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

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.

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

10.1101/069955 ◽

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.

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Oxidative stress-mediated epigenetic regulation by G-quadruplexes

NAR Cancer ◽

10.1093/narcan/zcab038 ◽

2021 ◽

Vol 3 (3) ◽

Author(s):

Aaron M Fleming ◽

Cynthia J Burrows

Keyword(s):

Oxidative Stress ◽

Base Excision Repair ◽

Excision Repair ◽

Gene Promoter ◽

Nuclease Activity ◽

G Quadruplex ◽

Biophysical Studies ◽

Base Excision ◽

The Impact

Abstract Many cancer-associated genes are regulated by guanine (G)-rich sequences that are capable of refolding from the canonical duplex structure to an intrastrand G-quadruplex. These same sequences are sensitive to oxidative damage that is repaired by the base excision repair glycosylases OGG1 and NEIL1–3. We describe studies indicating that oxidation of a guanosine base in a gene promoter G-quadruplex can lead to up- and downregulation of gene expression that is location dependent and involves the base excision repair pathway in which the first intermediate, an apurinic (AP) site, plays a key role mediated by AP endonuclease 1 (APE1/REF1). The nuclease activity of APE1 is paused at a G-quadruplex, while the REF1 capacity of this protein engages activating transcription factors such as HIF-1α, AP-1 and p53. The mechanism has been probed by in vitro biophysical studies, whole-genome approaches and reporter plasmids in cellulo. Replacement of promoter elements by a G-quadruplex sequence usually led to upregulation, but depending on the strand and precise location, examples of downregulation were also found. The impact of oxidative stress-mediated lesions in the G-rich sequence enhanced the effect, whether it was positive or negative.

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

International Journal of Molecular Sciences ◽

10.3390/ijms22031137 ◽

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.

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

Molecular and Cellular Biology ◽

10.1128/mcb.01357-08 ◽

2008 ◽

Vol 29 (3) ◽

pp. 794-807 ◽

Cited By ~ 31

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.

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

Carcinogenesis ◽

10.1093/carcin/bgn250 ◽

2008 ◽

Vol 30 (1) ◽

pp. 2-10 ◽

Cited By ~ 344

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

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

Chemical Communications ◽

10.1039/c3cc41129j ◽

2013 ◽

Vol 49 (50) ◽

pp. 5630 ◽

Cited By ~ 103

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

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

Chemical Communications ◽

10.1039/c5cc05010c ◽

2015 ◽

Vol 51 (72) ◽

pp. 13744-13747 ◽

Cited By ~ 42

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.

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

BioMed Research International ◽

10.1155/2013/152909 ◽

2013 ◽

Vol 2013 ◽

pp. 1-9 ◽

Cited By ~ 3

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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