Accessibility and conservation in bacterial small RNA-mRNA interactions and implications for genome-wide target predictions

Bacterial small RNAs (sRNAs) are a class of structural RNAs that often regulate mRNA targets via post-transcriptional base pair interactions. In this study, we assessed the accessibility and conservation of the interaction sites and 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, and collected genome-wide information on 5’ untranslated regions of annotated genes. Then, features of the confirmed interactions were compared to a set of non-interactions. We found that the interaction sites both in sRNA and target are more accessible than in the negative data. Furthermore, interaction sites in the sRNAs, but not in the targets, show high sequence conservation. The base pairing between sRNA and target was not found to be generally conserved across more distantly related species. We then present two approaches to constrain the region of interaction initiation to (1) well-accessible regions in both interaction partners or (2) unstructured conserved sRNA regions derived from reliability profiles of multiple sRNA alignments. Using these constraints, genome-wide target predictions were improved in terms of specificity.