G-quadruplex structures affect the immune response to bacterial infection in mouse macrophages.

Macrophages orchestrate immunity via transcriptional reprogramming, largely controlled by the master regulator NF-κB. However, mechanisms of promoter selection remain enigmatic. Here, we reveal that DNA secondary structures called G-quadruplexes (G4s) modulate the macrophage transcriptome during inflammation. By investigating the G4 ligand pyridostatin (PDS) in lipopolysaccharide-stimulated macrophages, we establish that G4 stabilization significantly decreases the inflammatory response without affecting mitochondrial metabolism or pathogen clearance. Instead, NF-κB-dependent transcription of activation markers and proinflammatory cytokines is selectively repressed. Using chromatin accessibility profiling, NF-κB ChIP, and in silico predictions, we demonstrate that G4 stabilization sterically hinders NF-κB promoter occupancy. Furthermore, PDS stabilizes transient, transcription-induced G4s, prematurely shutting down transcription and reverting local chromatin to a dormant state. Thus, G4 formation represents a potential strategy to modulate dysregulated macrophage activation.