Focal ischemia induces genome-wide accumulation of R-loops in the brain

Ischemic stroke induces rapid changes in transcriptional regulatory mechanisms across diverse genomic regions of the brain. These alterations fine-tune gene expression patterns to orchestrate post-stroke pathological responses. Precise control of these processes is critical for limiting brain damage and facilitating long-term neurological recovery. During transcription, RNA can hybridize with the DNA template to form three-stranded RNA:DNA hybrids, termed R-loops. Accumulation of R-loops leads to altered transcriptional fidelity, DNA damage, and genomic instability in several pathological conditions. We currently evaluated the effect of stroke on R-loops in mice subjected to transient focal ischemia. Focal ischemia significantly induced R-loop accumulation and DNA damage in the peri-infarct cortex compared with sham. Immunoprecipitated RNA:DNA hybrids sequencing showed strand and site-specific accumulation of R-loops across the genome, with increased R-loops signal at long-noncoding RNA-associated genomic regions. Gene ontology analysis of genes associated with significantly altered R-loops indicated that they regulate several biological functions, including action potential, axonogenesis, apoptosis, chromatin remodeling, dendrite morphogenesis, and synapse organization, which play a significant role in functional recovery after stroke. Overall, our results indicated a potential role of R-loops in modulating ischemic stroke pathophysiology. Targeting R-loops might be a promising strategy to improve post-stroke recovery.