Ana Pombo

Midbrain dopamine neurons (DNs) are the first responders to the acute exposure of cocaine and are central to the development of drug addiction. Following a single cocaine injection, DNs undergo synaptic and transcriptional changes that are resolved within days but preserve a long-term cellular memory of the exposure by a mechanism that remains unknown. To investigate whether persistent alterations in 3D genome organization are involved in the cellular memory of an acute drug exposure, we applied Genome Architecture Mapping (GAM), single nucleus transcriptomics (snRNA-seq) and chromatin accessibility mapping (snATAC-seq) in the mouse midbrain 24 hours or 14 days after a single injection of cocaine or saline control. We found that DNs retain extensive chromatin reorganization 14 days after a single exposure across multiple genomic scales, including topologically associating domains (TADs), chromatin condensation and looping interactions, which affect genes previously associated with chronic cocaine addiction, synaptic plasticity and metabolic adaptation.To assess whether altered 3D genome structure 14 days post exposure has consequences for the transcriptional responses to cocaine, we re-exposed animals to a second injection of cocaine after 14 days of abstinence. Transcriptional responses were more extensive and often did not match the direction or intensity of changes seen upon the first exposure. Importantly, transcriptional responses following re-injection occurred predominantly at genes with reorganized chromatin architecture. Together, these findings identify 3D genome remodelling as a key mechanism underlying cellular memory of cocaine exposure, providing new insight into the earliest molecular events in addiction and the plasticity of the genome.

Max Delbrück Center for Molecular Medicine, Berlin Institute for Medical Systems Biology, Epigenetic Regulation and Chromatin Architecture Group, Berlin, Germany.

Department of Biology and Department of Molecular Biology and Genetics, Johns Hopkins University, Baltimore, MD, USA.