A systematic survey in Arabidopsis thaliana of transcription factors that modulate circadian parameters

Shigeru Hanano, Ralf Stracke, Marc Jakoby, Thomas Merkle, Malgorzata A Domagalska, Bernd Weisshaar, Seth J Davis

Research output: Contribution to journalA1: Web of Science-articlepeer-review


BACKGROUND: Plant circadian systems regulate various biological processes in harmony with daily environmental changes. In Arabidopsis thaliana, the underlying clock mechanism is comprised of multiple integrated transcriptional feedbacks, which collectively lead to global patterns of rhythmic gene expression. The transcriptional networks are essential within the clock itself and in its output pathway.

RESULTS: Here, to expand understanding of transcriptional networks within and associated to the clock, we performed both an in silico analysis of transcript rhythmicity of transcription factor genes, and a pilot assessment of functional phenomics on the MYB, bHLH, and bZIP families. In our in silico analysis, we defined which members of these families express a circadian waveform of transcript abundance. Up to 20% of these families were over-represented as clock-controlled genes. To detect members that contribute to proper oscillator function, we systematically measured rhythmic growth via an imaging system in hundreds of misexpression lines targeting members of the transcription-factor families. Three transcription factors were found that conferred aberrant circadian rhythms when misexpressed: MYB3R2, bHLH69, and bHLH92.

CONCLUSION: Transcript abundance of many transcription factors in Arabidopsis oscillates in a circadian manner. Further, a developed pipeline assessed phenotypic contribution of a panel of transcriptional regulators in the circadian system.

Original languageEnglish
Article number182
JournalBMC Genomics
Publication statusPublished - 2008
Externally publishedYes


  • Arabidopsis
  • Arabidopsis Proteins
  • Base Sequence
  • Basic Helix-Loop-Helix Transcription Factors
  • Basic-Leucine Zipper Transcription Factors
  • Circadian Rhythm
  • DNA Primers
  • DNA, Plant
  • Feedback
  • Gene Expression Profiling
  • Gene Expression Regulation, Plant
  • Gene Regulatory Networks
  • Genes, Plant
  • Genes, myb
  • Mutation
  • Phenotype
  • Photoperiod
  • Plants, Genetically Modified
  • Transcription Factors
  • Journal Article
  • Research Support, Non-U.S. Gov't


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