[SMaLS] Transcription Creates Transient Boundaries that Confine Supercoiling and Coordinate Gene Expression

Speaker: Lili Yang (Postdoc, Yeung group, UCSB)
Title: Transcription Creates Transient Boundaries that Confine Supercoiling and Coordinate Gene Expression
Abstract: DNA supercoiling is generated by torsional stress created during transcription and DNA replication and, in turn, modulates gene expression. However, despite its pervasive involvement, understanding the dynamics of transcription-induced supercoiling remains a major challenge. This difficulty arises in part because supercoiling has traditionally been treated, in theory, as a globally distributed physical property.
Here, we find that transcription-induced supercoiling is intrinsically localized by using a single-molecule imaging platform that enables direct visualization of transcription on individual, topologically unconstrained DNA molecules. RNA polymerase (RNAP) activity alone is sufficient to generate and dynamically confine supercoiling without fixed topological constraints or externally applied torsional stress. This localization emerges from the collective action of multiple simultaneously transcribing RNAPs, which act as transient topological barriers and define dynamic supercoiling domains. In contrast, single-gene transcription fails to produce stable supercoiling, highlighting the essential role of multi-gene transcription activity.
Importantly, we further observe that transcription-induced supercoiling has direct and spatially restricted effects on gene expression. Activation of transcription leads to coordinated upregulation of clusters of neighboring genes that are spatially co-localized, indicating that supercoiling is generated and acts within confined regions. These results demonstrate that the influence of transcription-generated supercoiling spreads over limited genomic distances, providing a physical mechanism for localized gene co-regulation.
Together, our findings establish a new framework in which DNA supercoiling is not a globally diffusive property, but a dynamically generated and spatially confined structure defined by transient, RNAP-mediated boundaries. This perspective reconciles the physical behavior of DNA with the spatial precision of gene regulation and provides a mechanistic basis for local coordination of gene expression.