Innocenti Nicolas, Golumbeanu Monica, Fouquier d'Hérouël Aymeric, Lacoux Caroline, Bonnin Rémy A, Kennedy Sean P, Wessner Françoise, Serror Pascale, Bouloc Philippe, Repoila Francis, Aurell Erik
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.
Department of Biosystems Science and Engineering, ETH Zürich, CH-4058, Basel, Switzerland SIB Swiss Institute of Bioinformatics, University of Basel, CH-4056, Basel, Switzerland.
RNA. 2015 May;21(5):1018-30. doi: 10.1261/rna.048470.114. Epub 2015 Mar 3.
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.
粪肠球菌是医院感染的第三大病因。为了获得该细菌转录组织的首张快照，我们采用了一种改良的RNA测序方法，能够区分初级5' RNA末端和加工后的5' RNA末端。我们还通过确认大肠杆菌中的已知特征来验证我们的方法。我们绘制了粪肠球菌中的559个转录起始位点（TSS）和352个加工位点（PSS）。通过盲法基序搜索检索到了所绘制转录起始位点之前的SigA和SigN依赖性启动子的典型特征。我们发现了85个新的假定调控RNA、小RNA和反义RNA，以及72个转录反义组织。所呈现的数据构成了对细菌RNA景观的重要洞察，也是朝着全面推断转录和转录后水平调控过程迈出的一步。
