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References from Emergence of supercoiling-mediated regulatory networks through the evolution of bacterial chromosome organization. Local targets link to admitted publications; unresolved targets remain external evidence.
DNA supercoiling - a global transcriptional regulator for enterobacterial growth?
10.1038/nrmicro1088 · 2005 · External reference
Estimation of the effect of coumermycin A1 on Salmonella typhimurium promoters by using random operon fusions
10.1128/jb.169.10.4431-4435.1987 · 1987 · External reference
Genomic transcriptional response to loss of chromosomal supercoiling in Escherichia coli
10.1186/gb-2004-5-11-r87 · 2004 · External reference
DNA supercoiling is a fundamental regulatory principle in the control of bacterial gene expression
10.1007/s12551-016-0205-y · 2016 · External reference
DNA topoisomerases: structure, function, and mechanism
10.1146/annurev.biochem.70.1.369 · 2001 · External reference
Bacterial DNA supercoiling and [ATP]/[ADP] ratio: changes associated with salt shock
10.1128/jb.173.12.3914-3917.1991 · 1991 · External reference
DNA topology and adaptation of Salmonella typhimurium to an intracellular environment
10.1098/rstb.2000.0598 · 2000 · External reference
Role of the LysR-type transcriptional regulator PecT and DNA supercoiling in the thermoregulation of pel genes, the major virulence factors in Dickeya dadantii
10.1111/1462-2920.12198 · 2014 · External reference
10.1016/j.csbj.2019.07.013 · 2019 · Admitted local publication
Supercoiling of the DNA template during transcription
10.1073/pnas.84.20.7024 · 1987 · External reference
High-resolution, genome-wide mapping of positive supercoiling in chromosomes
2021 · External reference
Interaction between transcribing RNA polymerase and topoisomerase I prevents R-loop formation in E. coli
10.1038/s41467-022-32106-5 · 2022 · External reference
Psoralen mapping reveals a bacterial genome supercoiling landscape dominated by transcription
10.1093/nar/gkac244 · 2022 · External reference
Topological domain structure of the Escherichia coli chromosome
10.1101/gad.1207504 · 2004 · External reference
Transcription-induced barriers to supercoil diffusion in the Salmonella typhimurium chromosome
10.1073/pnas.0307550101 · 2004 · External reference
DNA supercoiling in bacteria: state of play and challenges from a viewpoint of physics based modeling
10.3389/fmicb.2023.1192831 · 2023 · External reference
Bacterial genome architecture shapes global transcriptional regulation by DNA supercoiling
10.1093/nar/gkz300 · 2019 · External reference
Clinically relevant mutant DNA gyrase alters supercoiling, changes the transcriptome, and confers multidrug resistance
10.1128/mbio.00273-13 · 2013 · External reference
The genome of Streptococcus pneumoniae is organized in topology-reacting gene clusters
10.1093/nar/gkq106 · 2010 · External reference
What is a supercoiling-sensitive gene? Insights from topoisomerase I inhibition in the Gram-negative bacterium Dickeya dadantii
10.1093/nar/gkac679 · 2022 · External reference
Genomic analysis of the regulatory elements and links with intrinsic DNA structural properties in the shrunken genome of Buchnera
10.1186/1471-2164-14-73 · 2013 · External reference
Determination of the gene regulatory network of a genome-reduced bacterium highlights alternative regulation independent of transcription factors
2019 · External reference
Long-term experimental evolution in Escherichia Coli. I. Adaptation and divergence during 2,000 generations
10.1086/285289 · 1991 · External reference
Revisiting the design of the long-term evolution experiment with Escherichia coli
10.1007/s00239-023-10095-3 · 2023 · External reference
Long-term experimental evolution in Escherichia coli. XII. DNA topology as a key target of selection
10.1534/genetics.104.035717 · 2005 · External reference
Parallel genetic and phenotypic evolution of DNA superhelicity in experimental populations of Escherichia coli
10.1093/molbev/msq099 · 2010 · External reference
DNA supercoiling and prokaryotic transcription
10.1016/0092-8674(89)90574-6 · 1989 · External reference
DNA supercoiling and transcription: topological coupling of promoters
10.1017/s0033583500005825 · 1996 · External reference
Torsion-mediated interaction between adjacent genes
10.1371/journal.pcbi.1003785 · 2014 · External reference
Thermoregulation of virB transcription in Shigella flexneri by sensing of changes in local DNA superhelicity
10.1128/jb.177.4.1094-1097.1995 · 1995 · External reference
Activation and silencing of leu-500 promoter by transcription-induced DNA supercoiling in the Salmonella chromosome
10.1046/j.1365-2958.2000.02015.x · 2000 · External reference
Transcriptional coupling between the divergent promoters of a prototypic LysR-type regulatory system, the ilvYC operon of Escherichia coli
10.1073/pnas.96.25.14294 · 1999 · External reference
Long-distance cooperative and antagonistic RNA polymerase dynamics via DNA supercoiling
2019 · External reference
Biophysical constraints arising from compositional context in synthetic gene networks
2017 · External reference
Towards a better control of engineered circuit transcription in bacterial genomes
10.3390/applmicrobiol5010017 · 2025 · External reference
The complete genome sequence of Escherichia coli K-12
10.1126/science.277.5331.1453 · 1997 · External reference
Transcription-coupled DNA supercoiling dictates the chromosomal arrangement of bacterial genes
10.1093/nar/gkw007 · 2016 · External reference
Impact of Salmonella genome rearrangement on gene expression
10.1002/evl3.305 · 2022 · External reference
Genome structural variation in Escherichia coli O157:H7
2021 · External reference
Conserved units of co-expression in bacterial genomes: an evolutionary insight into transcriptional regulation
10.1371/journal.pone.0155740 · 2016 · External reference
A spatially resolved stochastic model reveals the role of supercoiling in transcription regulation
10.1371/journal.pcbi.1009788 · 2022 · External reference
Collective polymerase dynamics emerge from DNA supercoiling during transcription
10.1016/j.bpj.2022.09.026 · 2022 · External reference
Supercoiling-mediated feedback rapidly couples and tunes transcription
10.1016/j.celrep.2022.111492 · 2022 · External reference
Assessing in vivo the impact of gene context on transcription through DNA supercoiling
10.1093/nar/gkad688 · 2023 · External reference
Construction of a genetic toggle switch in Escherichia coli
10.1038/35002131 · 2000 · External reference
Role of the discriminator sequence in the supercoiling sensitivity of bacterial promoters
10.1128/msystems.00978-21 · 2021 · External reference
Modulation of transcription by DNA supercoiling: a deletion analysis of the Escherichia coli gyrA and gyrB promoters
10.1073/pnas.84.12.4185 · 1987 · External reference
Quantitative contribution of the spacer length in the supercoiling-sensitivity of bacterial promoters
10.1093/nar/gkac579 · 2022 · External reference
Local genetic context shapes the function of a gene regulatory network
10.7554/elife.65993 · 2021 · External reference
Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection
10.1038/msb4100050 · 2006 · External reference
Evolution of evolvability in gene regulatory networks
10.1371/journal.pcbi.1000112 · 2008 · External reference
Stochastic model of supercoiling-dependent transcription
10.1103/physrevlett.117.018101 · 2016 · External reference
DNA supercoiling and transcription in bacteria: a two-way street
10.1186/s12860-019-0211-6 · 2019 · External reference
The transcriptome of streptococcus pneumoniae induced by local and global changes in supercoiling
10.3389/fmicb.2017.01447 · 2017 · External reference
A genome-wide evolutionary simulation of the transcription-supercoiling coupling
2022 · External reference
A fundamental regulatory mechanism operating through OmpR and DNA topology controls expression of Salmonella pathogenicity islands SPI-1 and SPI-2
2012 · External reference
How long does it take to fix a favorable mutation, and why should we care?
10.1086/708187 · 2020 · External reference
10.1145/2833157.2833162
10.1145/2833157.2833162 · External reference
