Endogenous Promoter G-quadruplexes Scaffold Apurinic/apyrimidinic Endonuclease (APE1) to Drive Gene Expression

G-quadruplexes (G4s) are non-canonical DNA secondary structures enriched at promoters, yet their regulatory role in transcription remains elusive. While G4-ligand-based studies suggest transcriptional repression, their prevalence at oncogene promoters and correlation with high expression suggest a positive regulatory role. Here, we provide direct genetic evidence that promoter G4s function as positive activators of gene expression through a novel mechanism. By selectively mutating endogenous promoter G4 motifs, we demonstrate that G4 loss significantly impairs oncogene expression. Using the endogenous CXCL1 promoter G4 as an example, we revealed that loss of a single promoter G4 motif led to a marked down-regulation of CXCL1 expression as well as inhibition of cellular functions such as cell migration and invasion. Mechanistically, we identified apurinic/apyrimidinic endonuclease (APE1), a multifunctional DNA repair and redox factor, as a G4-binding protein which was recruited to promoters via its unique N-terminus. Subsequently, the redox activity of APE1 enhances transcription factor binding at G4-containing promoters, driving a pro-metastatic gene expression program. Disruption of the G4-APE1 interaction, either genetically or pharmacologically, suppresses gene expression and impairs tumor cell malignant traits. Our findings establish a direct genetic link and mechanistic basis for promoter G4s as crucial drivers of oncogene expression and tumor progression.