Promoter G‐quadruplex sequences are targets for base oxidation and strand cleavage during hypoxia‐induced gene transcription

The G‐quadruplex (G4), a non‐B DNA motif that can form in certain G‐rich sequences, is often located near transcription start sites in growth regulatory genes. We previously showed that G4s play a role in regulating hypoxia‐induced transcriptional responses in pulmonary artery endothelial cells. G4s are regarded as stable structures and there is uncertainty regarding the events governing their assembly and disassembly. Because G repeats are uniquely sensitive to oxidative damage, and since G4 sequences have been documented as “hot spots” for genetic mutation and DNA translocation, we hypothesized that G4 sequences could be affected by the base excision pathway of DNA repair (BER). We used a PCR‐based technique to monitor the level of base oxidation near multiple promoter G4 sequences in genes during transcriptional activation or repression by hypoxia. The frequency of base oxidation in promoter G4 sequences was related to the expression state of the genes. Chromatin immunoprecipitation assays showed that BER enzymes were recruited to, and DNA strand breaks transiently formed in G4s during hypoxic exposure. These findings suggest that the oxidant stress in hypoxia causes oxidative base modifications, recruitment of BER enzymes, and transient strand breaks in G4 promoter sequences that may dictate G4 integrity and transcriptional modulation. Supported by NIH and AHA.