Supercoiling-mediated feedback rapidly couples and tunes transcription

Abstract

Transcription induces a wave of DNA supercoiling, altering the binding affinity of RNA polymerases and reshaping the biochemical landscape of gene regulation. As supercoiling rapidly diffuses, transcription dynamically reshapes the regulation of proximal genes, forming a complex feedback loop. The resulting intergene coupling may provide a mechanism to control transcriptional variance in engineered gene networks and explain the behavior of co-localized native circuits. However, a theoretical framework is needed for integrating both biophysical and biochemical transcriptional regulation to investigate the role of supercoiling-mediated feedback within multi-gene systems. Here, we model transcriptional regulation under the influence of supercoiling-mediated polymerase dynamics, allowing us to identify patterns of expression that result from physical intergene coupling and explore integration of this biophysical model with a set of canonical biochemical gene regulatory systems. We find that gene syntax--the relative ordering and orientation of genes--defines the expression profiles, variance, burst dynamics, and intergene correlation of two-gene systems. By applying our model to both a synthetic toggle switch and the endogenous zebrafish segmentation network, we find that supercoiling can enhance or weaken conventional biochemical regulatory strategies such as mRNA- and protein-mediated feedback loops. Together, our results suggest that supercoiling couples behavior between neighboring genes, representing a novel regulatory mechanism. Integrating biophysical regulation into the analysis and design of gene regulation provides a framework for enhanced understanding of native networks and engineering of synthetic gene circuits.

Emergence of Supercoiling-Mediated Regulatory Networks through the Evolution of Bacterial Chromosome Organization

“…We found that evolved genomes in the model are enriched in divergent pairs of always-active genes, as well as in convergent pairs that act as bistable toggle switches (Gardner et al, 2000; Johnstone and Galloway, 2022); the evolution of such systems substantiates the theoretical predictions made by models that explicitly describe the movement of RNA polymerases during gene transcription, such as Sevier and Hormoz (2021). Then, we showed that the local organization of the genome into convergent or divergent pairs of genes is not sufficient to explain the transcriptional response of individuals to different environments, but that larger subnetworks can be required to selectively inhibit genes in specific environments.…”

“…Moreover, integrating a model of gene regulation by DNA supercoiling into a more comprehensive evolutionary model of the genome that allows for classical gene regulation via transcription factors, such as the model presented in Crombach and Hogeweg (2008), would help shed light on the coevolution between the different modes of gene regulation that are available to bacterial genomes. Finally, from an experimental perspective, a better understanding of the regulatory interactions caused by the transcription-supercoiling coupling could help design more reliable synthetic genetic constructs, as explored in Johnstone and Galloway (2022).…”

“…For evolutionists, it provides a plausible evolutionary rationale for the observed conservation of local gene order between closely related bacteria (Junier and Rivoire, 2016) and along evolutionary histories (Brinza et al, 2013). Finally, for synthetic biologists, it provides a theory to help predict in finer detail the gene transcription levels that can be expected from a given gene syntax (Johnstone and Galloway, 2022), which could help design more robust genetic circuits.…”