Neuronal activity-driven 3D chromatin dynamics in cortical pyramidal neurons depend on SATB2

Neuronal activity induces widespread changes in chromatin organization, yet the mechanisms of activity-dependent 3D genome remodelling remain incompletely understood. Here, we identify SATB2 as a key regulator of activity-dependent 3D chromatin dynamics in cortical pyramidal neurons. Using primary cultures from floxed and Satb2 conditional knockout mice, we combined Hi-C and chromatin accessibility mapping to capture rapid 3D epigenome reorganization following neuronal stimulation. Within 1 h of activation, floxed neurons exhibited enhanced chromatin interactions, increased chromatin accessibility, and the emergence of a novel activity-dependent (AD) compartment enriched for SATB2 binding sites. The AD compartment harbours metabolic and housekeeping genes that undergo transient repression upon neuronal activation, thereby prioritizing translation of long synaptic transcripts. Loss of SATB2 disrupted these activity-induced changes, including chromatin accessibility, long-range interactions, and AD compartment formation, resulting in attenuated induction and repression of key activity-regulated genes. These findings establish SATB2 as a central organizer of activity-dependent chromatin architecture dynamics, required for coordinated activation and repression of activity-regulated genes in cortical pyramidal neurons.