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Orchestrated Transcription of Key Pathways in Arabidopsis by the Circadian Clock
Stacey L. Harmer,1John B. Hogenesch,2Marty Straume,3Hur-Song Chang,4Bin Han,4Tong Zhu,4Xun Wang,4Joel A. Kreps,4Steve A. Kay12*
Like most organisms, plants have endogenous biological
clocks that coordinate internal events with the external environment.We used high-density oligonucleotide microarrays to examine geneexpression in Arabidopsis and found that 6% of the more
than 8000genes on the array exhibited circadian changes in
steady-statemessenger RNA levels. Clusters of circadian-regulated
genes werefound in pathways involved in plant responses to light and
otherkey metabolic pathways. Computational analysis of cycling genesallowed the identification of a highly conserved promoter motifthat we
found to be required for circadian control of gene expression.Our
study presents a comprehensive view of the temporal
compartmentalizationof physiological pathways by the circadian clock
in a eukaryote.
1 Department of Cell Biology, Scripps Research
Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.
2 Genomics Institute of the Novartis Research
Foundation, 3115 Merryfield Row, La Jolla, CA 92121, USA.
3 Center for Biomathematical Technology, NSF Center
for Biological Timing, Division of Endocrinology and Metabolism,
Department of Internal Medicine, University of Virginia,
Charlottesville, VA 22904, USA.
4 Novartis
Agricultural Discovery Institute, 3115 Merryfield Row, San Diego, CA
92121, USA.
*
To whom correspondence should be addressed. E-mail:
stevek{at}scripps.edu
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