Staphylococcal regulatory RNAs

An overflow of regulatory RNAs (sRNAs) was identified in a wide range of bacteria. We designed and implemented a new resource for the hundreds sRNAs identified in Staphylococci, with primary focus on the human pathogen Staphylococcus aureus. The ‘Staphylococcal Regulatory RNA Database’ compiled all published data in a single interface including genetic locations, sequences and other features. SRD proposes a simplified and unified identifier for Staphylococcal regulatory RNAs (srn) based on the sRNA’s genetic location in S. aureus strain N315 which served as a reference. SRD provides a list of 575 srn potentially exempt of repeated sequences. For each sRNA, their experimental support(s) is provided, allowing the user to individually assess their validness and significance. RNAseq analysis performed on strains N315, NCTC8325 and Newman allowed us to improve the initial annotation and to dress a list of 159 RNAseq independent transcribed sRNAs. SRD is the first sRNA database centered on a genus since the comparison of the srn contents within 32 Staphylococcal genomes revealed a poor conservation between species. It is a user-friendly and scalable device with the possibility to submit new sequences which should rapidly spread in the literature.

Specific features of SRD:

In depth manual curation of sRNAs
Novel and simple annotation of sRNAs identified in S. aureus : srn for Staphylococcus RiboNucleotide
GFF files downloadable for further RNAseq analysis
BLAST server and intaRNA program implemented
Prediction of sRNA structures available
Visualization of the distribution of sRNA on corresponding chromosomes

if you use SRD, please cite SRD: a Staphylococcus regulatory RNA database. Sassi M, Augagneur Y, Mauro T, Ivain L, Chabelskaya S, Hallier M, Sallou O, Felden B. RNA. 2015 Mar 24. PMID:25805861

SRD updated on 07/11/2017

Staphylococcal regulatory RNAs

Heatmap based on the presence (black) and absence (red) of srn sequences in Staphylococcus genomes.

Links to other sRNA databases and platforms