Whole-genome mapping of 5′ RNA ends in bacteria by tagged sequencing: a comprehensive view in Enterococcus faecalis

  1. Erik Aurell1,9
  1. 1Department of Computational Biology, KTH Royal Institute of Technology, AlbaNova University Center, SE-10691 Stockholm, Sweden
  2. 2INRA, UMR1319 Micalis, Domaine de Vilvert, F-78352, Jouy-en-Josas, France
  3. 3AgroParisTech, UMR Micalis, Domaine de Vilvert, F-78350, Jouy-en-Josas, France
  4. 4Department of Biosystems Science and Engineering, ETH Zürich, CH-4058, Basel, Switzerland
  5. 5SIB Swiss Institute of Bioinformatics, University of Basel, CH-4056, Basel, Switzerland
  6. 6Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4362, Esch-sur-Alzette, Luxembourg
  7. 7Institut de Génétique et Microbiologie, Université Paris-Sud, CNRS, UMR8621, F-91405, Orsay, France
  8. 8INRA, MetaGenoPolis US1367, Domaine de Vilvert, F-78350, Jouy-en-Josas, France
  9. 9Department of Information and Computer Science, Aalto University, FI-02150 Espoo, Finland
  1. Corresponding authors: francis.repoila{at}jouy.inra.fr, eaurell{at}kth.se

Abstract

Enterococcus faecalis is the third cause of nosocomial infections. To obtain the first snapshot 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 (TSSs) and 352 processing sites (PSSs) in E. faecalis. A blind motif search retrieved canonical features of SigA- and SigN-dependent promoters preceding transcription start sites mapped. We discovered 85 novel putative regulatory RNAs, small- and antisense RNAs, and 72 transcriptional antisense organizations. Presented data constitute a significant insight into bacterial RNA landscapes and a step toward the inference of regulatory processes at transcriptional and post-transcriptional levels in a comprehensive manner.

Keywords

Footnotes

  • Abbreviations: asRNA, antisense RNA; BHI, brain-heart infusion; dRNA-seq, differential RNA-seq; IGR, intergenic region; ORF, open reading frame; ppRNome, primary and processed transmission; PSS, processing site; PTS, phosphor-sugar transfer systems; RNA-seq, RNA sequencing; Sdh, serine-dehydratase; sRNA, small RNA; TSS, transcription start site; UTR, untranslated region

  • Article published online ahead of print. Article and publication date are at http://www.rnajournal.org/cgi/doi/10.1261/rna.048470.114.

  • Received October 7, 2014.
  • Accepted December 22, 2014.

This article is distributed exclusively by the RNA Society for the first 12 months after the full-issue publication date (see http://rnajournal.cshlp.org/site/misc/terms.xhtml). After 12 months, it is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.

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