title: Global transcriptome analysis reveals circadian regulation of key pathways in plant growth and development.
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.
  
  
  CONCLUSIONS
  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.
authors: Department of Plant Biology, College of Biological Sciences, One Shields Avenue, University of California, Davis, California 95616, USA.
authors: Michael F
authors: MF
authors: Covington
authors: Julin N
authors: JN
authors: Maloof
authors: Marty
authors: M
authors: Straume
authors: Steve A
authors: SA
authors: Kay
authors: Stacey L
authors: SL
authors: Harmer
mesh_terms: D000040:Abscisic Acid / Q000096:biosynthesis; D017360:Arabidopsis / Q000235:genetics / Q000254:growth & development* / Q000378:metabolism; D029681:Arabidopsis Proteins / Q000235:genetics* / Q000502:physiology; D002940:Circadian Rhythm; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D018745:Genome, Plant; D020411:Oligonucleotide Array Sequence Analysis; D020133:Reverse Transcriptase Polymerase Chain Reaction; D015398:Signal Transduction / Q000235:genetics; D013729:Terpenes / Q000378:metabolism; D014157:Transcription Factors / Q000235:genetics* / Q000502:physiology
chemical_list: D029681:Arabidopsis Proteins; D013729:Terpenes; D014157:Transcription Factors; D000040:Abscisic Acid