title: Genome-wide gene expression profiling in Arabidopsis thaliana reveals new targets of abscisic acid and largely impaired gene regulation in the abi1-1 mutant.
abstract: The phytohormone abscisic acid (ABA) plays important regulatory roles in many plant developmental processes including seed dormancy, germination, growth, and stomatal movements. These physiological responses to ABA are in large part brought about by changes in gene expression. To study genome-wide ABA-responsive gene expression we applied massively parallel signature sequencing (MPSS) to samples from Arabidopsis thaliana wildtype (WT) and abi1-1 mutant seedlings. We identified 1354 genes that are either up- or downregulated following ABA treatment of WT seedlings. Among these ABA-responsive genes, many encode signal transduction components. In addition, we identified novel ABA-responsive gene families including those encoding ribosomal proteins and proteins involved in regulated proteolysis. In the ABA-insensitive mutant abi1-1, ABA 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 ABA-responsive genes in WT Arabidopsis thaliana. 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 ABA. Regulation of the majority of the genes by ABA was impaired in the ABA-insensitive mutant abi1-1. However, a subset of genes continued to be appropriately regulated by ABA, which suggests the presence of at least two ABA signaling pathways, only one of which is blocked in abi1-1.
authors.affiliation: Laboratory of Plant Molecular Biology, The Rockefeller University, 1230 York Avenue, New York, NY 10021, USA.
authors.forename: Stefan
authors.initials: S
authors.lastname: Hoth
authors.forename: Michele
authors.initials: M
authors.lastname: Morgante
authors.forename: Juan-Pablo
authors.initials: JP
authors.lastname: Sanchez
authors.forename: Michael K
authors.initials: MK
authors.lastname: Hanafey
authors.forename: Scott V
authors.initials: SV
authors.lastname: Tingey
authors.forename: Nam-Hai
authors.initials: NH
authors.lastname: Chua
mesh_terms: D000040:Abscisic Acid / Q000494:pharmacology*; D017360:Arabidopsis / Q000235:genetics*; D001483:Base Sequence; D017931:DNA Primers; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant / Q000187:drug effects*; D018745:Genome, Plant; D009154:Mutation
chemical_list: D017931:DNA Primers; D000040:Abscisic Acid