Symposium V: From the soil to the seed

Abs # 50001: Developmental genomics: A global map of gene activity in the Arabidopsis root

Presenter:	Birnbaum, Kenneth , kdb4348@nyu.edu
Authors	Birnbaum, Kenneth  (A)   Shasha, Dennis E. (A)   Wang, Jean Y (B)   Jung, Jee W (A)   Lambert, Georgina M. (C)   Galbraith, David W (C)   Benfey, Philip N (B)
Affiliations:	(A): New York University (B): Duke University (C): University of Arizona, Tuscon
Web Site:	http://homepages.nyu.edu/~kdb4348/

Control over gene expression plays a large role in determining cell fate and patterning in plant development. Thus, genomic approaches to development require cell type or tissue specific expression profiles. We have developed a cell-type specific profiling method in which we protoplast plant cells expressing GFP in specific cell types, isolate marked protoplasts using a fluorescence activated cell sorter, and analyze transcription in single cell type populations with microarrays. Controls showed minimal changes in gene expression during the rapid protoplasting procedure. We also validated these “digital” expression patterns against more than 30 genes with known expression patterns in the root, showing an error rate of about 6%. This showed that the digital expression map yielded an accurate and reproducible view of gene expression in the Arabidopsis root. The majority of root-expressed transcripts are differentially regulated within the root, supporting the view that morphological specificity lies in transcriptional regulation at the cell and tissue level. These data were used to search for localized patterns that give clues to gene function and regulation. Clusters of co-expressed genes within domains of the root identify sets of genes responding to localized developmental cues such as hormones. We have developed computational methods of promoter analysis that allow us to account for combinatorial regulation of gene clusters by transcription factors. These analyses have yielded testable hypotheses on the regulatory elements involved in orchestrating root development. In addition, the data shows that gene duplication plays a paradoxical role in organ development. First, the potential for genetic redundancy is extremely high. For example, the majority of root-expressed transcription factors have a close duplicate with a similar expression pattern. Forward genetics appears to be biased away from discovering this large group of genes, suggesting that many co-expressed duplicated genes have functional overlap. Second, gene duplication also frequently results in pairs of similar genes with distinct expression domains within the root. In some cases, entire pathways exhibit these parallel expression patterns in a coordinated fashion. The implication is that gene duplication events frequently contribute to tissue and cell type specialization.