ArticleNature biotechnology2009
The transcription unit architecture of the Escherichia coli genome.
Article in Nature biotechnology, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 168 papers.
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Who cites it
168 citing papers in PubMed.
- Intersegmental transfers drive target search in an RNA-targeting CRISPR system.bioRxiv : the preprint server for biology · 2026Article
- Important role in transcription start site selection for the RNA polymerase II-TFIIE-TFIIH interface in Saccharomyces cerevisiae.Genetics · 2026Article
- CRAGE-RB-PI-seq reveals transcriptional dynamics of plant-associated bacteria during root colonization.Nature communications · 2026Article
- RNA polymerase II-TFIIE-TFIIH interface functions in transcription start site selection inbioRxiv : the preprint server for biology · 2025Article
- Unraveling the Prevalence and Multifaceted Roles of Accessory Peptide Deformylases in Bacterial Adaptation and Resistance.Molecular biology and evolution · 2025Article
- Multi-omics analysis reveals the genetic basis for rapid COmSystems · 2025Article
- Promoter-proximal transcription-translation coupling controls early transcription in Escherichia coli.Nucleic acids research · 2025Article
- Determination of the transcription unit landscape and associated regulatory elements inMicrobiology spectrum · 2025Article
- Article
- 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
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- Genomic SELEX Screening of Regulatory Targets of Transcription Factors.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Model-driven experimental design workflow expands understanding of regulatory role of Nac inNAR genomics and bioinformatics · 2023Article
- Purification and Characterization of Authentic 30S Ribosomal Precursors Induced by Heat Shock.International journal of molecular sciences · 2023Article
- Engineering nonphotosynthetic carbon fixation for production of bioplastics by methanogenic archaea.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Genome-wide promoter assembly inGenome research · 2022Article
- Quantitative Control for Stoichiometric Protein Synthesis.Annual review of microbiology · 2021Article
- Review
- The transcriptional landscape of a rewritten bacterial genome reveals control elements and genome design principles.Nature communications · 2021Article
- Article
108 more citing papers are in PubMed but not listed here.
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Authors and funding
8 authors.
Funding
Abstract
Bacterial genomes are organized by structural and functional elements, including promoters, transcription start and termination sites, open reading frames, regulatory noncoding regions, untranslated regions and transcription units. Here, we iteratively integrate high-throughput, genome-wide measurements of RNA polymerase binding locations and mRNA transcript abundance, 5' sequences and translation into proteins to determine the organizational structure of the Escherichia coli K-12 MG1655 genome. Integration of the organizational elements provides an experimentally annotated transcription unit architecture, including alternative transcription start sites, 5' untranslated region, boundaries and open reading frames of each transcription unit. A total of 4,661 transcription units were identified, representing an increase of >530% over current knowledge. This comprehensive transcription unit architecture allows for the elucidation of condition-specific uses of alternative sigma factors at the genome scale. Furthermore, the transcription unit architecture provides a foundation on which to construct genome-scale transcriptional and translational regulatory networks.
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Registered trials
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