Genome-wide gene expression profiling in XXXX reveals new targets of abscisic acid and largely impaired gene regulation in the abi1-1 mutant.

@entity2272 @entity958
The phytohormone abscisic acid ( @entity2272 ) plays important regulatory roles in many plant developmental processes including seed dormancy, germination, growth, and stomatal movements. These physiological responses to @entity2272 are in large part brought about by changes in gene expression. To study genome-wide @entity2272 -responsive gene expression we applied massively parallel signature sequencing (MPSS) to samples from @entity958 wildtype (WT) and abi1-1 mutant seedlings. We identified 1354 genes that are either up- or downregulated following @entity2272 treatment of WT seedlings. Among these @entity2272 -responsive genes, many encode signal transduction components. In addition, we identified novel @entity2272 -responsive gene families including those encoding ribosomal proteins and proteins involved in regulated proteolysis. In the @entity2272 -insensitive mutant abi1-1, @entity2272 regulation of about 84.5% and 6.9% of the identified genes was impaired or strongly diminished, respectively; however, 8.6% of the genes remained appropriately regulated. Compared to other methods of gene expression analysis, the high sensitivity and specificity of MPSS allowed us to identify a large number of @entity2272 -responsive genes in WT @entity958 . The database given in our supplementary material (http://jcs.biologists.org/supplemental) provides researchers with the opportunity to rapidly assess whether genes of interest may be regulated by @entity2272 . Regulation of the majority of the genes by @entity2272 was impaired in the @entity2272 -insensitive mutant abi1-1. However, a subset of genes continued to be appropriately regulated by @entity2272 , which suggests the presence of at least two @entity2272 signaling pathways, only one of which is blocked in abi1-1.
