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

TL;DR

This study provides a comprehensive map of transcription start and processing sites in Enterococcus faecalis using a modified RNA-seq approach, revealing novel regulatory RNAs and transcriptional organizations to understand bacterial gene regulation.

Contribution

It introduces a modified RNA-seq method to distinguish primary from processed RNA ends and maps transcriptional features in E. faecalis for the first time.

Findings

Mapped 559 transcription start sites in E. faecalis

Discovered 95 novel regulatory RNAs and 72 antisense organizations

Validated approach by confirming features in E. coli

Abstract

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.