Whole-genome mapping of 5′ RNA ends in bacteria by tagged sequencing: a comprehensive view in Enterococcus faecalis
2015 (English)In: RNA, ISSN 1355-8382Article in journal (Refereed) Published
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.
Place, publisher, year, edition, pages
RNA Society , 2015.
primary RNA, processed RNA, promoter, RNA degradation, Enterococcus faecalis
Bioinformatics and Systems Biology Microbiology Genetics
Research subject Biological Physics
IdentifiersURN: urn:nbn:se:kth:diva-163570DOI: 10.1261/rna.048470.114ISI: 000353068400022ScopusID: 2-s2.0-84928006918OAI: oai:DiVA.org:kth-163570DiVA: diva2:801237
FunderSwedish Research Council, 621-2012-2982
QC 201504172015-04-082015-04-082015-09-30Bibliographically approved