ◽  
Point Mutations ◽  
Gc Content ◽  
Unknown Origin ◽  
Unknown Etiology ◽  
Mutational Signatures ◽  
Dna Damage And Repair ◽  
Disease Etiology ◽  
Repair Processes ◽  
A Genome

Abstract Although not all somatic mutations are cancer drivers, their mutational signatures, i.e. the patterns of genomic alterations at a genome-wide scale, provide insights into past exposure to mutagens, DNA damage and repair processes. Computational deconvolution of somatic mutation patterns and expert curation pan-cancer studies have identified a number of mutational signatures associated with point mutations, dinucleotide substitutions, insertions and deletions, and rearrangements, and have established etiologies for a subset of these signatures. However, the mechanisms underlying nearly one-third of all mutational signatures are not yet understood. The signatures with established etiology and those with hitherto unknown origin appear to have some differences in strand bias, GC content and nucleotide context diversity. It is possible that some of the hitherto ‘unknown’ signatures predominantly occur outside gene regions. While nucleotide contexts might be adequate to establish etiologies of some mutational signatures, in other cases additional features, such as broader (epi)genomic contexts, including chromatin, replication timing, processivity and local mutational patterns, may help fully understand the underlying DNA damage and repair processes. Nonetheless, remarkable progress in characterization of mutational signatures has provided fundamental insights into the biology of cancer, informed disease etiology and opened up new opportunities for cancer prevention, risk management, and therapeutic decision making.

scholarly journals Oxidative DNA Damage and Repair: Significance and Biomarkers

2006 ◽  
Vol 136 (10) ◽  
pp. 2687S-2689S ◽  
Author(s):  
Lynnette R. Ferguson ◽  
Martin Philpott ◽  
Nishi Karunasinghe
Keyword(s):  
Dna Damage ◽  
Oxidative Dna Damage ◽  
Dna Damage And Repair
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