The traditional view of the genome is based on the dogma that genetic information flows from DNA to RNA to protein. Genes have essentially been synonymous with proteins, with RNA viewed primarily as an intermediate template for protein translation. Intriguingly, only ~2% of the human genome encodes proteins, and the number of protein-coding genes (~20,000) is similar between humans and the simple nematode worm.I have been involved with the analysis of a large-scale transcriptome study, intiated by the RIKEN Genomic Sciences Centre in Japan. As part of this work, it was discovered that the genome carries instructions for tens of thousands of “non protein-coding RNAs” (ncRNAs)(please refer to Appendix A to view the original articles that appeared in Science). The significance of these ncRNAs remains a matter of intense interest and debate. Some have argued that these ncRNAs are simply transcriptional noise, while others have suggested that they comprise a critical regulatory system, which directs the complex patterns of gene expression that underlie differentiation and development.To investigate this further, I have conducted a series of studies that explore the expression and evolution of ncRNAs in mammals. Firstly, I established a comprehensive, on-line database of ncRNAs. This collection provides information on more than twenty thousand ncRNAs, and has proven a valuable resource for ncRNA studies. Secondly, I have systematically analyzed the conservation of known functional ncRNA subsets. I found that small ncRNAs (microRNAs and snoRNAs) were well-conserved similar to protein-coding sequences, whereas longer functional ncRNAs were not. These results indicate that long ncRNAs are evolving more rapidly than other functional genomic elements, and suggest that many of the recently-discovered ncRNAs – most of which are long and of unknown significance – might still be functional, despite having poor sequence conservation. Thirdly, I have shown that many ncRNAs are derived from genuine transcripts, whose expression appears regulated in a biologically-relevant manner. Fourthly, I helped develop a computational strategy to identify extremely large ncRNAs and discovered >60 novel candidates, several of which were characterized experimentally. Prior to this work, only a handful of extremely large ncRNAs had been previously described, and these play critical roles in processes such as genomic imprinting and X chromosome inactivation. This study represented the first systematic discovery of extremely large ncRNAs. Finally, I designed custom microarrays and profiled ncRNA expression across the development of CD8+ T cells. CD8+ T cells serve an important role in immunity by killing virus-infected and tumour cells, and transit through a series of functionally-distinct developmental stages. I found that ~200 novel ncRNAs are dynamically expressed during CD8+ T cell development.Taken together, my findings indicate that ncRNAs are a major, regulated output of the mammalian genome, and are consistent with the notion that ncRNAs represent an important, previously-unrecognised biological control system.
| Identifer | oai:union.ndltd.org:ADTP/245299 |
| Creators | Pang, Ken Chung-Ren |
| Source Sets | Australiasian Digital Theses Program |
| Language | English |
| Detected Language | English |
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