Accessibility and conservation: General features of bacterial small RNA–mRNA interactions?

Bacterial small RNAs (sRNAs) are a class of structural RNAs that often regulate mRNA targets via post-transcriptional base pair interactions. We determined features that discriminate functional from non-functional interactions and assessed the influence of these features on genome-wide target predictions. For this purpose, we compiled a set of 71 experimentally verified sRNA–target pairs from Escherichia coli and Salmonella enterica. Furthermore, we collected full-length 5′ untranslated regions by using genome-wide experimentally verified transcription start sites. Only interaction sites in sRNAs, but not in targets, show significant sequence conservation. In addition to this observation, we found that the base pairing between sRNAs and their targets is not conserved in general across more distantly related species. A closer inspection of RybB and RyhB sRNAs and their targets revealed that the base pairing complementarity is only conserved in a small subset of the targets. In contrast to conservation, accessibility of functional interaction sites is significantly higher in both sRNAs and targets in comparison to non-functional sites. Based on the above observations, we successfully used the following constraints to improve the specificity of genome-wide target predictions: the region of interaction initiation must be located in (1) highly accessible regions in both interaction partners or (2) unstructured conserved sRNA regions derived from reliability profiles of multiple sRNA alignments. Aligned sequences of homologous sRNAs, functional and non-functional targets, and a sup document with sup tables, figures and references are available at www.bioinf.uni-freiburg.de/Supplements/srna-interact-feat/.