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The Plant Cell, Vol. 14, 2481-2494, October 2002, Copyright © 2002,
American Society of Plant Biologists

Expression Profile Analysis of the Low-Oxygen Response in Arabidopsis Root Cultures

Erik Jan Klok1,a, Iain W. Wilsona, Dale Wilsonb, Scott C. Chapmanc, Rob M. Ewingd, Shauna C. Somervillee, W. James Peacocka, Rudy Dolferusa and Elizabeth S. Dennisa

a Commonwealth Scientific and Industrial Research Organization Plant Industry, Canberra, Australian Capital Territory 2601, Australia
b Commonwealth Scientific and Industrial Research Organization Mathematical and Information Sciences, Macquarie University, North Ryde, New South Wales, Australia
c Commonwealth Scientific and Industrial Research Organization Plant Industry, Long Pocket Laboratories, Indooroopilly, Queensland 4068, Australia
d Incyte Genomics, Palo Alto, California 94043
e Department of Plant Biology, Carnegie Institution of Washington, Stanford, California 94305

1 To whom correspondence should be addressed. E-mail erikjan.klok{at}csiro.au; fax 61-2-6246-5000

We used DNA microarray technology to identify genes involved in the low-oxygen response of Arabidopsis root cultures. A microarray containing 3500 cDNA clones was screened with cDNA samples taken at various times (0.5, 2, 4, and 20 h) after transfer to low-oxygen conditions. A package of statistical tools identified 210 differentially expressed genes over the four time points. Principal component analysis showed the 0.5-h response to contain a substantially different set of genes from those regulated differentially at the other three time points. The differentially expressed genes included the known anaerobic proteins as well as transcription factors, signal transduction components, and genes that encode enzymes of pathways not known previously to be involved in low-oxygen metabolism. We found that the regulatory regions of genes with a similar expression profile contained similar sequence motifs, suggesting the coordinated transcriptional control of groups of genes by common sets of regulatory factors.




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