Regulation of transcription patterns, poly(ADP-ribose), and RNA-DNA hybrids by the ATM protein kinase
The ATM protein kinase is a master regulator of the DNA damage response and also an important sensor of oxidative stress in mammals. Loss of ATM or its ability to be activated by reactive oxygen species (ROS) generates high levels of ROS and an excess of single-strand DNA breaks in non-dividing human cells. Here we map locations of poly-ADP-ribose and RNA-DNA hybrid accumulation genome-wide in post-mitotic human neurons with ATM inhibition and find that these locations are coincident with promoter regions, active transcription histone marks, and sequences with high GC content. Antioxidant treatment reverses the accumulation of R-loops in transcribed regions, consistent with the central role of ROS in promoting these lesions. In A-T patient cerebellum tissue, RNAseq analyses show large-scale transcriptional changes that correlate with both expression level and GC content of transcribed genes. Based on these results we postulate that transcription-associated lesions accumulate in ATM-deficient neurons and that the single-strand breaks and PARylation at these sites ultimately generate changes in transcription that compromise cerebellum function and lead to neurodegeneration of this tissue over time in A-T patients. Overall design: chromatin immunoprecipitation (poly-ADP-ribose ChIPseq and R-ChIP), RNAseq