Topoisomerase-mediated resolution of negative DNA supercoiling sustains human transcription and gene activation

Abstract

Transcription generates DNA supercoiling that can influence gene expression, but how transcription-associated supercoiling shapes RNA polymerase II (RNAPII) dynamics in human cells remain poorly understood. Here, we show that topoisomerase-mediated resolution of negative DNA supercoiling is required for productive transcription. Acute topoisomerase perturbation causes negative supercoiling to accumulate around transcription start sites (TSS), with greater negative supercoiling accumulation associated with stronger transcription reduction. Elevated negative supercoiling behind the elongating RNAPII, but not positive supercoiling ahead, is associated with reduced RNAPII elongation rates. Using NOTE-seq2 to simultaneously profile newly synthesized and total RNA in single cells, we further demonstrate that acute TOP1 depletion increases gene expression noise by reducing both transcriptional burst size and frequency. Mechanistically, negative supercoiling accumulation at TSS increases RNAPII promoter occupancy and promoter-proximal pausing, providing a potential basis for reduced burst size. Micro-C analysis shows that TOP1 depletion largely preserves chromatin compartments and TADs but weakens short-range chromatin loops, including enhancer-promoter interactions, likely contributing to reduced burst frequency. Finally, during T-cell activation, impaired resolution of negative supercoiling compromises rapid gene upregulation and attenuates the transcriptional activation program. Together, these findings establish topoisomerase-mediated resolution of negative DNA supercoiling as a key mechanism linking DNA topological homeostasis to RNAPII dynamics, chromatin looping, and rapid gene activation.