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Assessing in vivo the impact of gene context on transcription through DNA supercoiling

Gene context can have significant impact on gene expression but is currently not integrated in quantitative models of gene regulation despite known biophysical principles and quantitative in vitro measurements. Conceptually, the simplest gene context consists of a single gene framed by two topologic...

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Autores principales: Boulas, Ihab, Bruno, Lisa, Rimsky, Sylvie, Espeli, Olivier, Junier, Ivan, Rivoire, Olivier
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10570042/
https://www.ncbi.nlm.nih.gov/pubmed/37667073
http://dx.doi.org/10.1093/nar/gkad688
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author Boulas, Ihab
Bruno, Lisa
Rimsky, Sylvie
Espeli, Olivier
Junier, Ivan
Rivoire, Olivier
author_facet Boulas, Ihab
Bruno, Lisa
Rimsky, Sylvie
Espeli, Olivier
Junier, Ivan
Rivoire, Olivier
author_sort Boulas, Ihab
collection PubMed
description Gene context can have significant impact on gene expression but is currently not integrated in quantitative models of gene regulation despite known biophysical principles and quantitative in vitro measurements. Conceptually, the simplest gene context consists of a single gene framed by two topological barriers, known as the twin transcriptional-loop model, which illustrates the interplay between transcription and DNA supercoiling. In vivo, DNA supercoiling is additionally modulated by topoisomerases, whose modus operandi remains to be quantified. Here, we bridge the gap between theory and in vivo properties by realizing in Escherichia coli the twin transcriptional-loop model and by measuring how gene expression varies with promoters and distances to the topological barriers. We find that gene expression depends on the distance to the upstream barrier but not to the downstream barrier, with a promoter-dependent intensity. We rationalize these findings with a first-principle biophysical model of DNA transcription. Our results are explained if TopoI and gyrase both act specifically, respectively upstream and downstream of the gene, with antagonistic effects of TopoI, which can repress initiation while facilitating elongation. Altogether, our work sets the foundations for a systematic and quantitative description of the impact of gene context on gene regulation.
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spelling pubmed-105700422023-10-14 Assessing in vivo the impact of gene context on transcription through DNA supercoiling Boulas, Ihab Bruno, Lisa Rimsky, Sylvie Espeli, Olivier Junier, Ivan Rivoire, Olivier Nucleic Acids Res NAR Breakthrough Article Gene context can have significant impact on gene expression but is currently not integrated in quantitative models of gene regulation despite known biophysical principles and quantitative in vitro measurements. Conceptually, the simplest gene context consists of a single gene framed by two topological barriers, known as the twin transcriptional-loop model, which illustrates the interplay between transcription and DNA supercoiling. In vivo, DNA supercoiling is additionally modulated by topoisomerases, whose modus operandi remains to be quantified. Here, we bridge the gap between theory and in vivo properties by realizing in Escherichia coli the twin transcriptional-loop model and by measuring how gene expression varies with promoters and distances to the topological barriers. We find that gene expression depends on the distance to the upstream barrier but not to the downstream barrier, with a promoter-dependent intensity. We rationalize these findings with a first-principle biophysical model of DNA transcription. Our results are explained if TopoI and gyrase both act specifically, respectively upstream and downstream of the gene, with antagonistic effects of TopoI, which can repress initiation while facilitating elongation. Altogether, our work sets the foundations for a systematic and quantitative description of the impact of gene context on gene regulation. Oxford University Press 2023-09-05 /pmc/articles/PMC10570042/ /pubmed/37667073 http://dx.doi.org/10.1093/nar/gkad688 Text en © The Author(s) 2023. Published by Oxford University Press on behalf of Nucleic Acids Research. https://creativecommons.org/licenses/by-nc/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial License (https://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
spellingShingle NAR Breakthrough Article
Boulas, Ihab
Bruno, Lisa
Rimsky, Sylvie
Espeli, Olivier
Junier, Ivan
Rivoire, Olivier
Assessing in vivo the impact of gene context on transcription through DNA supercoiling
title Assessing in vivo the impact of gene context on transcription through DNA supercoiling
title_full Assessing in vivo the impact of gene context on transcription through DNA supercoiling
title_fullStr Assessing in vivo the impact of gene context on transcription through DNA supercoiling
title_full_unstemmed Assessing in vivo the impact of gene context on transcription through DNA supercoiling
title_short Assessing in vivo the impact of gene context on transcription through DNA supercoiling
title_sort assessing in vivo the impact of gene context on transcription through dna supercoiling
topic NAR Breakthrough Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10570042/
https://www.ncbi.nlm.nih.gov/pubmed/37667073
http://dx.doi.org/10.1093/nar/gkad688
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