Multiple products from functional RNA gene loci

The most commonly understood role of RNA is as an intermediate in the decoding of genetic information in DNA into the proteins that carry out the majority of known structural and functional roles in the cell. A few other classes of functional RNA (fRNA) molecules, such as transfer RNAs, ribosomal RNAs and spliceosomal RNAs, are expressed from their own genes (so-called RNA genes), but were long assumed to be unusual specialised cases. However, it is becoming clear that RNA molecules have many previously unimagined functions, including regulation of gene expression, as guide molecules, in imprinting, dosage compensation, catalysis and structure. Particular RNA classes have also been implicated in disease, including cancer. A number of new RNA classes have been discovered, including microRNAs (in 2001), riboswitches (in 2002) and piwi-associated RNAs (in 2006). Over 2000 functional RNA genes can now be identified in the human genome, making up around 10% of the total gene count. While there has been rapid progress in identifying novel RNAs, the functions of the majority of new discoveries are unknown. In addition, computational studies and large-scale transcriptional data predict that the majority of RNA genes remain to be discovered. There are hints that there may be as many RNA genes as there are protein-coding genes. Just as post-genomic science begins to approach understanding of the complete set of protein structures and functions encoded in the genome, the importance of the roles of RNA in regulating cellular processes is becoming clear. Previous work (including our own) has shown that many classes of functional RNA molecules are expressed from gene loci that also make proteins or other RNA products. This observation fundamentally challenges our concept of the gene. For example, a researcher who knocks-out a gene will likely assume that an observed phenotype is the result of loss of protein function. However, an ignored fRNA product, such as a microRNA, expressed from the same locus may regulate the expression of other genes, confounding the interpretation of experimental data. The proposed research aims to use the context of RNA gene loci in the genome to understand their function. For example, if a single gene or transcript produces a functional RNA and a translated protein at the same time in the same cells under the same conditions, we predict that the RNA and protein will have related functions, or be involved in related pathways. A few known examples, such as small nucleolar RNAs expressed from introns of ribosomal protein genes, suggest that this is the case, but no large-scale systematic study has been reported. The work will examine whether intronic RNAs are indeed processed from the host transcript, or expressed from their own promoters. We will test whether co-expressed RNA and protein products function in the same pathways. Finally, we will use our improved understanding of intronic RNA characteristics to predict novel functional RNAs.

The past decade has seen a paradigm shift in our understanding of the roles of RNA molecules in cellular biology. A number of novel classes of functional RNA (fRNA) have been identified (eg microRNAs, riboswitches, piwi-associated RNAs), and significant numbers of non-protein-coding genes in previously known classes continue to be placed in complete genome sequences(eg snoRNAs, bacterial sRNAs). Recent computational analyses predict that there may be tens of thousands of RNA genes in the mammalian genome, the vast majority of which remain to be identified. In addition, the functions of many classes, and the precise molecular actions of almost all RNA genes, remain unknown. A significant proportion of known eukaryotic RNA genes appear to be processed from introns of other genes (termed host genes), mostly encoding proteins, but also long transcripts without protein-coding potential. The observation that multiple distinct functional products may be expressed in parallel from a single locus has dramatic consequences for our understanding of the nature of the gene and functional gene networks. Thorough description of this phenomenon is vital for our understanding of the non-protein-coding component of the genome, and for correct interpretation of experimental genetic data and transcriptomic datasets. This proposal seeks to determine and analyse the functional relationships between multiple protein and RNA products from fRNA loci. The work will catalogue all transcripts that express multiple RNA/protein and RNA/RNA products, and determine the sequence and structure characteristics which differentiate them from other mRNAs. The co-expression of host gene and fRNA will be investigated, including the possibility that intronic RNAs may be transcribed independently of the host gene. The core of the proposal is to use newly described host gene/RNA relationships to predict the functions of uncharacterised RNAs, and to discover novel fRNA genes.