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

Abstract

The interaction of mammals with a novel environment (NE) results in structural and functional changes in multiple brain areas, including the hippocampus. This experience-dependent circuit reorganization is driven in part by changes in gene expression however, the dynamic sensory experience-driven chromatin states and the diverse cell type specific gene expression programs that are regulated by novel experiences are not well described. We employed single- nucleus multiomics (snRNA- and ATAC-seq) and bulk RNA-seq of the hippocampal DG, CA3, and CA1 regions to characterize the temporal evolution of cell-type-specific chromatin accessibility and gene expression changes that occur in 14 different cell types of the hippocampus upon exposure of mice to a novel environment. We observe strong hippocampal regional specificity in excitatory neuron chromatin accessibility and gene expression as well as great diversity in the inhibitory neuron and non-neuronal transcriptional responses. The novel environment-regulated genes in each cell type were enriched for genes that encode secreted factors, and cell-type-specific expression of their cognate receptors identified promising candidates for the modulation of learning and memory processes. Our characterization of the effect of novel experience on chromatin revealed thousands of cell-type-specific changes in chromatin accessibility. Coordinated analysis of chromatin accessibility and gene expression changes within individual cell types identified Fos/AP-1 as a key driver of novel experience-induced changes in chromatin accessibility and cell-type-specific gene expression. Together, these data provide a rich resource of hippocampal chromatin accessibility and gene expression profiles across diverse cell types in response to novel experience, a physiological stimulus that affects learning and memory.