Open Access Highly Accessed Research article

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

Shigeru Hanano13, Ralf Stracke12, Marc Jakoby1, Thomas Merkle2, Malgorzata A Domagalska14, Bernd Weisshaar12 and Seth J Davis1*

Author Affiliations

1 Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, D-50829 Cologne, Germany

2 Bielefeld University, Department of Biology, Chair of Genome Research, D-33594 Bielefeld, Germany

3 Research Institute for Biological Sciences OKAYAMA Okayama 716-1241 Japan

4 Department of Biology, University of York. PO Box 373, York, YO10 5YW; UK

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BMC Genomics 2008, 9:182  doi:10.1186/1471-2164-9-182

Published: 21 April 2008



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.


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.


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.