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The Arabidopsis Translatome browser for visualization of translated mRNAs
Achievement/Results
NSF-ChemGen Integrative Graduate Education and Research Trainee Program fellow Charles Jang established an in silico platform for visualization of the distinct patterns of expression of over 17,000 genes in the model plant Arabidopsis thaliana. A question not easily addressed in a multicellular organism is, where and when is an individual gene active?
Researchers at the University of California, Riverside’s Center for Plant Cell Biology developed methods to capture messenger RNAs undergoing translation in cells of specific identity within multicellular organs. Charles Jang adapted the Electronic Fluorescent Pictograph (eFP) format developed by Nicholas Provart at the University of Toronto to display schematic representations of cell-specific expression data obtained for 21 mRNA populations under two growth conditions. The different mRNA populations included samples for root epidermis, cortex, endodermis, stele and phloem companion cells, as well as the shoot epidermis, guard cells, trichomes, mesophyll, bundle sheath and phloem companion cells. The dataset defined groups of genes with enriched or limited expression in individual cell types. By use of the Arabidopsis Translatome web browser, investigators can visualize the domains of expression of individual genes, examining the whole seedling or focusing on the root or shoot. Development of the Arabidopsis Translatome efp database for recognition of differentially expressed genes was supervised by biologist Julia Bailey-Serres and bioinformaticist Thomas Girke.
The Arabidopsis Translatome web browser: http://efp.ucr.edu/.
An eFP tool for visualization of Polysomal mRNAs (“Translatomes”) in Discrete Cell Populations of Arabidopsis Seedlings: Control and Hypoxia Stressed.
Mustroph, A., Zanetti, M.E., Jang, C.J., Holtan, H.E., Repetti, P.P., Galbraith, D.W., Girke, T. and Bailey-Serres, J. (2009), Profiling the Arabidopsis translatome in discrete cell types resolves altered cell-specific priorities in response to hypoxia. PNAS. 106(44):18843-18848. Online supplement: http://www.pnas.org/content/106/44/18843/suppl/...
Address Goals
The Arabidopsis Translatome web browser and the associated publication in the Proceedings of the National Academy of science are freely available via the web for other researchers. Users can visualize data for individual Arabidopsis genes. This tool and the accompanying dataset provide a rich source of gene expression information for plant biologists.
