Regulatory mechanisms employed by cis-encoded antisense RNAs.

Bacterial small regulatory RNAs that act by base-pairing can be divided into two classes: cis-encoded and trans-encoded antisense RNAs. The former--mainly discovered in plasmids, phages and transposons--are encoded in the same DNA locus and are therefore completely complementary to their targets over a long sequence stretch. Regulatory mechanisms employed by these RNAs encompass inhibition of primer maturation or RNA pseudoknot formation, transcriptional attenuation, inhibition of translation or promotion of RNA degradation or cleavage. Although the final product of antisense RNA/target RNA binding is a full duplex that is degraded by RNase III, inhibition does not require complete duplex formation. By contrast, in many cases, partially paired binding intermediates have been shown to be sufficient for the biological function.