Characterization of structural features for small regulatory RNAs in Escherichia coli genomes

Small regulatory RNAs are highly abundant noncoding RNAs (ncRNA) found in bacterial genomes. These small regulatory ncRNAs (sRNAs) can regulate the synthesis of proteins by mediating mRNA transcription, translation and stability. Furthermore, they also control the activity of specific proteins by binding to them. In this study, we present a general computational approach for identifying the distinct structure of sRNAs in the Escherichia coli (E. coli) genome by a quantitative measure, Ediff that is the energy difference between the optimal structure folded from a sequence segment and its corresponding optimal restrained structure where all base pairings formed in the original optimal structure are excluded. Our results indicate that most of the known small ncRNAs in E. coli K12 have very high normalized Ediff scores with high statistical significance. These sRNAs have distinct well-ordered structures that are both thermodynamically stable and uniquely folded.