Arabidopsis 2010: Development of a genome-scale cell type-specific gene expression map

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Pattern formation in developmental fields is a dynamic process. It involves generation of specific cell types in a correct spatio-temporal sequence. Therefore, deciphering gene networks that underlie cell fate transitions requires new approaches aimed at assaying genome scale expression patterns of genes at a single cell type resolution. Shoot apical meristems (SAMs) of higher plants harbor a set of stem-cells and provide cells for the development of all the above-ground biomass of plants. Most of the important pattern formation events such as maintenance of stem-cell identity, specification and differentiation of leaf/flower primordia, and the temporal control of transition from vegetative to reproductive program are determined in the SAMs. Genetic analysis has revealed molecular and hormonal pathways involved in stem-cell maintenance, organ differentiation and flowering time. However, limited information is available as to how different pathways interact with each other to function as a network in specifying different cell types and their function. A major requirement for analyzing developmental gene networks is to determine gene expression profiles of different cell types, at a single cell type resolution. In this project, the PI and the co-PI will combine novel experimental approaches and bioinformatics analysis to generate a cell type-specific, genome-scale, expression map of the Arabidopsis shoot apex. The experimental methods of protoplasting SAMs cells, FACS-mediated sorting of fluorescently labeled protoplasts, fluorescently tagged transgenic seeds, the cell type specific microarray data, the relevant scripts and analysis tools such as PostgreSQL for the database backend, Python for its interface and R, JavaScript and Perl libraries for the online analysis and graphical tools will be available for download (www.CySAM.org). In addition, training will be provided for a post-doctoral fellow, and graduate and under-graduate students in designing new methods of isolation and separation of fluorescently labeled protoplasts and bioinformatic analysis of microarray data. The Center for Plant Cell Biology (CEPCEB) at UCR runs an NSF-sponsored REU program for undergraduates without research experience. Most students for this program are recruited from community colleges. The undergraduate students for this project will be recruited from the REU program and they will be exposed to state-of-the art cell isolation, genomic and bioinformatic technologies.