Profiling cell-type-specific transcriptional changes and DNA break sites in response to contextual fear learning

Neuronal activity generates DNA double-strand breaks (DSBs) in vitro and in vivo, and these breaks facilitate the rapid transcriptional induction of immediate early genes (IEGs). Yet the locations of these DSBs in vivo and their relation to brain function remains unclear. Here, following contextual fear conditioning in mice, we profiled the locations of DSBs genome-wide along with transcriptomic changes in neurons and glia in two brain regions. Interestingly, while DSB-susceptible genes induced by fear learning in neurons are predominately involved in synaptic processes, we also observe increased DNA breaks at genes upregulated in glia. Both activity-regulated and proteostasis-related transcription factors appear to govern these gene expression changes across cell types. Finally, we find that glia but not neurons have a robust transcriptional response to glucocorticoids, and these are sites of DSBs. Overall, our data show that fear learning rapidly induces transcriptional changes at genes important for brain function, including stress-responsive genes in glia, and this correlates with hotspots of DSBs. gH2AX foci and total RNA profiling in neurons and glia of the hippocampus and medial prefrontal cortex