Human AP endonuclease inefficiently removes abasic sites within G4 structures compared to duplex DNA

Reactive 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-7,8dihydroguanine (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.

show abstract

“…S4). Lastly, the AP is strongly bound by APE1 in a G-quadruplex fold, but the cleavage kinetics are attenuated, as previously described 21 .…”

Section: Resultssupporting

confidence: 55%

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

Fleming

Ding

Burrows

2016

Preprint

156

View full text Add to dashboard Cite

show abstract

“…laboratory and others, and it was found that APE1 binds APs in G4s, but the cleavage rate was highly attenuated (12,19). The attenuated cleavage by APE1 on the promoter may provide the trigger to increase the rate of transcription observed by allowing APE1 to idle on the G4/G5 structural motif.…”

Section: Significancementioning

confidence: 94%

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

Fleming

Ding

Burrows

2017

Proc. Natl. Acad. Sci. U.S.A.

294

432

View full text Add to dashboard Cite

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.

show abstract

“…The G-quadruplex fold is favored because the 5 th G track allows extrusion of the damaged G run into a large loop while maintaining the fold. The AP site is then presented to APE1 and bound by this protein; consequently, the reaction kinetics are highly attenuated by the G4 structure prolonging APE1 binding [42] and aiding in the possible recruitment of other activating transcription factors for gene induction (e.g., HIF1-α) [13]. These initial studies identify an intertwining of G oxidation in PQS elements to provide a structural switch for recruitment of BER proteins to activate transcription (Fig.…”

Section: Og Activates Mrna Synthesis By Facilitating Promoter G-qumentioning

confidence: 99%

8-Oxo-7,8-dihydroguanine, friend and foe: Epigenetic-like regulator versus initiator of mutagenesis

2017

View full text Add to dashboard Cite

A high flux of reactive oxygen species during oxidative stress results in oxidative modification of cellular components including DNA. Oxidative DNA “damage” to the heterocyclic bases is considered deleterious because polymerases may incorrectly read the modifications causing mutations. A prominent member in this class is the oxidized guanine base 8-oxo-7,8-dihydroguanine (OG) that is moderately mutagenic effecting G→T transversion mutations. Recent reports have identified that formation of OG in G-rich regulatory elements in the promoters of the VEGF, TNFα, and SIRT1 genes can increase transcription via activation of the base excision repair (BER) pathway. Work in our laboratory with the G-rich sequence in the promoter of VEGF concluded that BER drives a shift in structure to a G-quadruplex conformation leading to gene activation in mammalian cells. More specifically, removal of OG from the duplex context by 8-oxoguanine glycosylase 1 (OGG1) produces an abasic site (AP) that destabilizes the duplex, shifting the equilibrium toward the G-quadruplex fold because of preferential extrusion of the AP into a loop. The AP is bound but inefficiently cleaved by apurinic/apyrimidinic endoDNase I (APE1) that likely allows recruitment of activating transcription factors for gene induction. The ability of OG to induce transcription ascribes a regulatory or epigenetic-like role for this oxidatively modified base. We compare OG to the 5-methylcytosine (5mC) epigenetic pathway including its oxidized derivatives, some of which poise genes for transcription while also being substrates for BER. The mutagenic potential of OG to induce only ~one-third the number of mutations (G→T) compared to deamination of 5mC producing C→T mutations is described. These comparisons blur the line between friendly epigenetic base modifications and those that are foes, i.e. DNA “damage,” causing genetic mutations.

show abstract

Human AP endonuclease inefficiently removes abasic sites within G4 structures compared to duplex DNA

Cited by 33 publications

References 49 publications

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

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

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

8-Oxo-7,8-dihydroguanine, friend and foe: Epigenetic-like regulator versus initiator of mutagenesis

Contact Info

Product

Resources

About