Circadian oscillations in clock gene expression lead to a global rhythm of large parts of the transcriptome. (a) Oscillations of the Arabidopsis thaliana clock genes across the day. The open bar refers to day, the dark bar refers to night. The numbers indicate hours after lights on. Please note that the amplitude of the oscillations is arbitrarily chosen to be equal for all transcripts. (b) Blueprint of the circadian oscillator in Arabidopsis thaliana. The core loop consists of the Myb-type transcription factors CCA1 and LHY, and the Pseudo response regulator TOC1, which reciprocally regulate each others' oscillations. Interconnected with the core loop are the morning and the evening loops. In the morning loop, CCA1 and LHY activate PRR5, PRR7 and PRR9, which in turn leads to inhibition of CCA1 and LHY. In the evening loop, the evening complex (EC), a protein complex consisting of ELF3, ELF4 and LUX, inhibits expression of PRR9 and perhaps other PRRs. EC components are themselves rhythmic through repression by CCA1 and LHY. Additional transcription factors, such as RVE8 and CHE, modulate these interconnected loops. (c) Oscillations in the output genes can be accomplished through direct binding of rhythmically expressed clock proteins to phase modules in their promoters or via intermediate transcription factors (TF). In this way, transcripts are directed to different times of the day. As one example, components involved in metabolizing sugars produced through photosynthesis peak early in the day, and components involved in starch degradation, in turn, peak in the middle of the night .
Staiger et al. Genome Biology 2013 14:208 doi:10.1186/gb-2013-14-6-208