Goldberg, B. I. | bioRxiv Science

bioRxiv2025

Chromosomal Topological Domain Formation Modulates Transcription and the Coupling of Neighboring Genes in Escherichia coli

Chromosomal topology and transcription are tightly coupled, yet the quantitative impact of topological constraints on transcription, supercoiling, and the potential coupling between neighboring genes in vivo remains unclear. In this work, we constructed synthetic chromosomal domains in Escherichia coli that contained two genes inside a topology-controllable domain and a third gene outside. Using three-color single-molecule fluorescence in situ hybridization (smFISH), we measured transcription output from the three genes in individual cells under conditions in which gene orientation, domain formation state, and global chromosomal supercoiling density were varied. We found that topological domain formation repressed transcription, diminished gene orientation-dependent differences in transcription, and modulated the supercoiling sensitivity of genes located both within and near the domain. Relaxing global negative supercoiling through gyrase inhibition broadly repressed transcription; increasing global negative supercoiling level through topoisomerase I inhibition repressed highly expressed genes, while activating lowly expressed ones. Besides single-gene effects, we also observed an intrinsic coupling between neighboring genes with a non-monotonic dependence on the underlying supercoiling state, which shifted with domain topology and gene syntax. Our results establish chromosome topology as a major regulator of both transcription levels and the coupling between adjacent genes.

biophysics↗

bioRxiv2025

Differential effect of supercoiling on bacterial transcription in topological domains

DNA supercoiling (SC), the over- and under-winding of DNA, is generated by transcription as described in the twin-domain model. Conversely, SC also impacts transcription through torsional stress. SC therefore regulates transcription independent of transcription factor binding, the classic protein-based transcription regulatory mechanism, particularly in the context of chromosomal topological domains and the actions of topoisomerases. SC-coupled transcription has inspired several computational models, but a systematic and quantitative assessment of the parameters controlling this complex interplay is missing. There is also a lack of comparison to various experimental results regarding the effects of topological variables such as topoisomerase binding rates and domain size on transcription strength and noise. In this work we developed a quantitative model to describe SC-coupled transcription. We analyzed the effects of topoisomerase activities on the transcription of a single isolated gene with varying promoter strengths and in a topological domain of varying sizes. These simulations revealed qualitatively different roles of the two topoisomerases. Topoisomerase I is specifically required for strongly expressed genes that may be hindered by stalled RNAP, whereas gyrase activity favors the expression of all genes by enhancing transcription initiation and modulating the burstiness of transcription. A new analysis of transcriptomics data in several bacterial species showed that these simulations replicate a global relationship between promoters strength and response to variations in topoisomerase activities. Our work demonstrates how SC contributes to differential gene regulation and transcriptional bursting in mechanistic details and unites computational and experimental work. Author SummaryWe are interested in understanding how bacteria regulate the expression of their genes. One mechanism by which bacteria can do so is through the over- and under-winding of their DNA, termed DNA supercoiling. Because bacteria can use enzymes called topoisomerases to regulate the supercoiling level of their DNA, these enzymes can serve as gene regulators. It is difficult, however, to understand how topoisomerases act as gene regulators through experiments alone. Currently, there is no method of measuring the supercoiling level along a stretch of DNA over an extended period of time in living cells. We therefore developed a computational model of gene transcription coupled to supercoiling dynamics. Unlike some previously existing models, we consider continuous response curves of topoisomerases activities in response to the local supercoiling level and the ability of gyrase to perform several catalytic cycles per binding event. We also perform extensive comparisons between our model and existing gene expression and transcriptomics data, which is essential to ensuring the biological relevance of computational modeling efforts. We replicate and provide detailed explanations for several experimental observations, including the connection between supercoiling and transcriptional bursts and the selective gene expression modulation by topoisomerase inhibition that is based on the promoter strength.

biophysics↗