How transient activation of mature neuronal circuits leads to changes in gene expression and properties in neurons over the short- and long- term is a fundamental question in neurobiology and has significant implications for understanding neuronal plasticity, learning and mem-

VOLUME 20 | NUMBER 3 | MARCH 2017 nature neurOSCIenCe How transient activation of mature neuronal circuits leads to changes in gene expression and properties in neurons over the shortand longterm is a fundamental question in neurobiology and has significant implications for understanding neuronal plasticity, learning and memory, and brain disorders1. Epigenetic mechanisms play a crucial role in regulating neuronal gene expression, and neuronal activity is known to alter epigenetic landmarks, such as DNA methylation and histone modifications2–11. These epigenetic changes not only regulate which genes become activated or suppressed but also modify the dynamics of gene expression12. Regulation of chromatin opening is an important regulatory mechanism for the precise control of gene expression patterns. Global changes in chromatin accessibility occur during cell differentiation when cells with the same genome establish their identities through distinct gene expression patterns. Previous genome-wide studies of different tissues and cell types, including those in the nervous system, have revealed tissueand cell-type-specific landscapes of chromatin accessibility13–16. Whether large-scale changes in chromatin accessibility occur after cell differentiation and maturation in vivo is unclear. Specifically, in the nervous system, whether and to what extent neuronal activity may reshape the accessible chromatin landscape in neurons and induce transient and sustained biological outcomes are largely unknown. Here we examined the impact of acute neuronal activation on chromatin accessibility and gene expression in dentate granule neurons over time in the adult mouse brain in vivo. RESULTS Widespread chromatin accessibility changes induced by neuronal activation To investigate whether neuronal activation induces changes in chromatin accessibility, we employed an assay for transposase-accessible chromatin using sequencing (ATAC-seq) for sensitive and quantitative measurement of chromatin accessibility across the gemome17 (Online Methods). We performed ATAC-seq of biological replicates (n = 3 or 4 for each condition) of microdissected dentate gyri before (E0 thereafter) and 1 h (E1 thereafter) after synchronous neuronal activation via electroconvulsive stimulation18–20, a procedure currently used to treat patients with drug-resistant depression21. Our previous studies have shown that this in vivo preparation is highly enriched for dentate granule neurons (over 90%) and such treatment switches most neurons from an inactive state that reflects the presumed sparse coding in the dentate gyrus22 to an active state18–20. We identified 89,946 and 114,959 open chromatin regions at E0 and E1, respectively (P < 1 × 10−5; Supplementary Table 1). We compared our data set to previously published chromatin-accessibility profiles of different tissues and cell types (Supplementary Table 2). The signature of open chromatin regions at the basal state (E0) is closer to those of different neuronal subtypes than to those of astrocytes or other non-neural tissues (Supplementary Fig. 1). We identified 16,882 open chromatin regions that occurred in dentate gyrus neurons but not in other cell types or tissues examined (Supplementary Table 3). Consistent with previous findings13,23,24, open chromatin sites exhibited a broad