Promoter G-quadruplex folding precedes transcription and is controlled by chromatin

Four stranded DNA G-quadruplex (G4) structures are common features of the human genome that are primarily found in active promoters associated with elevated transcription. Here, we explore the relationship between the folding of G4s in promoters, transcription and chromatin state. Transcriptional inhibition by DRB or by triptolide reveals that promoter G4 formation, as assessed G4 ChIP-seq, is not reliant on transcriptional activity. Establishing a link between G4 formation and chromatin accessibility, we demonstrate that chromatin compaction leads to loss of promoter G4s accompanied by a corresponding loss of RNA polymerase II (Pol II). Furthermore, pre-treatment of cells with a G4-stabilising ligand can mitigate Pol II loss at promoters induced by chromatin compaction. Overall, our findings show that G4 formation is fostered in accessible chromatin and does not require active transcription. Furthermore, our findings suggest that G4s have a role to recruit Pol II to promote transcription. K562 cells profiling by G4-ChIP-seq upon DRB, TPL; K562 cells profiling by G4-ChIP-seq, Pol2-ChIP-seq and Atac-seq upon pyPDS, Hypoxia, Hypoxia plus pyPDS or DMSO, Normoxia plus pyPDS or DMSO. U2OS cells profiling by G4-ChIP-seq in Hypoxia and Normoxia in triplicates.