Genome-wide Mapping of Endogenous G-quadruplexes Unravels Their Roles in Enhancer Architecture across Human Cell Lines

We found that G4 structures assist to shape the nucleosome positioning and nucleosome depleted regions on enhancers. Moreover, many transcription factor (TF) clusters tend to co-target G4 on enhancers, leading to widespread enhancer transcriptional signals. These TFs further influenced the chromatin interactions between G4 enhancers and their target genes. Additionally, G4 enhancers harbored significantly higher enrichment of expression quantitative trait locus than typical enhancers, suggesting G4 enhancers displayed more enhancer regulatory activity. Overall design: We used BG4 ChIP-seq method to target all endogenous G4 structures in the LnCap cell line and described the relationship between enhancers and G4s.