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


CONCLUSIONS
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.
Hanano
Shigeru
S
Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, D-50829 Cologne, Germany. sh_hanano@bio-ribs.com
Stracke
Ralf
R
Jakoby
Marc
M
Merkle
Thomas
T
Domagalska
Malgorzata A
MA
Weisshaar
Bernd
B
Davis
Seth J
SJ
D017360:Arabidopsis / Q000235:genetics* / Q000502:physiology*; D029681:Arabidopsis Proteins / Q000235:genetics* / Q000502:physiology*; D001483:Base Sequence; D051792:Basic Helix-Loop-Helix Proteins / Q000235:genetics / Q000502:physiology; D050976:Basic-Leucine Zipper Transcription Factors / Q000235:genetics / Q000502:physiology; D002940:Circadian Rhythm / Q000235:genetics* / Q000502:physiology*; D017931:DNA Primers / Q000235:genetics; D018744:DNA, Plant / Q000235:genetics; D005246:Feedback; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D053263:Gene Regulatory Networks / Q000235:genetics / Q000502:physiology; D017343:Genes, Plant; D020570:Genes, myb; D009154:Mutation; D010641:Phenotype; D017440:Photoperiod; D030821:Plants, Genetically Modified; D014157:Transcription Factors / Q000235:genetics* / Q000502:physiology*
D029681:Arabidopsis Proteins; D051792:Basic Helix-Loop-Helix Proteins; D050976:Basic-Leucine Zipper Transcription Factors; D017931:DNA Primers; D018744:DNA, Plant; D014157:Transcription Factors