Bioinformatic discovery of novel RNA elements in genome and transcript sequences.
Bioinformatic discovery of novel RNA elements in genome and transcript sequences.
Chris Brown1, Ambarish Biswas1,2, Stewart Stevens1, Gareth Gillard1, Rob Lawry3, Artemio Mendoza3 and Peter Fineran2.
1. Biochemistry, University of Otago
2. Microbiology and Immunology, University of Otago
3. Bioprotection CORE, Lincoln University.
The untranslated regions of mRNAs commonly contain RNA elements that determine where, when or how effectively the mRNA is translated. This allows cells to respond rapidly to their environment and when they are mutated may result in disease. Some of these elements are well characterised- these may be structured (e.g. the Iron Responsive Element) or unstructured (e.g. the AU Rich element).
However, the high level of conservation in mRNAs' UTRs and discovery of mutations that cause disease in UTRs suggest there are many more undiscovered elements. We have been developing computational models to describe (1,2) and discover (3) these elements and search for them in mRNA sequences. There are a surprising number of potential new elements in the human genome.
Non-coding RNAs (ncRNAs) are been growing in variety and importance. Indeed one of the most striking observations from the recently completed ENCODE project was that there are almost as many ncRNAs as protein coding mRNAs in the human genome. However, in many genome and transcriptome studies they are ignored.
We have been using a variety of techniques to discover ncRNAs in different species, using published genomes and RNA-Seq. I will outline examples from our recently published and unpublished studies, focusing on the bioinformatic discovery of ncRNAs in diverse species- bacteria (4), fungi and the NZ sea urchin kina (5).
1. Jacobs et al (2009) Nucl Acids Res 37:D72,
2. Stevens et al (2011) RNA Biol 8:792,
3. Chen and Brown (2012) Nucl Acids Res 40:8862, 4. Biswas et al (2013) RNA Biol 10:817, 5. Gillard et al (2014) BMC Genomics 15:45.