Orchestrated Transcription of Key Pathways in Arabidopsis by the Circadian Clock

Abstract

Like most organisms, plants have endogenous biological clocks that coordinate internal events with the external environment. We used high-density oligonucleotide microarrays to examine gene expression in Arabidopsis and found that 6% of the more than 8000 genes on the array exhibited circadian changes in steady-state messenger RNA levels. Clusters of circadian-regulated genes were found in pathways involved in plant responses to light and other key metabolic pathways. Computational analysis of cycling genes allowed the identification of a highly conserved promoter motif that we found to be required for circadian control of gene expression. Our study presents a comprehensive view of the temporal compartmentalization of physiological pathways by the circadian clock in a eukaryote.

Comparison of global responses to mild deficiency and excess copper levels in Arabidopsis seedlings

“…55 In light of this, some Cu-regulated categories in our microarray well fit processes that have been previously reported to be circadian clock-regulated: ion homeostasis, osmotic stress responses and cell growth. 56,57 The SDH1-2 expression increased at Cu levels of 5 mM in the growth medium (Fig. 6b), which represented Cu supra-optimal supply (>20 mg Cu per gram of dry weight) (Fig.…”

Perchance to dream: Solving the mystery of sleep through genetic analysis

“…Although the function of "clock" genes in generating circadian rhythms is now firmly established, their implication in other molecular pathways is likely given their wide-spread expression throughout the organism and the large number and diversity of genes controlling fundamental biologic processes that are under the influence of "clock" genes in Arabidopsis, Drosophila, and the mouse (Harmer et al, 2000;Claridge-Chang et al, 2001;McDonald and Rosbash, 2001;Rutter et al, 2001;Panda et al, 2002a;Storch et al, 2002;Ueda et al, 2002). The distinct roles of circadian and homeostatic components in sleep regulation are often difficult to discern (Dijk and Czeisler, 1994).…”

Spatiotemporal Analysis of Localized Circadian Arrhythmias in Plant Roots

“…In higher plants, circadian clocks play crucial roles in regulating numerous biological processes, including gene expression, photosynthesis, water use, and flowering (Harmer, 2000;Nohales and Kay, 2016). An important characteristic of circadian clocks is their entrainment to environmental time cues (zeitgebers) such as changes in external light and temperature cycles (Nakamichi et al, 2004;Higashi et al, 2014).…”