Manuscript: Novel environment exposure drives temporally defined and region-specific chromatin accessibility and gene expression changes in the hippocampus

Erin E. Duffy1*, Lisa Traunmüller1*, Hanqing Liu1, Stella Sanalidou1, Elena G. Assad1, Senmiao Sun1,2, Naeem S. Pajarillo1, Nancy Niu1, Eric. C. Griffith1, and Michael E. Greenberg1

Author affiliations
1.	Department of Neurobiology, Harvard Medical School, Boston, MA, USA
2.	Program in Neuroscience, Harvard Medical School, Boston, MA, USA
* both authors contributed equally

Curiosity-driven interactions with novel cues in our environment represent a common behavioral trait across the animal kingdom. Exposure to a novel environment (NE) reshapes the brain by driving structural and functional changes in multiple brain areas, including the hippocampus. This experience-dependent circuit reorganization is thought to be driven in part by changes in gene expression. While NE exposure has been shown to rapidly induce the expression of FOS and other immediate-early gene transcription factors (IEG TFs), the downstream IEG-driven gene effectors that serve to mediate NE-dependent circuit remodeling, as well as the DNA regulatory elements that drive the expression of these effectors, remain largely unclear. We employed a combination of hippocampal single-nuclei multiomics and bulk RNA sequencing from the CA1, CA3, and DG regions to systematically characterize NE-driven gene expression and chromatin accessibility changes downstream of IEG induction over time. We observe strong region-specificity in excitatory neuron late-response gene programs as well as diversity in inhibitory neuron and non-neuronal gene responses. In addition, prolonged exposure to NE caused more robust induction of late-response genes in bulk RNA sequencing, suggesting that sustained environmental stimulation is more effective at triggering long-lasting molecular changes that support memory formation. Notably, chromatin-level analyses revealed thousands of cell type-specific changes in chromatin accessibility in response to NE exposure. Coordinated analysis of both chromatin accessibility and gene expression within individual cells revealed the AP-1 motif as a major predictor of cell-type-specific late-response gene expression. Together, these data provide a rich resource of hippocampal gene expression and chromatin accessibility changes in response to a physiological stimulus, with implications for learning and memory.