Accessibility and conservation: general features of bacterial small RNA-mRNA interactions?
| Autor: | Andreas S. Richter, Rolf Backofen |
|---|---|
| Rok vydání: | 2012 |
| Předmět: |
Untranslated region
Sequence analysis Base pair Molecular Sequence Data target prediction Biology RyhB Conserved sequence Bacterial small RNA IntaRNA Escherichia coli RNA Messenger bacteria Molecular Biology Base Pairing Conserved Sequence Phylogeny Genetics Binding Sites Base Sequence Models Genetic Sequence Analysis RNA conservation RNA Salmonella enterica Cell Biology Gene Expression Regulation Bacterial accessibility RNA Bacterial Genes Bacterial Transfer RNA RNA–RNA interaction RNA Small Untranslated RNA Interference sRNA Algorithms Research Paper |
| Zdroj: | RNA Biology |
| ISSN: | 1555-8584 |
| Popis: | 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 and (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 supplementary document with supplementary tables, figures and references are available at http://www. bioinf.uni-freiburg.de/Supplements/srna-interact-feat. |
| Databáze: | OpenAIRE |
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