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A Genome-Wide Evolutionary Simulation of the Transcription-Supercoiling Coupling

Théotime Grohens 1, 2 Sam Meyer 3, 4 Guillaume Beslon 1, 2 
1 BEAGLE - Artificial Evolution and Computational Biology
LIRIS - Laboratoire d'InfoRmatique en Image et Systèmes d'information, Inria Grenoble - Rhône-Alpes, LBBE - Laboratoire de Biométrie et Biologie Evolutive - UMR 5558
3 CRP - Chromatine et Régulation de la Pathogénie bactérienne
MAP - Microbiologie, adaptation et pathogénie
Abstract : DNA supercoiling (SC), 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 negative SC levels facilitate the opening of the DNA double helix at gene promoters, and increase the associated expression levels. Different levels of SC have been measured in bacteria exposed to different environments, leading to the hypothesis that SC variation can be an environmental response. Moreover, DNA transcription has been shown to generate local variations in the SC level, and therefore to impact the transcription 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 (TSC). We show that, in this model, a simple change in global DNA SC is sufficient to trigger differentiated responses in gene expression levels via the TSC. Then, studying our model in the light of evolution, we demonstrate that this SC-mediated non-linear response to environmental change can serve as the basis for the evolution of specialized phenotypes, through the selection of a specific genomic architecture.
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Submitted on : Tuesday, July 6, 2021 - 2:51:57 PM
Last modification on : Tuesday, October 25, 2022 - 4:24:59 PM


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  • HAL Id : hal-03242696, version 2


Théotime Grohens, Sam Meyer, Guillaume Beslon. A Genome-Wide Evolutionary Simulation of the Transcription-Supercoiling Coupling. ALIFE 2021 - Conference on Artificial Life, Jul 2021, Prague, Czech Republic. ⟨hal-03242696v2⟩



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