ArticleBMC bioinformatics2015
Revisiting operons: an analysis of the landscape of transcriptional units in E. coli.
Article in BMC bioinformatics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed, 47 citations in OpenAlex.
- An end-to-end computational framework for "Record-seq" transcriptional recording data.Bioinformatics (Oxford, England) · 2026Article
- A transcription unit based systems biology study onFrontiers in microbiology · 2026Article
- Bacterial gene 5' ends have unusual mutation rates that can mislead tests of selection.PLoS biology · 2025Article
- Article
- Role of a TonB-dependent receptor and an oxygenase in iron-dependent copper resistance inJournal of bacteriology · 2025Article
- Cross-evaluation of E. coli's operon structures via a whole-cell model suggests alternative cellular benefits for low- versus high-expressing operons.Cell systems · 2024Article
- Exopolysaccharide Biosynthesis inInternational journal of molecular sciences · 2023Article
- Genome-wide promoter assembly inGenome research · 2022Article
- Genome-scale analysis of genetic regulatory elements in Streptomyces avermitilis MA-4680 using transcript boundary information.BMC genomics · 2022Article
- Does the Pachytene Checkpoint, a Feature of Meiosis, Filter Out Mistakes in Double-Strand DNA Break Repair and as a side-Effect Strongly Promote Adaptive Speciation?Integrative organismal biology (Oxford, England) · 2022Article
- Article
- Redefining fundamental concepts of transcription initiation in bacteria.Nature reviews. Genetics · 2020Review
- Transcriptional Organization of the Stability Module of Broad-Host-Range Plasmid RA3, from the IncU Group.Applied and environmental microbiology · 2020Article
- Complete genome sequence and annotation of the laboratory reference strain Shigella flexneri serotype 5a M90T and genome-wide transcriptional start site determination.BMC genomics · 2020Article
- The Transcription Unit Architecture ofFrontiers in microbiology · 2019Article
- The Transcriptional landscape of Streptococcus pneumoniae TIGR4 reveals a complex operon architecture and abundant riboregulation critical for growth and virulence.PLoS pathogens · 2018Article
- RECTA: Regulon Identification Based on Comparative Genomics and Transcriptomics Analysis.Genes · 2018Article
- Trees, fungi and bacteria: tripartite metatranscriptomics of a root microbiome responding to soil contamination.Microbiome · 2018Article
- BAC-BROWSER: The Tool for Visualization and Analysis of Prokaryotic Genomes.Frontiers in microbiology · 2018Article
- Mining Novel Constitutive Promoter Elements in Soil Metagenomic Libraries inFrontiers in microbiology · 2018Article
Corrections and comments
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Authors and funding
6 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundBacterial operons are considerably more complex than what were thought. At least their components are dynamically rather than statically defined as previously assumed. Here we present a computational study of the landscape of the transcriptional units (TUs) of E. coli K12, revealed by the available genomic and transcriptomic data, providing new understanding about the complexity of TUs as a whole encoded in the genome of E. coli K12. RESULTS AND
conclusionOur main findings include that (i) different TUs may overlap with each other by sharing common genes, giving rise to clusters of overlapped TUs (TUCs) along the genomic sequence; (ii) the intergenic regions in front of the first gene of each TU tend to have more conserved sequence motifs than those of the other genes inside the TU, suggesting that TUs each have their own promoters; (iii) the terminators associated with the 3' ends of TUCs tend to be Rho-independent terminators, substantially more often than terminators of TUs that end inside a TUC; and (iv) the functional relatedness of adjacent gene pairs in individual TUs is higher than those in TUCs, suggesting that individual TUs are more basic functional units than TUCs.
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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.