RNA Polymerase-II-generated DNA supercoils destabilize nucleosomes

The twin supercoiled domain model posits that, as RNA Polymerase II (Pol II) transcribes a gene, it generates negative and positive supercoils upstream and downstream respectively, but little is known about the functional consequence in vivo of the resulting torsional strain. Here we provide a method for high resolution mapping of DNA supercoils using next-generation sequencing, and show that the level of supercoiling is correlated with gene expression in Drosophila cells. Inhibition of topoisomerases, enzymes that relieve torsional strain, leads to accumulation of supercoils surrounding gene bodies and of Pol II at the transcription start sites. Topoisomerase I inhibition results in increased nascent RNA transcripts with Topoisomerase II inhibition shows little change in nascent RNA levels. Despite these different effects on transcription, inhibition of either enzyme results in increased nucleosome turnover within gene bodies, suggesting that torsional stress contributes to destabilizing nucleosomes ahead of Pol II. 12 paired-end samples and 8 single-end samples were sequenced and analyzed.