RNA is beginning to take its place among the movers and shakers of biology. For decades, it was considered a background player in biology, a static carrier of genetic instructions from big daddy DNA. Now, however, RNA and its analysis are coming into the spotlight in an ever-expanding arena. New players bearing acronyms such as piRNA, siRNA, shRNA, and ncRNA are now regulars in scientific lexicons (and, perhaps more importantly, Wikipedia).
Emerging trends and new advances in the field are reviewed in this article, including revolutionary tools for transcriptomic analyses, deciphering how pathogens subvert immune systems, and new modeling methods to better delineate RNA structure/function.
Piwi-interacting RNAs (piRNAs) are a new chapter in the emerging story of RNA biology. These small, noncoding RNAs (ncRNA) were discovered from a search for ncRNAs that interacted with the Drosophila signaling protein called Piwi. Two classes of piRNAs have been discovered. One set is abundant in germ cells and a second set is present in somatic cells and has a role in regulation of mRNA from early embryos and gonads.
The recent discovery of piRNAs in the central nervous system (CNS) was a surprise, reported Kenneth S. Kosik, M.D., professor and director, Neuroscience Research Institute, University of California, Santa Barbara.
“We are interested in how synapses of the CNS are locally regulated,” he said. “Since their discovery in 2006, the roles of piRNAs have continued to expand. We performed deep sequencing as a nonbiased approach toward searching for any category of small RNAs in the hippocampus, a brain region commonly used in studies of plasticity and studies of local translation in neuronal dendrites, an important facet of plasticity. Among the small RNA sequences observed were a set of piRNAs.”
Dr. Kosik and colleagues prepared small RNA libraries made by extracting RNA from male mouse hippocampus tissue to capture a large number of RNAs.
“We found a set of small RNAs in the size range of 24–31 base pairs, which is characteristic of piRNAs and quite distinct from the smaller ~21 nt microRNAs. We searched the piRNA database and found annotated sequences that corresponded to those in our sample. Then we confirmed our results by co-immunoprecipitating the piRNAs with the protein they bind to in the mouse (termed MIWI).”
The scientists also validated the results by performing in situ hybridization for several of the piRNAs. “Interestingly, we found that one piRNA extended out to dendrites; it was not confined to the neuron body. The dendrite is a site for a great deal of control over RNA and protein synthesis. These results may help us understand the plasticity of the nervous system.
“While we don’t know if piRNAs will have a role here, it certainly opens up the doors to explore if they are players. Minimally these studies revealed that piRNAs should no longer be considered as limited to the germ line. It is becoming increasingly clear that we need to think more broadly about them.”