G-quadruplex structures as modulators of alternative promoter usage.

The precise regulation of gene transcription relies on promoters, and the selection of specific promoters for a particular gene is a key determinant of transcript diversity. However, the regulatory mechanisms governing promoter selection are not fully understood. G-quadruplexes (G4s) are unique DNA noncanonical secondary structures that have emerged as important regulators of gene expression. In this study, we systematically analyzed the relationship between G4 structures and alternative promoters (APs) in two cancer cell lines, K562 and HepG2, by integrating native elongating transcript-cap analysis of gene expression and G4 ChIP-seq datasets. We identified 573 differentially utilized APs (|fold change| > 2, false discovery rate < 0.05), 26% of which being associated with G4 structures within 100 base pairs. Notably, G4-associated promoters predominantly exhibited increased activity, suggesting that G4s generally promote AP selection. Furthermore, treatment with G4 ligands induced the generation of APs, suggesting that the stabilization of G4 structures may modulate AP usage. Collectively, these findings provide new insights into the G4-based mechanisms that regulate transcript isoform diversity.