Widespread transmission of DNA supercoiling and selective topoisomerase utilization regulates torsional stress within the neuronal genome [RNA-Seq]

Here we utilized psoralen crosslinking and sequencing (TMP-seq) to assess the distribution of underwound DNA at high resolution in postmitotic neurons. We report that supercoiling propagates widely (> 200 kb) from the sites of active RNAPII and that its distribution is constrained by chromosome compartments and by specific nucleosome configurations, including H3K27me3-rich regions and broad distributions of active promoter-related chromatin marks.

Underwound DNA does not accrue upstream of expressed genes in postmitotic neurons, which could shield them from cumulative torsional stress. Inhibiting either transcription or TOP1 affect underwound DNA levels genome-wide; however, supercoiling at the boundaries of expressed genes is minimally perturbed, indicating that dynamic supercoiling is not locally confined to sites of RNAPII activity at expressed genes. Surprisingly, TOP1 inhibition elevates supercoiling but stimulates nascent transcription at most genes and other sites of transcription, including enhancers, suggesting that torsional stress generally favors transcription, and that topoisomerase activity is not essential for transcription at most genes.