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Preprint WatchModerateOctober 4th, 2026

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

Lyu, J.; Ahmed, A.; Biswas, I.; Li, S.; Chen, C.

Acute TOP1 depletion increases gene expression noise by reducing both transcriptional burst size and frequency, with negative supercoiling accumulation at transcription start sites increasing RNA polymerase II promoter occupancy and promoter-proximal pausing.

Moderate contradiction

1 prior failure

Two documented clinical failures match this mechanism, or a single Phase 3 failure is on record.

This preprint assigns TOP1 a housekeeping role in sustaining productive transcription, where acute depletion raises expression noise and slows RNA polymerase II elongation across genes generally rather than in tumor cells selectively. Claidex holds one TOP1 failure on file, cbx-12-top1-phlip-exatecan-platinum-resistant-ovarian-phase2-termination, recorded as an efficacy failure. A target whose inhibition degrades transcription broadly offers a narrow therapeutic window that depends on differential dependence rather than differential expression, which is the assumption most TOP1-directed delivery strategies make. The finding does not contradict the Claidex record, and it does supply a mechanistic reason why improving tumor delivery of a TOP1 poison may not widen that window.

Abstract excerpt

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.

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This is an automated contradiction flag, not an editorial judgment on the preprint's quality. Flags identify where the preclinical literature and the clinical failure record diverge.