title: SRD: a Staphylococcus regulatory RNA database.
abstract: An overflow of regulatory RNAs (sRNAs) was identified in a wide range of bacteria. We designed and implemented a new resource for the hundreds of sRNAs identified in Staphylococci, with primary focus on the human pathogen Staphylococcus aureus. The "Staphylococcal Regulatory RNA Database" (SRD, http://srd.genouest.org/) compiled all published data in a single interface including genetic locations, sequences and other features. SRD proposes novel and simplified identifiers for Staphylococcal regulatory RNAs (srn) based on the sRNA's genetic location in S. aureus strain N315 which served as a reference. From a set of 894 sequences and after an in-depth cleaning, SRD provides a list of 575 srn exempt of redundant sequences. For each sRNA, their experimental support(s) is provided, allowing the user to individually assess their validity and significance. RNA-seq analysis performed on strains N315, NCTC8325, and Newman allowed us to provide further details, upgrade the initial annotation, and identified 159 RNA-seq independent transcribed sRNAs. The lists of 575 and 159 sRNAs sequences were used to predict the number and location of srns in 18 S. aureus strains and 10 other Staphylococci. A comparison of the srn contents within 32 Staphylococcal genomes revealed a poor conservation between species. In addition, sRNA structure predictions obtained with MFold are accessible. A BLAST server and the intaRNA program, which is dedicated to target prediction, were implemented. SRD is the first sRNA database centered on a genus; it is a user-friendly and scalable device with the possibility to submit new sequences that should spread in the literature.
authors: Inserm U835 Biochimie Pharmaceutique, Rennes University, 35043 Rennes, France.
authors: Mohamed
authors: M
authors: Sassi
authors: Inserm U835 Biochimie Pharmaceutique, Rennes University, 35043 Rennes, France.
authors: Yoann
authors: Y
authors: Augagneur
authors: Inserm U835 Biochimie Pharmaceutique, Rennes University, 35043 Rennes, France.
authors: Tony
authors: T
authors: Mauro
authors: Inserm U835 Biochimie Pharmaceutique, Rennes University, 35043 Rennes, France.
authors: Lorraine
authors: L
authors: Ivain
authors: Inserm U835 Biochimie Pharmaceutique, Rennes University, 35043 Rennes, France.
authors: Svetlana
authors: S
authors: Chabelskaya
authors: Inserm U835 Biochimie Pharmaceutique, Rennes University, 35043 Rennes, France.
authors: Marc
authors: M
authors: Hallier
authors: Institut de Recherche en Informatique et Systèmes Aléatoires, Rennes University, 35043 Rennes, France.
authors: Olivier
authors: O
authors: Sallou
authors: Inserm U835 Biochimie Pharmaceutique, Rennes University, 35043 Rennes, France.
authors: Brice
authors: B
authors: Felden
mesh_terms: D001483:Base Sequence; D002874:Chromosome Mapping; D019295:Computational Biology; D030561:Databases, Nucleic Acid; D015964:Gene Expression Regulation, Bacterial / Q000235:genetics*; D016680:Genome, Bacterial; D010802:Phylogeny; D012329:RNA, Bacterial / Q000235:genetics*; D058727:RNA, Small Untranslated; D017423:Sequence Analysis, RNA; D012984:Software; D013211:Staphylococcus aureus / Q000235:genetics*
chemical_list: D012329:RNA, Bacterial; D058727:RNA, Small Untranslated
keywords: RNA-seq; Staphylococcus aureus; bacteria; database; sRNA identification; sRNA targets; small regulatory RNAs