scholarly journals Oxidative DNA damage is epigenetic by regulating gene transcription via base excision repair

2016 ◽  
Author(s):  
Aaron M. Fleming ◽  
Yun Ding ◽  
Cynthia J. Burrows
Keyword(s):  
Base Excision Repair ◽  
Oxidative Dna Damage ◽  
Excision Repair ◽  
Gene Activation ◽  
Gene Promoters ◽  
Abasic Site ◽  
Protein Activity ◽  
Modified Dna ◽  
G Quadruplex ◽  
Base Excision

AbstractReactive oxygen species (ROS) have emerged as important cellular signaling agents for survival. Herein, we demonstrate that ROS-mediated oxidation of DNA to yield 8-oxo-7,8-dihydroguanine (OG) in gene promoters is a signaling agent for gene activation. Enhanced gene expression occurs when OG is formed in guanine-rich, potential G-quadruplex sequences (PQS) in promoter coding strands to initiate base excision repair (BER) by 8-oxoguanine DNA glycosylase (OGG1) yielding an abasic site (AP). The AP enables melting of the duplex to unmask the PQS to adopt a G-quadruplex fold in which apurinic/apyrimidinic endonuclease 1 (APE1) binds, but inefficiently cleaves, the AP for activation of VEGF or NTHL1 genes. This concept allowed identification of 61 human DNA repair genes that might be activated by this mechanism. Identification of the oxidatively-modified DNA base OG as guiding protein activity on the genome and altering cellular phenotype ascribes an epigenetic role to OG.

scholarly journals Oxidative DNA damage is epigenetic by regulating gene transcription via base excision repair

2017 ◽  
Vol 114 (10) ◽  
pp. 2604-2609 ◽  
Author(s):  
Aaron M. Fleming ◽  
Yun Ding ◽  
Cynthia J. Burrows
Keyword(s):  
Base Excision Repair ◽  
Oxidative Dna Damage ◽  
Excision Repair ◽  
Luciferase Reporter ◽  
Luciferase Expression ◽  
Gene Promoters ◽  
Modified Dna ◽  
G Quadruplex ◽  
Base Excision ◽  
The Impact

Reactive oxygen species (ROS) have emerged as important cellular-signaling agents for cellular survival. Herein, we demonstrate that ROS-mediated oxidation of DNA to yield 8-oxo-7,8-dihydroguanine (OG) in gene promoters is a signaling agent for gene activation. Enhanced gene expression occurs when OG is formed in guanine-rich, potential G-quadruplex–forming sequences (PQS) in promoter-coding strands, initiating base excision repair (BER) by 8-oxoguanine DNA glycosylase (OGG1), yielding an abasic site (AP). The AP enables melting of the duplex to unmask the PQS, adopting a G-quadruplex fold in which apurinic/apyrimidinic endonuclease 1 (APE1) binds, but inefficiently cleaves, the AP for activation of vascular endothelial growth factor (VEGF) or endonuclease III-like protein 1 (NTHL1) genes. These details were mapped via synthesis of OG and AP analogs at single-nucleotide precision within the promoter of a luciferase reporter system. The reporters were analyzed in human and mouse cells while selectively knocking out or down critical BER proteins to identify the impact on luciferase expression. Identification of the oxidatively modified DNA base OG to guide BER activity in a gene promoter and impact cellular phenotype ascribes an epigenetic role to OG.

scholarly journals Removal of Oxidative DNA Damage via FEN1-Dependent Long-Patch Base Excision Repair in Human Cell Mitochondria

2008 ◽  
Vol 28 (16) ◽  
pp. 4975-4987 ◽  
Author(s):  
Pingfang Liu ◽  
Limin Qian ◽  
Jung-Suk Sung ◽  
Nadja C. de Souza-Pinto ◽  
Li Zheng ◽  
...  
Keyword(s):  
Dna Damage ◽  
Base Excision Repair ◽  
Oxidative Dna Damage ◽  
Excision Repair ◽  
Subcellular Fractionation ◽  
Major Type ◽  
Abasic Site ◽  
Intact Cells ◽  
Base Excision ◽  
Extent Of Damage

ABSTRACT Repair of oxidative DNA damage in mitochondria was thought limited to short-patch base excision repair (SP-BER) replacing a single nucleotide. However, certain oxidative lesions cannot be processed by SP-BER. Here we report that 2-deoxyribonolactone (dL), a major type of oxidized abasic site, inhibits replication by mitochondrial DNA (mtDNA) polymerase γ and interferes with SP-BER by covalently trapping polymerase γ during attempted dL excision. However, repair of dL was detected in human mitochondrial extracts, and we show that this repair is via long-patch BER (LP-BER) dependent on flap endonuclease 1 (FEN1), not previously known to be present in mitochondria. FEN1 was retained in protease-treated mitochondria and detected in mitochondrial nucleoids that contain known mitochondrial replication and transcription proteins. Results of immunofluorescence and subcellular fractionation studies were also consistent with the presence of FEN1 in the mitochondria of intact cells. Immunodepletion experiments showed that the LP-BER activity of mitochondrial extracts was strongly diminished in parallel with the removal of FEN1, although some activity remained, suggesting the presence of an additional flap-removing enzyme. Biological evidence for a FEN1 role in repairing mitochondrial oxidative DNA damage was provided by RNA interference experiments, with the extent of damage greater and the recovery slower in FEN1-depleted cells than in control cells. The mitochondrial LP-BER pathway likely plays important roles in repairing dL lesions and other oxidative lesions and perhaps in normal mtDNA replication.

scholarly journals Effect of DNA Glycosylases OGG1 and Neil1 on Oxidized G-Rich Motif in the KRAS Promoter

2021 ◽  
Vol 22 (3) ◽  
pp. 1137
Author(s):  
Annalisa Ferino ◽  
Luigi E. Xodo
Keyword(s):  
Oxidative Stress ◽  
Base Excision Repair ◽  
Excision Repair ◽  
Start Site ◽  
Dna Glycosylases ◽  
Repair Pathway ◽  
Transcription Start ◽  
G Quadruplex ◽  
Base Excision ◽  
Regulatory Functions

The promoter of the Kirsten ras (KRAS) proto-oncogene contains, upstream of the transcription start site, a quadruplex-forming motif called 32R with regulatory functions. As guanine under oxidative stress can be oxidized to 8-oxoguanine (8OG), we investigated the capacity of glycosylases 8-oxoguanine glycosylase (OGG1) and endonuclease VIII-like 1 (Neil1) to excise 8OG from 32R, either in duplex or G-quadruplex (G4) conformation. We found that OGG1 efficiently excised 8OG from oxidized 32R in duplex but not in G4 conformation. By contrast, glycosylase Neil1 showed more activity on the G4 than the duplex conformation. We also found that the excising activity of Neil1 on folded 32R depended on G4 topology. Our data suggest that Neil1, besides being involved in base excision repair pathway (BER), could play a role on KRAS transcription.

scholarly journals MSH2–MSH6 stimulates DNA polymerase η, suggesting a role for A:T mutations in antibody genes

2005 ◽  
Vol 201 (4) ◽  
pp. 637-645 ◽  
Author(s):  
Teresa M. Wilson ◽  
Alexandra Vaisman ◽  
Stella A. Martomo ◽  
Patsa Sullivan ◽  
Li Lan ◽  
...  
Keyword(s):  
Dna Polymerase ◽  
Base Excision Repair ◽  
Somatic Hypermutation ◽  
Excision Repair ◽  
Cytidine Deaminase ◽  
Abasic Site ◽  
Cell Extracts ◽  
Activation Induced Cytidine Deaminase ◽  
Base Excision

Activation-induced cytidine deaminase deaminates cytosine to uracil (dU) in DNA, which leads to mutations at C:G basepairs in immunoglobulin genes during somatic hypermutation. The mechanism that generates mutations at A:T basepairs, however, remains unclear. It appears to require the MSH2–MSH6 mismatch repair heterodimer and DNA polymerase (pol) η, as mutations of A:T are decreased in mice and humans lacking these proteins. Here, we demonstrate that these proteins interact physically and functionally. First, we show that MSH2–MSH6 binds to a U:G mismatch but not to other DNA intermediates produced during base excision repair of dUs, including an abasic site and a deoxyribose phosphate group. Second, MSH2 binds to pol η in solution, and endogenous MSH2 associates with the pol in cell extracts. Third, MSH2–MSH6 stimulates the catalytic activity of pol η in vitro. These observations suggest that the interaction between MSH2–MSH6 and DNA pol η stimulates synthesis of mutations at bases located downstream of the initial dU lesion, including A:T pairs.

scholarly journals Dynamic Compartmentalization of Base Excision Repair Proteins in Response to Nuclear and Mitochondrial Oxidative Stress

2008 ◽  
Vol 29 (3) ◽  
pp. 794-807 ◽  
Author(s):  
Lyra M. Griffiths ◽  
Dan Swartzlander ◽  
Kellen L. Meadows ◽  
Keith D. Wilkinson ◽  
Anita H. Corbett ◽  
...  
Keyword(s):  
Oxidative Stress ◽  
Dna Damage ◽  
Dna Repair ◽  
Base Excision Repair ◽  
Oxidative Dna Damage ◽  
Excision Repair ◽  
Intracellular Localization ◽  
Genotoxic Stress ◽  
Mitochondrial Oxidative Stress ◽  
Base Excision

ABSTRACT DNAs harbored in both nuclei and mitochondria of eukaryotic cells are subject to continuous oxidative damage resulting from normal metabolic activities or environmental insults. Oxidative DNA damage is primarily reversed by the base excision repair (BER) pathway, initiated by N-glycosylase apurinic/apyrimidinic (AP) lyase proteins. To execute an appropriate repair response, BER components must be distributed to accommodate levels of genotoxic stress that may vary considerably between nuclei and mitochondria, depending on the growth state and stress environment of the cell. Numerous examples exist where cells respond to signals, resulting in relocalization of proteins involved in key biological transactions. To address whether such dynamic localization contributes to efficient organelle-specific DNA repair, we determined the intracellular localization of the Saccharomyces cerevisiae N-glycosylase/AP lyases, Ntg1 and Ntg2, in response to nuclear and mitochondrial oxidative stress. Fluorescence microscopy revealed that Ntg1 is differentially localized to nuclei and mitochondria, likely in response to the oxidative DNA damage status of the organelle. Sumoylation is associated with targeting of Ntg1 to nuclei containing oxidative DNA damage. These studies demonstrate that trafficking of DNA repair proteins to organelles containing high levels of oxidative DNA damage may be a central point for regulating BER in response to oxidative stress.

scholarly journals Base excision repair of oxidative DNA damage and association with cancer and aging

2008 ◽  
Vol 30 (1) ◽  
pp. 2-10 ◽  
Author(s):  
S. Maynard ◽  
S. H. Schurman ◽  
C. Harboe ◽  
N. C. de Souza-Pinto ◽  
V. A. Bohr
Keyword(s):  
Dna Damage ◽  
Base Excision Repair ◽  
Oxidative Dna Damage ◽  
Excision Repair ◽  
Base Excision

Detection of base excision repair enzyme activity using a luminescent G-quadruplex selective switch-on probe

2013 ◽  
Vol 49 (50) ◽  
pp. 5630 ◽  
Author(s):  
Ka-Ho Leung ◽  
Hong-Zhang He ◽  
Victor Pui-Yan Ma ◽  
Hai-Jing Zhong ◽  
Daniel Shiu-Hin Chan ◽  
...  
Keyword(s):  
Enzyme Activity ◽  
Base Excision Repair ◽  
Excision Repair ◽  
Repair Enzyme ◽  
G Quadruplex ◽  
Base Excision

A fluorescent G-quadruplex probe for the assay of base excision repair enzyme activity

2015 ◽  
Vol 51 (72) ◽  
pp. 13744-13747 ◽  
Author(s):  
Chang Yeol Lee ◽  
Ki Soo Park ◽  
Hyun Gyu Park
Keyword(s):  
Enzyme Activity ◽  
Base Excision Repair ◽  
Fluorescence Enhancement ◽  
Excision Repair ◽  
High Sensitivity ◽  
Repair Enzyme ◽  
Quadruplex Structure ◽  
G Quadruplex ◽  
Base Excision ◽  
Novel Strategy

A G-quadruplex probe incorporating 2-AP is utilized to develop a novel strategy to accurately determine UDG activity. The excision reaction promoted by UDG is designed to trigger the formation of G-quadruplex structure with significant fluorescence enhancement of 2-AP within the probe. By employing this strategy, UDG activity can be reliably determined with high sensitivity and specificity.

scholarly journals R-loops promote trinucleotide repeat deletion through DNA base excision repair enzymatic activities

2020 ◽  
Vol 295 (40) ◽  
pp. 13902-13913
Author(s):  
Eduardo E. Laverde ◽  
Yanhao Lai ◽  
Fenfei Leng ◽  
Lata Balakrishnan ◽  
Catherine H. Freudenreich ◽  
...  
Keyword(s):  
Base Excision Repair ◽  
Trinucleotide Repeat ◽  
Excision Repair ◽  
Enzymatic Activities ◽  
Cag Repeat ◽  
Abasic Site ◽  
Dna Damage And Repair ◽  
Dna Base Excision Repair ◽  
Treatment And Prevention ◽  
Base Excision

Trinucleotide repeat (TNR) expansion and deletion are responsible for over 40 neurodegenerative diseases and associated with cancer. TNRs can undergo somatic instability that is mediated by DNA damage and repair and gene transcription. Recent studies have pointed toward a role for R-loops in causing TNR expansion and deletion, and it has been shown that base excision repair (BER) can result in CAG repeat deletion from R-loops in yeast. However, it remains unknown how BER in R-loops can mediate TNR instability. In this study, using biochemical approaches, we examined BER enzymatic activities and their influence on TNR R-loops. We found that AP endonuclease 1 incised an abasic site on the nontemplate strand of a TNR R-loop, creating a double-flap intermediate containing an RNA:DNA hybrid that subsequently inhibited polymerase β (pol β) synthesis of TNRs. This stimulated flap endonuclease 1 (FEN1) cleavage of TNRs engaged in an R-loop. Moreover, we showed that FEN1 also efficiently cleaved the RNA strand, facilitating pol β loop/hairpin bypass synthesis and the resolution of TNR R-loops through BER. Consequently, this resulted in fewer TNRs synthesized by pol β than those removed by FEN1, thereby leading to repeat deletion. Our results indicate that TNR R-loops preferentially lead to repeat deletion during BER by disrupting the balance between the addition and removal of TNRs. Our discoveries open a new avenue for the treatment and prevention of repeat expansion diseases and cancer.

scholarly journals The Effect ofMsh2Knockdown on Toxicity Induced bytert-Butyl-hydroperoxide, Potassium Bromate, and Hydrogen Peroxide in Base Excision Repair Proficient and Deficient Cells

2013 ◽  
Vol 2013 ◽  
pp. 1-9 ◽  
Author(s):  
N. Cooley ◽  
R. H. Elder ◽  
A. C. Povey
Keyword(s):  
Dna Damage ◽  
Base Excision Repair ◽  
Oxidative Dna Damage ◽  
Excision Repair ◽  
Shrna Expression ◽  
Cellular Toxicity ◽  
Dna Mismatch ◽  
Shrna Expression Vector ◽  
Repair Systems ◽  
Base Excision

The DNA mismatch repair (MMR) and base excision repair (BER) systems are important determinants of cellular toxicity following exposure to agents that cause oxidative DNA damage. To examine the interactions between these different repair systems, we examined whether toxicity, induced byt-BOOH and KBrO3, differs in BER proficient (Mpg+/+,Nth1+/+) and deficient (Mpg−/−,Nth1−/−) mouse embryonic fibroblasts (MEFs) followingMsh2knockdown of between 79 and 88% using an shRNA expression vector.Msh2knockdown inNth1+/+cells had no effect ont-BOOH and KBrO3induced toxicity as assessed by an MTT assay; knockdown inNth1−/−cells resulted in increased resistance tot-BOOH and KBrO3, a result consistent with Nth1 removing oxidised pyrimidines.Msh2knockdown inMpg+/+cells had no effect ont-BOOH toxicity but increased resistance to KBrO3; inMpg−/−cells,Msh2knockdown increased cellular sensitivity to KBrO3but increased resistance to t-BOOH, suggesting a role forMpgin removing DNA damage induced by these agents. MSH2 dependent and independent pathways then determine cellular toxicity induced by oxidising agents. A complex interaction between MMR and BER repair systems, that is, exposure dependent, also exists to determine cellular toxicity.

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