Direct effects on gene transcription revealed by global and CRISPR-targeted oxidative DNA damage

Oxidative stress induces rapid expression changes of specific genes. However, whether these changes are due to direct and local DNA oxidation and whether they depend on the repair machinery is still debated. Here, we show by total RNA-Seq that upon oxidative stress, many genes are either rapidly repressed or activated. The early transcriptional response also includes the activation of many read-through RNAs. Importantly, degradation of the endogenous OGG1 DNA glycosylase showed that the early repression of these genes partially depends on OGG1, therefore demonstrating that these genome expression changes are due to the processing of oxidized DNA. We further demonstrate by ChIPseq against total or S5-phosphorylated RNA polymerase II that transcriptional regulation by oxidative stress involves changes in the recruitment of RNA polymerase II to transcription start sites. Finally, through the use of a chemoptogenetic system allowing the targeting of ROS to chosen genomic loci, we were able to reproduce repression of some genes through the local induction of oxidative DNA damage at their promoters, demonstrating that local DNA oxidation directly affects transcription of genes. Altogether, our results show that local oxidative DNA damage leads to alterations in the activity of specific promoters by a mechanism dependent on repair processes.