sRNAPredict: an integrative computational approach to identify sRNAs in bacterial genomes

Abstract

Small non-coding bacterial RNAs (sRNAs) play important regulatory roles in a variety of cellular processes. Nearly all known sRNAs have been identified in Escherichia coli and most of these are not conserved in the majority of other bacterial species. Many of the E.coli sRNAs were initially predicted through bioinformatic approaches based on their common features, namely that they are encoded between annotated open reading frames and are flanked by predictable transcription signals. Because promoter consensus sequences are undetermined for most species, the successful use of bioinformatics to identify sRNAs in bacteria other than E.coli has been limited. We have created a program, sRNAPredict, which uses coordinate-based algorithms to integrate the respective positions of individual predictive features of sRNAs and rapidly identify putative intergenic sRNAs. Relying only on sequence conservation and predicted Rho-independent terminators, sRNAPredict was used to search for sRNAs in Vibrio cholerae. This search identified 9 of the 10 known or putative V.cholerae sRNAs and 32 candidates for novel sRNAs. Small transcripts for 6 out of 9 candidate sRNAs were observed by Northern analysis. Our findings suggest that sRNAPredict can be used to efficiently identify novel sRNAs even in bacteria for which promoter consensus sequences are not available.

Mapping the regulon of Vibrio cholerae ferric uptake regulator expands its known network of gene regulation

“…1D). The intergenic region between VC0142 and VC0143 has a strong, validated vcFur ChIP peak and was shown previously to express an sRNA (41). Northern blots using probes against this sRNA showed it also was derepressed in the fur::Tn mutant (Fig.…”

“…These peaks are not located near the start site of any gene. Livny et al (41) identified an sRNA in the intergenic region between VC0142/ VC0143 during a computational screen for V. cholerae sRNAs. Our Northern blots showed increased expression of this sRNA in the fur::Tn mutant (Fig.…”

Transcriptomic profiling of the oyster pathogen Vibrio splendidus opens a window on the evolutionary dynamics of the small RNA repertoire in the Vibrio genus

“…A first integrative computational approach relying on intergenic sequence conservation and presence of a Rho-independent terminator led to the experimental validation of six new sRNAs (Livny et al 2005). However, because sRNAs are generally not conserved beyond closely related species, these computational screens have been quickly outpaced by high-throughput sequencing efforts (Croucher and Thomson 2010).…”

RNAspace.org: An integrated environment for the prediction, annotation, and analysis of ncRNA

“…The most effective ncRNA detection software are distributed as stand-alone applications Klein and Eddy 2003;Livny et al 2005;Washietl et al 2005), some of them address only specific classes of RNAs (Lowe and Eddy 1997;Laslett and Canbäck 2004;Schattner et al 2006;Lagesen et al 2007) or organisms (Klein et al 2002;Schattner 2002;Upadhyay et al 2005;Larsson et al 2008). The integration of these approaches for consistent ncRNA prediction and annotation remains the realm of bioinformatics experts.…”