Human NEIL3 Gene Expression Regulated by Epigenetic-Like Oxidative DNA Modification

Abstract

The NEIL3 DNA repair gene is induced in cells or animal models experiencing oxidative or inflammatory stress along with oxidation of guanine (G) to 8-oxo-7,8-dihydroguanine (OG) in the genome. We hypothesize that a G-rich promoter element that is a potential G-quadruplex-forming sequence (PQS) in NEIL3 is a site for introduction of OG with epigenetic-like potential for gene regulation. Activation occurs when OG is formed in the NEIL3 PQS located near the transcription start site. Oxidative stress either introduced by TNFα or synthetically incorporated into precise locations focuses the base excision repair process to read and catalyze removal of OG via OG-glycosylase I (OGG1), yielding an abasic site (AP). Thermodynamic studies showed that AP destabilizes the duplex, enabling a structural transition of the sequence to a G-quadruplex (G4) fold that positions the AP in a loop facilitated by the NEIL3 PQS having five G runs in which the four unmodified runs adopt a stable G4. This presents AP to apurinic/apyrimidinic endonuclease 1 (APE1) that poorly cleaves the AP backbone in this context according to in vitro studies, allowing the protein to function as a trans activator of transcription. The proposal is supported by chemical studies in cellulo and in vitro. Activation of NEIL3 expression via the proposed mechanism allows cells to respond to mutagenic DNA damage removed by NEIL3 associated with oxidative or inflammatory stress. Lastly, inspection of many mammalian genomes identified conservation of the NEIL3 PQS, suggesting this sequence was favorably selected to function as a redox switch with OG as the epigenetic-like regulatory modification.

Next-generation DNA damage sequencing

“…This loss of stability led to the formation of a new G4 structure with an abasic-site-containing loop, which facilitated the binding and stalling of APE1 to the AP site, further stimulating TF binding and activating transcription. [47][48][49][50] The emerging role of 8-oxodG as a transcriptional regulator highlights its biological and health relevance beyond classic toxicity aspects of DNA damage. However, genome-wide associations of 8-oxodG with gene expression and further with pathological processes are not understood due to the lack of precise location information of 8-oxodG in the genome.…”

On the epigenetic role of guanosine oxidation

“…In details, OGG1 recruitment on 8-oxo-dG generates an abasic site which unmasks the PQS, leading to the formation of a G-quadruplex where APE1 binds [140] and interacts with transcription factors [141]. This mechanism seems to be particularly relevant in human DNA repair genes, which display PQS enrichment in their promoter and 5′-UTR [142]. Notably, the same mechanism has been shown to be crucial for the expression of several genes such as VEGF [143,144], PCNA [145], NTHL [141], and, more recently, to the DNA repair gene NEIL3 [146].…”

“…This mechanism seems to be particularly relevant in human DNA repair genes, which display PQS enrichment in their promoter and 5′-UTR [142]. Notably, the same mechanism has been shown to be crucial for the expression of several genes such as VEGF [143,144], PCNA [145], NTHL [141], and, more recently, to the DNA repair gene NEIL3 [146]. Interestingly, another work by Burrows and colleague showed that, when 8-oxo-dG is incorporated in PQSs located in the template strand, the formation of G-quadruplex downregulates gene expression [147].…”

Multi-Omics Characterization of Inflammatory Bowel Disease-Induced Hyperplasia/Dysplasia in the Rag2−/−/Il10−/− Mouse Model

“…If present in a potential G-quadruplex-forming sequence of promoter, abasic sites can trigger a transition from B DNA to a G-quadruplex structure. This in turn can lead to gene activation via recruitment of purinic/apyrimidinic endonuclease 1 and transcription factors to abasic sites [ 20 ]. H. hepaticus -infected Rag2 −/− /Il10 −/− mice develop colon carcinomas by 4 to 8 months post infection [ 10 , 21 ].…”