Global transcriptional start site mapping using differential RNA sequencing reveals novel antisense RNAs in Escherichia coli
Open accessAbstract
While the model organism Escherichia coli has been the subject of intense study for decades, the full complement of its RNAs is only now being examined. Here we describe a survey of the E. coli transcriptome carried out using a differential RNA sequencing (dRNA-seq) approach, which can distinguish between primary and processed transcripts, and an automated prediction algorithm for transcriptional start sites (TSS). With the criterion of expression under at least one of three growth conditions examined, we predicted 14,868 TSS candidates, including 5,574 internal to annotated genes (iTSS) and 5,495 TSS corresponding to potential antisense RNAs (asRNAs). We examined expression of 14 candidate asRNAs by Northern analysis using RNA from wild-type E. coli and from strains defective for RNases III and E, two RNases reported to be involved in asRNA processing. Interestingly, nine asRNAs detected as distinct bands by Northern analysis were differentially affected by the rnc and rne mutations. We also compared our asRNA candidates with previously published asRNA annotations from RNA-seq data and discuss the challenges associated with these cross-comparisons. Our global transcriptional start site map represents a valuable resource for identification of transcription start sites, promoters, and novel transcripts in E. coli and is easily accessible, together with the cDNA coverage plots, in an online genome browser.
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For promoter library assembly, transcriptomic studies using RNA-seq can be used to identify promoters of various transcription intensities.
“For promoter library assembly, transcriptomic studies using RNA-seq can be used to identify promoters of various transcription intensities (Sharma and Vogel, 2014; Thomason et al., 2015).”
From Gas Fermentation—A Flexible Platform for Commercial Scale Production of Low-Carbon-Fuels and Chemicals from Waste and Renewable Feedstocks (2016) · cites this paper as Thomason et al., 2015
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- Authors
- Thomason, M. K., Bischler, T., Eisenbart, S. K., Förstner, K. U., Zhang, A., Herbig, A., Nieselt, K., Sharma, C. M., & Storz, G.
- Affiliations
- National Institutes of Health (US)
- University of Würzburg (DE)
- University of Tübingen (DE)
- ORCID
- Venue
- Journal of Bacteriology
- Publisher
- American Society for Microbiology
- Published
- 2015-01
- Volume
- 197
- Issue
- 1
- Pages
- 18-28
- ISSN
- 0021-9193 (ISSN-L)
- 1098-5530
- PMC
- PMC4288677
- OpenAlex
- W2137390416
- Cited by
- 335
- References
- 56
- Citations by year
- 2026: 10 · 2025: 15 · 2024: 30 · 2023: 39 · 2022: 22 · 2021: 31 · 2020: 29 · 2019: 37 · 2018: 40 · 2017: 33 · 2016: 25 · 2015: 18 · 2014: 4
- FWCI
- 17.51
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Journal of Bacteriology (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- MPG.PuRe (Max Planck Society) (submittedVersion, other-oa)
- Max Planck Digital Library (submittedVersion, other-oa)
- Funders
- Boehringer Ingelheim Fonds
- Deutscher Akademischer Austauschdienst
- Julius-Maximilians-Universität Würzburg
- National Institutes of Health
- National Institute of Child Health and Human Development
- Eunice Kennedy Shriver National Institute of Child Health and Human Development
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Bacterial Genetics and Biotechnology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Keywords
- Escherichia coli, transcription start sites, antisense RNA, transcriptome, RNase III, RNase E, promoter, novel transcripts, genome browser
- MeSH terms
- Chromosome Mapping, Escherichia coli, RNA, Bacterial, Gene Expression Regulation, Bacterial, RNA, Antisense, Genome, Bacterial, Sequence Analysis, RNA, Transcription Initiation Site, Transcriptome
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