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

Abstract

Reactive oxygen species (ROS) have emerged as important cellularsignaling 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 singlenucleotide 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.

Unveiling the non-repair face of the Base Excision Repair pathway in RNA processing: A missing link between DNA repair and gene expression?

“…A recently published paper gave a definitive prove to our previous findings and suggested a novel role of APE1 in epigenetic regulation, through modulating in a redox-mediated manner the DNMT1 expression and causing consequent suppression of Oct4 and Nanog expression through specific promoter methylation [56]. The epigenetic role of 8-oxoG modification was further supported by a recent publication showing a regulatory function of BER enzymes on specific gene expression by controlling the topological superstructure of G-quadruplex containing promoters, such as those of VEGF and NTHL1 genes [57], as also discussed in another article of this issue by A. Fleming and C. Burrows. All these studies highlight a new unsuspected function of oxidative DNA lesions as novel epigenetic mechanisms of gene regulation through the action of BER enzymes.…”

DNA damage mediates changes in neuronal sensitivity induced by the inflammatory mediators, MCP-1 and LPS, and can be reversed by enhancing the DNA repair function of APE1

“…Oxidative damage to DNA is known to alter the ability of transcription factors to recognize and bind promoter regions (Ziel et al, 2004, Gillespie et al, 2009, Pastukh et al, 2015), thus the DNA damage induced by inflammation might be reproducible because of damage to specific promoter/repressor regions of genes or transcription factors that are already activated by inflammation (Ruchko et al, 2009). Oxidative DNA damage, and specifically 8oxoG, has surfaced as a significant signaling mechanism for gene activation in promoter regions (Fleming et al, 2017). …”

Mitochondrial-epigenetic crosstalk in environmental toxicology

“…Although traditionally considered to inhibit transcription by blocking TF binding or stalling nuclear RNA polymerase II, ROS-mediated oxidation of DNA to 8-oxo-7,8-dihydroguanine (8-oxo-dG) in gene promoters can be serve as a signal for gene activation [64]. When 8-oxo-dG is formed in potential G-quadruplex forming sequences in a gene promoter, base excision repair by 8-oxoguanine DNA glycosylase OGG1 results in an abasic site that enables melting of the duplex and unmasking of G-quadruplex forming sequences [64]. These sequences can then adopt a G-quadruplex fold in which apurinic/apyrimidinic endonuclease 1 (APE1) binds but inefficiently cleaves the abasic site opposite the oxidized guanine and activates the adjacent gene [64].…”

“…When 8-oxo-dG is formed in potential G-quadruplex forming sequences in a gene promoter, base excision repair by 8-oxoguanine DNA glycosylase OGG1 results in an abasic site that enables melting of the duplex and unmasking of G-quadruplex forming sequences [64]. These sequences can then adopt a G-quadruplex fold in which apurinic/apyrimidinic endonuclease 1 (APE1) binds but inefficiently cleaves the abasic site opposite the oxidized guanine and activates the adjacent gene [64]. This mechanism has been demonstrated at two genes, VEGF and NTHL1 , in vitro [64], and is additionally supported by evidence of increased 8-oxo-dG levels and expression of genes involved in DNA repair, cell cycle, and stress response genes in response to infection or hypoxia [64].…”

“…These sequences can then adopt a G-quadruplex fold in which apurinic/apyrimidinic endonuclease 1 (APE1) binds but inefficiently cleaves the abasic site opposite the oxidized guanine and activates the adjacent gene [64]. This mechanism has been demonstrated at two genes, VEGF and NTHL1 , in vitro [64], and is additionally supported by evidence of increased 8-oxo-dG levels and expression of genes involved in DNA repair, cell cycle, and stress response genes in response to infection or hypoxia [64]. These data suggest that repair of oxidized DNA base 8-oxo-dG in a potential G-quadruplex sequence can serve as a structural switch in response to an oxidative environment (or, in severe cases, oxidative stress) by triggering folding that enhances adjacent gene transcription [64].…”