# G-quadruplex structures as modulators of alternative promoter usage

## TL;DR

This study shows that G-quadruplex DNA structures can influence how genes are transcribed by affecting promoter selection in cancer cells.

## Contribution

The study reveals a novel role of G-quadruplex structures in modulating alternative promoter usage and transcript diversity.

## Key findings

- 573 differentially utilized alternative promoters were identified in K562 and HepG2 cancer cell lines.
- 26% of these promoters were associated with G-quadruplex structures within 100 base pairs.
- G4 ligand treatment increased alternative promoter activity, suggesting G4 stabilization modulates promoter usage.

## Abstract

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.