Whole genome mapping of 5' RNA ends in bacteria by tagged sequencing : A comprehensive view in Enterococcus faecalis

Enterococcus faecalis is the third cause of nosocomial infections. To obtain the first comprehensive view of transcriptional organizations in this bacterium, we used a modified RNA-seq approach enabling to discriminate primary from processed 5'RNA ends. We also validated our approach by confirm...

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Published inarXiv.org
Main Authors Innocenti, Nicolas, Golumbeanu, Monica, d'Hérouël, Aymeric Fouquier, Lacoux, Caroline, Bonnin, Rémy A, Kennedy, Sean P, Wessner, Françoise, Serror, Pascale, Bouloc, Philippe, Repoila, Francis, Aurell, Erik
Format Paper Journal Article
LanguageEnglish
Published Ithaca Cornell University Library, arXiv.org 07.10.2014
Subjects
Bacteria
Bacterial proteins
E coli
Gene sequencing
Landscape
Mapping
Quantitative Biology - Biomolecules
Quantitative Biology - Genomics
Quantitative Biology - Quantitative Methods
Ribonucleic acid
RNA
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Summary:Enterococcus faecalis is the third cause of nosocomial infections. To obtain the first comprehensive view of transcriptional organizations in this bacterium, we used a modified RNA-seq approach enabling to discriminate primary from processed 5'RNA ends. We also validated our approach by confirming known features in Escherichia coli. We mapped 559 transcription start sites and 352 processing sites in E. faecalis. A blind motif search retrieved canonical features of SigA- and SigN-dependent promoters preceding TSSs mapped. We discovered 95 novel putative regulatory RNAs, small- and antisense RNAs, and 72 transcriptional antisense organisations. Presented data constitute a significant insight into bacterial RNA landscapes and a step towards the inference of regulatory processes at transcriptional and post-transcriptional levels in a comprehensive manner.
ISSN:2331-8422
DOI:10.48550/arxiv.1410.1925