RNAPII and DNA supercoiling regulate cohesin engagement in neurons

Chromatin looping by CTCF and cohesin is thought to be crucial for chromosome organization and gene transcription. Yet the precise relationships between CTCF, cohesin, and transcription in neurons are still poorly understood. To address this issue, we compared the occupancy of CTCF and the cohesin subunits, SMC1 and RAD21, relative to transcriptionally engaged RNAPII and as a function of stimulus-dependent transcription in cultured mouse cortical neurons. We show that CTCF and cohesin are enriched at transcription start sites (TSS) and that their levels increase with the level of transcriptionally engaged RNAPII, suggesting that RNAPII facilitates CTCF and cohesin occupancy. Unexpectedly, while neuronal stimulation caused widespread transcriptional activation, it resulted in the rapid genome-wide loss of SMC1 and RAD21 signals, including at the TSS of genes, loop anchors, and topologically associating domain boundaries. Activity-dependent reductions in cohesin were independent of CTCF but were mimicked by inhibiting either topoisomerase I or topoisomerase IIβ, which resolve torsional stress from DNA supercoiling. We show that neuronal stimulation elevates DNA supercoiling and that increasing torsional stress triggers the dissociation of cohesin from chromatin. Overall, these results suggest that modulation of torsional stress could be a physiologically relevant mechanism of regulating cohesin engagement and chromatin architecture.