Genome‐wide detection of oxidized base products in guanine quadruplex (G4) sequences by ChIP‐Seq analysis in hypoxic cells (887.1)

Reactive oxygen species (ROS) generated in hypoxic signaling cause a nuclear oxidant stress accompanied by oxidative DNA modifications. Detailed studies on a few genes show that these modifications are prominent in hypoxic responsive promoters (Al‐Mehdi et al, 2012) and G4 sequences in growth regulatory genes (Clark et al., 2012). The G4 damage in hypoxia was interesting because it did not relate to the transcriptional state of the gene, was often localized close to transcription start sites, and because mutations in G4 sequences have been linked to genomic instability and carcinogenesis. To gain more insight into the impact of hypoxia‐generated ROS on genomic integrity, we used ChIP‐Seq analysis to determine if G4 sequences immunoprecipitated by an antibody to the base damage product 8‐oxoguanine were enriched on a genome‐wide scale in pulmonary artery endothelial cells cultured in hypoxia for 3h. We found two notable differences between normoxic and hypoxic cells. First, DNA contigs from hypoxic cells were ≍1/3 the size of those from normoxic cells. Second, the number of 8‐oxoG harboring G4 sequences was enriched by ≍30 fold in hypoxia compared to normoxia. These findings suggest that ROS generated during hypoxic signaling cause widespread base damage in G4 sequences and thereby point to new mechanisms of disease‐causing mutations in this enigmatic gene regulatory region. Grant Funding Source : Supported by the NIH R01HL58234