Orchestrated transcription of key pathways in Arabidopsis by the circadian clock.

By S. Harmer, John B. Hogenesch, Martin Straume, H. Chang, B. Han, Tong Zhu, X. Wang, J. Kreps, Steve A. Kay. Science, 2000

1,714 citations recorded by the source corpus.

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.

Subfields: Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/fe670eb03eb4d0aa32329a12aede3276f5f977f7

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Molecular Biology

1. G. Coupland
2. C. R. McClung
3. Z. J. Chen
4. M. Schmid
5. Mark Stitt
6. Anusha Srikanth
7. S. Harmer
8. Alison M. Smith

In Plant Science

1. Z. J. Chen
2. C. R. McClung
3. G. Coupland
4. J. Takahashi
5. S. Harmer
6. M. Schmid
7. Mark Stitt
8. Anusha Srikanth

Citations in the corpus

• Minimal tool set for a prokaryotic circadian clock (2016, background): “Indeed, fbp also shows circadian expression patterns in Chlamydomonas reinhardtii [110] and Arabidopsis thaliana where its late-night peaks may reflect the great importance of these aldolases in higher plants for the mobilization of plastidic starch [111].”
• Plant Circadian Rhythms (2006, background): “Microarray analyses suggest that ;10% of all Arabidopsis genes regulated at the level of mRNA abundance and have identified multiple metabolic pathways under circadian control (Harmer et al., 2000; Schaffer et al., 2001).”
• The Arabidopsis sex1 Mutant Is Defective in the R1 Protein, a General Regulator of Starch Degradation in Plants, and Not in the Chloroplast Hexose Transporter (2001, result): “This finding is in agreement with those of Hammer et al. (2000), who observed that the SEX1 transcript was influenced by the circadian rhythms of the plant.”
• Mammalian circadian biology: elucidating genome-wide levels of temporal organization. (2004, background): “Schaffer R, Landgraf J, Accerbi M, Simon V, Larson M, Wisman E. Microarray analysis of diurnal and circadian-regulated genes in Arabidopsis.”
• Transcriptional Profiling Reveals Novel Interactions between Wounding, Pathogen, Abiotic Stress, and Hormonal Responses in Arabidopsis1,212 (2002, background): “Al- though the mechanism underlying the plant response to high salinity is not clear, gene activation has been widely documented to be an important response (Hasegawa et al., 2000).”
• Molecular Basis of Plant Cold Acclimation: Insights Gained from Studying the CBF Cold Response Pathway1 (2010, background): “The first indication that constant-light experiments were potentially missing important aspects of coldregulated gene expression was the finding that CBF3 and certain CBF regulon genes were subject to circadian regulation at normal growth temperatures (Harmer et al., 2000).”
• Plant Abiotic Stress (2005, background): “CBF expression is also influenced by the circadian rhythms (Harmer et al., 2000).”
• Sugars and Circadian Regulation Make Major Contributions to the Global Regulation of Diurnal Gene Expression in Arabidopsis[W][OA] (2005, background): “Figure 10A compares the time at which 373 circadian-regulated genes peak in a free-running circadian cycle (Harmer et al., 2000) and a diurnal light/dark cycle inCol-0.”