期刊
JOURNAL OF BACTERIOLOGY
卷 197, 期 1, 页码 18-28出版社
AMER SOC MICROBIOLOGY
DOI: 10.1128/JB.02096-14
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资金
- ZINF Young Investigator program of the Research Center for Infectious Diseases (ZINF) at the University of Wurzburg
- Bavarian BioSysNet Program
- Deutsche Forschungsgemeinshaft [Sh580/1-1]
- PROMOS travel scholarship (DAAD) of the University of Wurzburg
- Boehringer Ingelheim Fonds travel allowance
- EUNICE KENNEDY SHRIVER NATIONAL INSTITUTE OF CHILD HEALTH & HUMAN DEVELOPMENT [ZIAHD001608] Funding Source: NIH RePORTER
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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