Arabidopsis 2010: Next Generation Cellular Resolution Profiling of the Transcriptome and Epigenome

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The purpose of the project is to develop and apply methods to sequence translating messenger RNA from specific cell types. An important deficit in current experiments that obtain the list of active genes in plant tissue is that the tissue used comes from a mixture of different cell types, for example, it uses whole flowers or whole seedlings, each of which is made up of many different types of cells. The resulting data on active genes is useful, but is information on the activity of genes from many cells that have different collections of active genes. As cell-type-specific data are necessary to infer gene regulatory networks, current types of data are inadequate to understand a complex organ like a leaf, shoot, or flower. The research will use developing flowers as a system, will adapt existing methods and develop new methods to isolate cell-type specific RNA, and to perform detailed sequencing of the RNA from individual cell types of the developing flower. The result will be a set of tested methods that allow researchers to isolate messenger RNA from single cell types found in complex tissues, and therefore to record patterns and changing patterns of gene activity from each of the single cell types found in developing organs.Broader ImpactsThe broader impacts of the project are in three areas. First, the completion of the proposed research will result in new technologies for the entire plant science community to study RNA and gene activity at cellular resolution in virtually any cell type, which is expected to be crucial for the understanding of various questions from development to energy capture and response to the environment. All the methods and lines generated through this project, which will enable cell-type specific analysis in other laboratories, including those of young and starting researchers who would have to spend considerable time to make such lines, will be made freely available to the research community. Second, by being partly established within the environment of a much larger group of undergraduate students, graduate students, postdoctoral fellows and technical staff that are engaged in different research projects on Arabidopsis and animal development (the Meyerowitz laboratory and the personnel of the Caltech Jacobs Center for Genetics and Genomics), the project will provide familiarity with a variety of genomic technologies and approaches to a substantial pool of future independent investigators. This pool will include undergraduate summer researchers and students from underrepresented minorities recruited through established programs at Caltech. Finally, public outreach and training activities will include provision of the materials generated (especially images) for the "Grounding in Botany" program, a collaboration between the Meyerowitz lab and the Huntington Botanical Gardens, in which laboratory exercises using plants are developed by teachers for high school classrooms; and for a program in which graduate students and postdoctoral scholars from Caltech spend up to six weeks at the Exploratorium in San Francisco, teaching high school and elementary science teachers in a summer teacher training program.