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 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.
Department of Computational Biology, KTH Royal Institute of Technology, AlbaNova University Center, SE-10691 Stockholm, Sweden INRA, UMR1319 Micalis, Domaine de Vilvert, F-78352, Jouy-en-Josas, France AgroParisTech, UMR Micalis, Domaine de Vilvert, F-78350, Jouy-en-Josas, France.
Nicolas
N
Innocenti
Department of Biosystems Science and Engineering, ETH Zürich, CH-4058, Basel, Switzerland SIB Swiss Institute of Bioinformatics, University of Basel, CH-4056, Basel, Switzerland.
Monica
M
Golumbeanu
Department of Computational Biology, KTH Royal Institute of Technology, AlbaNova University Center, SE-10691 Stockholm, Sweden Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4362, Esch-sur-Alzette, Luxembourg.
Aymeric
A
Fouquier d'Hérouël
INRA, UMR1319 Micalis, Domaine de Vilvert, F-78352, Jouy-en-Josas, France AgroParisTech, UMR Micalis, Domaine de Vilvert, F-78350, Jouy-en-Josas, France.
Caroline
C
Lacoux
Institut de Génétique et Microbiologie, Université Paris-Sud, CNRS, UMR8621, F-91405, Orsay, France.
Rémy A
RA
Bonnin
INRA, MetaGenoPolis US1367, Domaine de Vilvert, F-78350, Jouy-en-Josas, France.
Sean P
SP
Kennedy
INRA, UMR1319 Micalis, Domaine de Vilvert, F-78352, Jouy-en-Josas, France AgroParisTech, UMR Micalis, Domaine de Vilvert, F-78350, Jouy-en-Josas, France.
Françoise
F
Wessner
INRA, UMR1319 Micalis, Domaine de Vilvert, F-78352, Jouy-en-Josas, France AgroParisTech, UMR Micalis, Domaine de Vilvert, F-78350, Jouy-en-Josas, France.
Pascale
P
Serror
Institut de Génétique et Microbiologie, Université Paris-Sud, CNRS, UMR8621, F-91405, Orsay, France.
Philippe
P
Bouloc
INRA, UMR1319 Micalis, Domaine de Vilvert, F-78352, Jouy-en-Josas, France AgroParisTech, UMR Micalis, Domaine de Vilvert, F-78350, Jouy-en-Josas, France.
Francis
F
Repoila
Department of Computational Biology, KTH Royal Institute of Technology, AlbaNova University Center, SE-10691 Stockholm, Sweden Department of Information and Computer Science, Aalto University, FI-02150 Espoo, Finland.
Erik
E
Aurell
D020121:5' Untranslated Regions / Q000235:genetics*; D002874:Chromosome Mapping / Q000379:methods*; D013293:Enterococcus faecalis / Q000235:genetics*; D015964:Gene Expression Regulation, Bacterial; D016680:Genome, Bacterial; D009691:Nucleic Acid Denaturation; D011401:Promoter Regions, Genetic / Q000235:genetics; D012323:RNA Processing, Post-Transcriptional; D012329:RNA, Bacterial / Q000235:genetics*; D017423:Sequence Analysis, RNA / Q000379:methods*; D016324:Sequence Tagged Sites; D024363:Transcription Initiation Site; D059467:Transcriptome
D020121:5' Untranslated Regions; D012329:RNA, Bacterial
Enterococcus faecalis; RNA degradation; primary RNA; processed RNA; promoter