Accessibility and evolutionary conservation mark bacterial small-RNA target-binding regions

Bacterial small noncoding RNAs have attracted much interest in recent years as posttranscriptional regu-lators of genes involved in diverse pathways. Small RNAs (sRNAs) are 50 to 400 nucleotides long and exert their regulatory function by directly base pairing with mRNA targets to alter their stability and/or affect their translation. This base pairing is achieved through a region of about 10 to 25 nucleotides, which may be located at various positions along different sRNAs. By compiling a data set of experimentally determined target-binding regions of sRNAs and systematically analyzing their properties, we reveal that they are both more evolutionarily conserved and more accessible than random regions. We demonstrate the use of these properties for computational identification of sRNA target-binding regions with high specificity and sensitivity. Our results show that these predicted regions are likely to base pair with known targets of an sRNA, suggesting that pointing out these regions in a specific sRNA can help in searching for its targets. Small noncoding RNAs are essential for the regulation of diverse processes in all kingdoms of life. The bacterial regula-tory RNAs, usually referred to as “small RNAs ” (sRNAs), vary in size between 50 and 400 nucleotides (63) and occasionally contain a short open reading frame (75). Many bacteria