Molecular Mechanisms of Stress Resistance miRCURY LNA™ microRNA Arrays
Dr. Shane Murray
Dr Shane Murray is a plant genomics expert at the Centre for Proteomic and Genomic Research (CPGR) in Cape Town, South Africa. The CPGR is a modern world class, high throughput biology research facility that provides state-of-the-art analytical services and technical expertise in the genomics and proteomics sectors.
1. What is the function of the Centre for Proteomic & Genomic Research? (Which areas of microRNA research are you involved in?)
The Centre for Proteomic and Genomic Research (CPGR) is a not-for-profit core research technology platform, funded by the South African government through its vehicles the Cape Biotech Trust and PlantBio. The mission of the CPGR is to stimulate excellent “omics” research, to support existing companies to facilitate the generation of new projects and to increase the number of suitably trained scientists in South Africa. While the CPGR has successfully used Exiqon's miRCURY arrays to profile miRNA expression in both human and plant samples, my interest is in cereal crops, in particular maize. Maize is an important crop in Africa and identification of the molecular controls of resistance to biotic and abiotic stresses is a major research goal.
2. In your opinion, why should researchers perform a microRNA profile in plants?
Profiling miRNAs in plants using an array-based approach is a good first approach. miRNA families are highly conserved, making it possible to identify known miRNAs expressed in different plant species under different conditions. miCURY miRNA arrays contain probes for the vast majority of validated plant miRNAs (as listed in miRBase), which makes them a good tool for this purpose. In addition, profiling expression of miRNAs can complement traditional transcript profiling to further unravel control of gene expression and can help validate miRNAs identified through bioinformatics approaches.
3. What has been your experience in microRNA profiling in plants?
In collaboration with the Council for Scientific and Industrial Research (CSIR), we have conducted a proof-of-concept study, comparing miRNA profiles in maize flowers and leaves, using the miRCURY LNA™ array and labeling kit from Exiqon. We obtained data of very high quality. Our preliminary analysis indicates that miRNAs involved in development in both Arabidopsis
and maize are differentially expressed in maize flowers.
4. What are your experiences of using the miRCURY LNA™ Array and the Labeling Kit from Exiqon with plant material?
5. In your opinion, what are the main advantages to using the miRCURY LNA™ Array and the Labeling kit compared to other types of microRNA array and labeling kits?
In my opinion, there are many advantages. Firstly, the miRCURY kit is really easy to use and we obtained good quality data. I particularly liked the spike-in controls, as a good method to determine the quality of the array. Secondly, the miRCURY arrays cover a wide range of species, allowing the identification of validated miRNAs in different species under different conditions. Thirdly, we use the Tecan HS4800Pro automated hybridization station for which Exiqon provides compatible protocols, further enhancing the ease of performing the assay and the quality of the data produced.
6. How do you validate the results from the microRNA arrays?
We are currently evaluating several qPCR approaches.
7. What is the biggest challenge when profiling microRNAs in plants?
This is difficult to say, as our proof of concept study went really well. Probably the same challenges apply as for full genome profiling: the necessity to grow and harvest plants under standard growth conditions, to extract good quality RNA (ensuring that small RNA species are not lost, in the case of miRNA profiling), to process the arrays routinely (we used a TECAN hybridization station, which reduces array-to-array variation) and to have access to good normalization and analysis packages for down-stream processing of the data.
8. How do you think the interest of microRNAs in plants will evolve in the next few years? We believe interest in miRNAs in plants will definitely increase in the next five years, as more and more papers are published linking miRNA expression to a particular stress response. A number of other research groups in South Africa have already expressed interest in using the Exiqon arrays.