Global transcriptome analysis reveals circadian regulation of key pathways in plant growth and development.

Genome Biology
Michael F CovingtonStacey L Harmer

Abstract

As nonmotile organisms, plants must rapidly adapt to ever-changing environmental conditions, including those caused by daily light/dark cycles. One important mechanism for anticipating and preparing for such predictable changes is the circadian clock. Nearly all organisms have circadian oscillators that, when they are in phase with the Earth's rotation, provide a competitive advantage. In order to understand how circadian clocks benefit plants, it is necessary to identify the pathways and processes that are clock controlled. We have integrated information from multiple circadian microarray experiments performed on Arabidopsis thaliana in order to better estimate the fraction of the plant transcriptome that is circadian regulated. Analyzing the promoters of clock-controlled genes, we identified circadian clock regulatory elements correlated with phase-specific transcript accumulation. We have also identified several physiological pathways enriched for clock-regulated changes in transcript abundance, suggesting they may be modulated by the circadian clock. Our analysis suggests that transcript abundance of roughly one-third of expressed A. thaliana genes is circadian regulated. We found four promoter elements, enriched in the pro...Continue Reading

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Citations

Jul 21, 2011·Protoplasma·David SeungJan Marc
Apr 22, 2009·Proceedings of the National Academy of Sciences of the United States of America·Patrick G StephensonMatthew J Terry
Oct 7, 2009·Proceedings of the National Academy of Sciences of the United States of America·Reetika RawatStacey L Harmer
Feb 6, 2010·Proceedings of the National Academy of Sciences of the United States of America·Bryan Thines, Frank G Harmon
Feb 4, 2011·Proceedings of the National Academy of Sciences of the United States of America·Kyoko BabaRishikesh P Bhalerao
Dec 1, 2010·Proceedings of the National Academy of Sciences of the United States of America·Matthew A JonesStacey L Harmer
Nov 2, 2011·Proceedings of the National Academy of Sciences of the United States of America·Ann AtwoodSteve A Kay
Feb 15, 2012·Proceedings of the National Academy of Sciences of the United States of America·Danielle GoodspeedMichael F Covington
Mar 2, 2012·Proceedings of the National Academy of Sciences of the United States of America·Georg Jander
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Methods Mentioned

BETA
environmental stresses
environmental stress
PCR

Software Mentioned

Weeder
AlignACE
Affymetrix MAS5 .
MapMan
Clustal
R
COSOPT
MotifSampler
Perl

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