ArticleCell systems2016
Insights into the Mechanisms of Basal Coordination of Transcription Using a Genome-Reduced Bacterium.
Article in Cell systems, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 23 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
23 citing papers in PubMed, 46 citations in OpenAlex.
- Differential effect of supercoiling on bacterial transcription in topological domains.PLoS computational biology · 2025Article
- A versatile plug and play bacterial chassis based on a fast-growing Mycoplasma species.Nucleic acids research · 2025Article
- Assessing in vivo the impact of gene context on transcription through DNA supercoiling.Nucleic acids research · 2023Article
- Comprehensive quantitative modeling of translation efficiency in a genome-reduced bacterium.Molecular systems biology · 2023Article
- Sub-operon promoter arrangement ofJournal of biosciences · 2023Article
- Quantitative contribution of the spacer length in the supercoiling-sensitivity of bacterial promoters.Nucleic acids research · 2022Article
- Polar mutagenesis of polycistronic bacterial transcriptional units using Cas12a.Microbial cell factories · 2022Article
- A genetic toolkit and gene switches to limit Mycoplasma growth for biosafety applications.Nature communications · 2022Article
- Role of the Discriminator Sequence in the Supercoiling Sensitivity of Bacterial Promoters.mSystems · 2021Article
- Article
- Benchmark of software tools for prokaryotic chromosomal interaction domain identification.Bioinformatics (Oxford, England) · 2020Article
- Redefining fundamental concepts of transcription initiation in bacteria.Nature reviews. Genetics · 2020Review
- Chromosomal Organization and Regulation of Genetic Function inEcoSal Plus · 2020Article
- Elucidating the Influence of Chromosomal Architecture on Transcriptional Regulation in Prokaryotes - Observing Strong Local Effects of Nucleoid Structure on Gene Regulation.Frontiers in microbiology · 2020Article
- Determination of the Gene Regulatory Network of a Genome-Reduced Bacterium Highlights Alternative Regulation Independent of Transcription Factors.Cell systems · 2019Article
- Bacterial genome architecture shapes global transcriptional regulation by DNA supercoiling.Nucleic acids research · 2019Article
- DNA Supercoiling: an Ancestral Regulator of Gene Expression in Pathogenic Bacteria?Computational and structural biotechnology journal · 2019Review
- Global analysis of sRNA target genes in Mycoplasma hyopneumoniae.BMC genomics · 2018Article
- Chromosomal organization of transcription: in a nutshell.Current genetics · 2018Review
- Mycoplasma pneumoniae from the Respiratory Tract and Beyond.Clinical microbiology reviews · 2017Review
Corrections and comments
- Erratum issued
Authors and funding
5 authors at 5 institutions in 3 countries.
Funding
Abstract
Coordination of transcription in bacteria occurs at supra-operonic scales, but the extent, specificity, and mechanisms of such regulation are poorly understood. Here, we tackle this problem by profiling the transcriptome of the model organism Mycoplasma pneumoniae across 115 growth conditions. We identify three qualitatively different levels of co-expression corresponding to distinct relative orientations and intergenic properties of adjacent genes. We reveal that the degree of co-expression between co-directional adjacent operons, and more generally between genes, is tightly related to their capacity to be transcribed en bloc into the same mRNA. We further show that this genome-wide pervasive transcription of adjacent genes and operons is specifically repressed by DNA regions preferentially bound by RNA polymerases, by intrinsic terminators, and by large intergenic distances. Taken together, our findings suggest that the basal coordination of transcription is mediated by the physical entities and mechanical properties of the transcription process itself, and that operon-like behaviors may strongly vary from condition to condition.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.