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 dynamically and independently of transcription factor binding, particularly in the context of chromosomal topological domains and the activity of topoisomerases in bacteria. In this work, we develop numerical simulations of SC-coupled transcription of a single gene within a topological domain, based on a model incorporating stochastic transcription and activities of topoisomerase I and gyrase. We explore the effect of several parameters not systematically assessed in previous works (role of topoisomerase activities, topological domain size, gene expression strength) and compare the simulation results to a diverse set of experimental observations ranging from in vitro transcription assays to transcriptomics datasets from various species. This model recapitulates the non-monotonic dependence of transcription in vitro with the superhelical density of the plasmid template. Simulations of in vivo transcription in a closed domain exhibit a qualitatively different role for the two topoisomerases, as well as qualitatively different regulatory behaviors depending on the promoter strength. Specifically, topoisomerase I is required for strongly expressed genes that may be hindered by stalled RNA Polymerase, whereas gyrase activity favors the expression of all genes by enhancing transcription initiation and modulating the burstiness of transcription. The simulations exhibit a new mechanism for transcription bursting mediated by negative SC accumulating at the promoter region and modulating the initiation rate, resulting in levels of burstiness compatible with values reported in cells. Finally, we analyze several transcriptomics datasets from a range of evolutionarily distant species and show that topoisomerase inhibition is systematically associated with the repression of highly expressed genes. Simulations show this behavior to occur within a limited parameter range and thus indicate a biologically relevant regime for the simulations. Overall, this work provides a more quantitative description of how SC contributes to differential gene regulation and transcriptional bursting in bacteria.

DNA supercoiling-the level of twisting and writhing of the DNA molecule around itself-plays an important role in the regulation of gene expression in bacteria by modulating promoter activity. The level of DNA supercoiling is a dynamic property of the chromosome which varies both at local and global scales, in response to both external factors such as environmental perturbations and internal factors including gene transcription. As such, local variations in supercoiling could in theory couple the expression levels of neighboring genes by creating feedback loops at the transcriptional level. However, the impact of such supercoiling-mediated interactions on the regulation of gene expression still remains uncertain. In this work, we study how this coupling between transcription and supercoiling could shape genome organization and help regulate gene transcription. We present a model of genome evolution in which individuals whose gene transcription rates are coupled to local supercoiling must adapt to two environments that induce different global supercoiling levels. In this model, we observe the evolution of whole-genome regulatory networks that provide control over gene expression by leveraging the transcription-supercoiling coupling, and show that the structure of these networks is underpinned by the organization of genes along the chromosome at several scales. Local variations in DNA supercoiling could therefore help jointly shape both gene regulation and genome organization during evolution.

DNA supercoiling, the level of under- or overwinding of the DNA polymer around itself, is widely recognized as an ancestral regulation mechanism of gene expression in bacteria. Higher levels of negative supercoiling facilitate the opening of the DNA double helix at gene promoters and thereby increase gene transcription rates. Different levels of supercoiling have been measured in bacteria exposed to different environments, leading to the hypothesis that variations in supercoiling could be a response to changes in the environment. Moreover, DNA transcription has been shown to generate local variations in the supercoiling level and, therefore, to impact the transcription rate of neighboring genes. In this work, we study the coupled dynamics of DNA supercoiling and transcription at the genome scale. We implement a genome-wide model of gene expression based on the transcription-supercoiling coupling. We show that, in this model, a simple change in global DNA supercoiling is sufficient to trigger differentiated responses in gene expression levels via the transcription-supercoiling coupling. Then, studying our model in the light of evolution, we demonstrate that this non-linear response to different environments, mediated by the transcription-supercoiling coupling, can serve as the basis for the evolution of specialized phenotypes.

SUMMARY: Transcription and DNA supercoiling are involved in a complex, dynamical and non-linear coupling that results from the basal interaction between DNA and RNA polymerase. We present the first software to simulate this coupling, applicable to a wide range of bacterial organisms. TwisTranscripT allows quantifying its contribution in global transcriptional regulation, and provides a mechanistic basis for the widely observed, evolutionarily conserved and currently unexplained co-regulation of adjacent operons that might play an important role in genome evolution. AVAILABILITY AND IMPLEMENTATION: TwisTranscripT is freely available at https://github.com/sammeyer2017/TwisTranscripT. It is implemented in Python3 and supported on MacOS X, Linux and Windows.

Motivation: Many DNA-binding proteins recognize their target sequences indirectly, by sensing DNA's response to mechanical distortion. ThreaDNA estimates this response based on high-resolution structures of the protein-DNA complex of interest. Implementing an efficient nanoscale modeling of DNA deformations involving essentially no adjustable parameters, it returns the profile of deformation energy along whole genomes, at base-pair resolution, within minutes on usual laptop/desktop computers. Our predictions can also be easily combined with estimations of direct selectivity through a generalized form of position-weight-matrices. The formalism of ThreaDNA is accessible to a wide audience. Results: We demonstrate the importance of indirect readout for the nucleosome as well as the bacterial regulators Fis and CRP. Combined with the direct contribution provided by usual sequence motifs, it significantly improves the prediction of sequence selectivity, and allows quantifying the two distinct physical mechanisms underlying it. Availability and implementation: Python software available at bioinfo.insa-lyon.fr, natively executable on Linux/MacOS systems with a user-friendly graphical interface. Galaxy webserver version available. Contact: [email protected]. Supplementary information: Supplementary data are available at Bioinformatics online.

DNA torsional stress is generated by virtually all biomolecular processes involving the double helix, in particular transcription where a significant level of stress propagates over several kilobases. If another promoter is located in this range, this stress may strongly modify its opening properties, and hence facilitate or hinder its transcription. This mechanism implies that transcribed genes distant of a few kilobases are not independent, but coupled by torsional stress, an effect for which we propose the first quantitative and systematic model. In contrast to previously proposed mechanisms of transcriptional interference, the suggested coupling is not mediated by the transcription machineries, but results from the universal mechanical features of the double-helix. The model shows that the effect likely affects prokaryotes as well as eukaryotes, but with different consequences owing to their different basal levels of torsion. It also depends crucially on the relative orientation of the genes, enhancing the expression of eukaryotic divergent pairs while reducing that of prokaryotic convergent ones. To test the in vivo influence of the torsional coupling, we analyze the expression of isolated gene pairs in the Drosophila melanogaster genome. Their orientation and distance dependence is fully consistent with the model, suggesting that torsional gene coupling may constitute a widespread mechanism of (co)regulation in eukaryotes.