Switcher Stories
Q&A with Dr. Pam Green and Dr. Blake Meyers
- How has the Genome Analyzer changed the scope of your research?
- What advantages does the Genome Analyzer offer to your field of research?
- Where do you plan on taking the Genome Analyzer next?
How has the Genome Analyzer changed the scope of your research?
Dr. Green: One of the key features of the Genome Analyzer is the depth of detection it offers. If we have one gene of interest and we want to know what small RNAs match with that gene, then having tremendous depth is important because we are looking throughout the genome. Conventional technologies give us limited information that often won’t allow us to test our hypothesis. Another important feature is the ability to study new organisms like Brachypodium dystachion. This plant is a brand new system that the community is just beginning to sequence now, which means a DNA microarray for messenger RNA profiling does not exist. When we were writing our grant to do small RNA profiling for Brachypodium, we thought Why don’t we just do mRNA profiling too? We can generate the data with the Genome Analyzer and essentially provide the field with baseline information without first needing to make a DNA microarray. Once the Brachypodium genome is ready, we can match this information to the genome sequence and the field will be jumpstarted with a lot of mRNA as well as small RNA gene expression information.
Sometimes we’ve turned to the Genome Analyzer to see what we find, other times we have a clear hypothesis. Either way, we still always discover other things we never expected to find. Because the data the Genome Analyzer generates is so extensive, it’s hard not to discover something that you didn’t expect when you do an experiment.
What advantages do you see the Genome Analyzer offering your field of research?
Dr. Meyers: If you work in a crop system with a small scientific community, you are somewhat on your own to develop those resources. With a technology like Genome Analyzer, it becomes much easier to develop a very rich set of genomic data set from which you can start to ask other questions. I think a lot of plant biologists, particularly those working in applied systems, are still working in a "discovery" phase. I think that they would have difficulty moving rapidly to the next phase in their research if technology like the Genome Analyzer wasn’t there to enable and advance this stage of discovery. One significant advantage is that this platform supports many different applications including ChIP-Seq, mRNA analysis, and small RNA analysis. For our epigenomics project, for example, the option to use all of these applications on a single platform is really powerful.
Where do you plan on taking the Genome Analyzer next?
Dr. Meyers: We are collaborating with Drs. Steve Jacobson and Matteo Pellegrini from the University of California, Los Angeles, as well as Dr. Guo-liang Wang of the Ohio State University on a rice epigenomics grant. We are hoping to use the Genome Analyzer to look at DNA histone modifications and DNA methylation in different rice varieties and mutants. As an example, there already have been a number of high impact papers in the human genome using ChIP-Seq. We intend to take a similar approach in rice.
Back to Dr. Green and Dr. Meyers’ Profiles.