Research

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

Michael F Covington^1,2 , Julin N Maloof¹ , Marty Straume^3,4 , Steve A Kay^5,6 and Stacey L Harmer¹

¹  Department of Plant Biology, College of Biological Sciences, One Shields Avenue, University of California, Davis, California 95616, USA

²  Present address: Department of Biochemistry and Cell Biology, Rice University, Main Street, Houston, Texas 77005, USA

³  Center for Biomathematical Technology, Box 800735, University of Virginia Health Sciences System, Charlottesville, Virginia 22908, USA

⁴  Present address: Customized Online Biomathematical Research Applications, Glenaire Drive, Charlottesville, Virginia 22901, USA

⁵  Department of Biochemistry, The Scripps Research Institute, North Torrey Pines Road, La Jolla, California 92037, USA

⁶  Present address: Section of Cell and Developmental Biology, University of California at San Diego, Gilman Drive, La Jolla, California 92093, USA

author email corresponding author email

Genome Biology 2008, 9:R130doi:10.1186/gb-2008-9-8-r130

Published:	18 August 2008

Subject areas: Genome studies, Physiology, Plant biology

Abstract

Background

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.

Results

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.

Conclusion

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 promoters of genes with four discrete phases, which may contribute to the time-of-day specific changes in the transcript abundance of these genes. Clock-regulated genes are over-represented among all of the classical plant hormone and multiple stress response pathways, suggesting that all of these pathways are influenced by the circadian clock. Further exploration of the links between the clock and these pathways will lead to a better understanding of how the circadian clock affects plant growth and leads to improved fitness.