Final Report Summary - FLAME (Long Intervening Noncoding RNAs (lincRNAs): Developmental Functions and Molecular Mechanisms of Action)
We have found that one of the conserved lncRNAs controls normal animal. Remarkably, this lncRNA controls behavior in adult zebrafish and mice by instructing destruction of another type of regulatory noncoding RNA in the cell called microRNA. We found that degradation of a specific microRNA in particular neurons of the adult brain is required for normal functioning of the cerebellum. If too much of the microRNA molecule is left in the brain, it leads to behavioral alterations in animals, including the impaired motor learning function. In addition, we identified the exact sequence in the lncRNA gene that triggers microRNA degradation. In summary, by demonstrating for the first time the physiological significance of microRNA degradation, directed by a genome-encoded lncRNA, our work resolves a longstanding question in the noncoding RNA field. In addition, our results point to these types of RNA sequences embedded in genome-encoded transcripts as potentially having broad in vivo relevance and serving as therapeutic targets in the future.
Another large achievement of the award was the development of a novel high-throughput technology that enables the identification of RNA–protein interactions in living cells. Because all cellular RNA transcripts are coated by RNA-binding proteins (RBPs) and, in particular, regulatory noncoding RNAs carry out their cellular functions through the diverse protein assemblies in which they are integrated, identifying the protein interaction partners of RNAs is critical to decipher their molecular functions. However, the RBP repertoire reported to bind various RNA transcripts is often skewed toward abundant and promiscuously binding proteins, which can confound functional interpretations. Due to its specific design, our new technology resolved two main obstacles when aiming to identify RNA-bound proteomes: it enabled the identification of proteins associated with RNAs expressed at low endogenous levels, and determined RNA region-specific proteomes allowing the assignment of protein binding to defined regions of a long full-length transcript. Moreover, our method not only identified previously known RNA-protein interactions but also identified novel functionally important RNA-protein interactions that evaded detection with previous methods, reinforcing the advantages of our technology. In summary, we have developed new tools and have established genetic in vivo systems to dissect the functions and mechanisms of action of lncRNAs. Our studies have demonstrated that sequence conservation can guide our understanding of lncRNA functions.