Complex Systems and Biological Physics Seminars

A Primary and Processed Bacterial Transcriptome in a Single View

by Nicolas Innocenti (KTH Computational Biology)

Europe/Stockholm
122:026

122:026

Description
Numerous studies performed on bacteria in the recent years have underlined the omnipresence of RNA-dependent regulatory processes. Although these global studies have been extremely valuable, their functional and regulatory insights remain incomplete, as primary and processed RNAs cannot be distinguished in classical transcriptomic experiments, hence transcriptional and post-transcriptional processes cannot be separated. Our group previously developed a method called 5’tagRACE (Fouquier et al., Nucleic Acids Res 2011) that enables to differentially ligate short RNA sequencing, called tags, to the 5’ ends of primary and processed RNAs. In this work we have coupled the 5'tagRACE with RNA-seq to distinguish primary and the processed RNAs, and unveil in a single experiment, the two transcriptomes (the ppRNome) building up the bacterial RNA landscape. While retaining all information present in a classical RNA-seq experiment, the presence of the tags allows direct probing of transcription start sites and helps in the detection of specific RNA cleavage sites. This approach is especially useful in regions with multiple overlapping or antisense transcripts. Most importantly, it allows distinguishing between variations in the expression level of a given genomic region due to changes in transcription from a similar effect due to regulated post-transcriptional activity, which constitutes a significant step towards the inference of regulatory cascades at transcriptional and post-transcriptional levels. As such, the presented method is a suitable tool for transcriptomic studies of transient behaviors in bacteria. My talk will present the study performed on Enterococcus faecalis, a commensal and opportunistic pathogen of the human gastro-intestinal tract. This is the very first ppRNome, available for the vancomycin resistant isolate V583.