BSRD: a repository for bacterial small regulatory RNA

Abstract

In bacteria, small regulatory non-coding RNAs (sRNAs) are the most abundant class of post-transcriptional regulators. They are involved in diverse processes including quorum sensing, stress response, virulence and carbon metabolism. Recent developments in high-throughput techniques, such as genomic tiling arrays and RNA-Seq, have allowed efficient detection and characterization of bacterial sRNAs. However, a comprehensive repository to host sRNAs and their annotations is not available. Existing databases suffer from a limited number of bacterial species or sRNAs included. In addition, these databases do not have tools to integrate or analyse high-throughput sequencing data. Here, we have developed BSRD (http://kwanlab.bio.cuhk.edu.hk/BSRD), a comprehensive bacterial sRNAs database, as a repository for published bacterial sRNA sequences with annotations and expression profiles. BSRD contains over nine times more experimentally validated sRNAs than any other available databases. BSRD also provides combinatorial regulatory networks of transcription factors and sRNAs with their common targets. We have built and implemented in BSRD a novel RNA-Seq analysis platform, sRNADeep, to characterize sRNAs in large-scale transcriptome sequencing projects. We will update BSRD regularly.

Figure 1.

Overview of BSRD design. The three main characteristics of BSRD are (i) comprehensive data collection from external databases and the literatures, (ii) comprehensive annotation and expression profiles for sRNAs and (iii) a novel RNA-Seq analysis platform, sRNADeep, for characterizing sRNAs from high-throughput sequencing data.

Figure 2.

Screenshots of the regulatory network page. (a) Overview of the regulatory network. (b) Each target gene in the network could be linked out to the UniProt database. (c) When clicking on relationship lines, the description of regulatory effects will be shown.