Extended supplementary data for manuscript: A single dose of cocaine rewires the 3D genome structure of midbrain dopamine neurons

Midbrain dopamine neurons (DNs) respond to a first exposure to addictive drugs and play key roles in chronic drug usage. As the synaptic and transcriptional changes that accompany an acute cocaine exposure are mostly resolved within hours and up to a few days, the long-term molecular changes that encode the cellular memory of the exposure within DNs remains unknown. To investigate whether a single cocaine exposure induces long-term changes in 3D genome structure of DNs, we applied Genome Architecture Mapping and single nucleus transcriptomic analyses in mouse midbrain. We found extensive rewiring of 3D genome architecture at 24h past exposure which lasts or worsens by 14 days, outlasting transcriptional responses. The cocaine-induced chromatin rewiring occurs at all genomic scales and affects genes with major roles in cocaine-induced synaptic changes. Cocaine exposure triggers extensive changes in chromatin condensation in post-synaptic and post-transcriptional regulatory genes, for example the unfolding of Rbfox1 which becomes most prominent 14 days post exposure. Finally, structurally remodeled genes are most expressed in a DN sub-type with low expression of the dopamine auto-receptor Drd2, a key feature of highly cocaine-sensitive cells. These results reveal an important role for long-lasting 3D genome remodelling in the cellular memory of a single cocaine exposure, providing new hypotheses for understanding the inception of drug addiction and 3D genome plasticity.