Stealth regulation: biological circuits with small RNA switches.

So you thinkyou finally understand the regulation of your favorite gene? The transcriptional regulators have been identified; the signaling cascades that regulate synthesis and activity of the regulators have been found. Possibly you have found that the regulator is itself unstable, and that instability is necessary for proper regulation. Time to lookfor a new project, or retire and rest on your laurels? Not so fast—there’s more. It is rapidly becoming apparent that another whole level of regulation lurks, unsuspected, in both prokaryotic and eukaryotic cells, hidden from our notice in part by the transcription-based approaches that we usually use to study gene regulation, and in part because these regulators are very small targets for mutagenesis and are not easily found from genome sequences alone. These stealth regulators, operating below our radar, if not that of the cell, are small regulatory RNAs, acting to control the translation and degradation of many messengers. These RNAs can be potent and multifunctional, allowing new signaling pathways to cross-regulate targets independently of the transcriptional signals for those targets, introducing polarity within operons, and explaining some puzzles in well-studied regulatory circuits. The importance of small regulatory RNAs was first appreciated in the elegant studies of plasmid-encoded antisense RNAs. The few apparently unusual cases of noncoding regulatory RNAs encoded in the bacterial chromosome has expanded over the last decade, and the role such RNA regulators play in both stimulating and inhibiting gene expression has been firmly established. As genome sequences have become available for many bacteria, it has become possible to search for additional members of this regulatory family, and, eventually, to begin to understand how they act at the molecular level. Simultaneously, researchers in eukaryotic systems were discovering the wonders of RNAi, a cellular strategy for protecting itself from RNA invaders, in which small double-stranded RNA molecules cause destruction of homologous messages. The discovery that developmental mutants in Caenorhabditis elegans define genes for two small RNA translational regulators, called small temporal RNAs (stRNAs) or microRNAs, and that these RNAs are processed by some of the same protein cofactors as is RNAi, have put regulatory RNAs in the spotlight in eukaryotes as well. Recent searches have confirmed that flies, worms, plants, and humans all harbor significant numbers of small RNAs likely to play regulatory roles. Along with the rapid expansion in RNAs doing interesting things, has come a proliferation of nomenclature. Noncoding RNAs (ncRNA) has been used recently, as the most general term (Storz 2002). Among the noncoding RNAs, the subclass of relatively small RNAs that frequently act as regulators have been called stRNAs (small temporal RNAs, eukaryotes) and sRNAs (small RNAs, prokaryotes), among others. Here, I will refer to the regulatory RNAs, which should be considered a subset of the ncRNAs. I review here the range of regulatory RNAs that have been identified and how they can be found, what we know about how they work, drawing lessons from the plasmid antisense molecules, and how they transduce regulatory signals. These stealthy RNAs may be the final level of unexpected regulatory circuitry in all of those systems we thought we were beginning to understand; now that we know they are there, we have some hope of understanding what it is they do and how they do it.