Microarray Analysis of Diurnal and Circadian-Regulated Genes in Arabidopsis

Schaffer, Robert J.; Landgraf, Jeff; Accerbi, Monica; Simon, Vernadette; Larson, Matt; Wisman, Ellen

doi:10.2307/3871157

Cited by 72 publications

(95 citation statements)

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“…However, if the clock system is reset by the light-to-dark transition at dusk, expression of these genes should rise at a constant time after transfer to DD regardless of when LL begins. Expression of PnLHY and PnTOC1 exhibited circadian rhythms peaking approximately at circadian time (CT) 0 in the subjective morning and CT 8 in the subjective evening, respectively, consistent with peak times in circadian expression of LHY and TOC1 in Arabidopsis, 24,25 (Figure 1B,E, H, K, Supplementary Figure 1A-D). Expression of both of these genes also began to rise constantly from transfer to LL, indicating that circadian phases in expression of PnLHY and PnTOC1 are set by the dark-to-light transition without being affected by light-to-dark transitions (Figure 1B,E, H, K, Supplementary Figure 1A-D).…”

supporting

confidence: 68%

Differential effects of light-to-dark transitions on phase setting in circadian expression among clock-controlled genes in Pharbitis nil

Hayama

Mizoguchi

Coupland

2018

Plant Signaling & Behavior

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The circadian clock is synchronized by the day-night cycle to allow plants to anticipate daily environmental changes and to recognize annual changes in day length enabling seasonal flowering. This clock system has been extensively studied in Arabidopsis thaliana and was found to be reset by the dark to light transition at dawn. By contrast, studies on photoperiodic flowering of Pharbitis nil revealed the presence of a clock system reset by the transition from light to dark at dusk to measure the duration of the night. However, a Pharbitis photosynthetic gene was also shown to be insensitive to this dusk transition and to be set by dawn. Thus Pharbitis appeared to have two clock systems, one set by dusk that controls photoperiodic flowering and a second controlling photosynthetic gene expression similar to that of Arabidopsis. Here, we show that circadian mRNA expression of Pharbitis homologs of a series of Arabidopsis clock or clock-controlled genes are insensitive to the dusk transition. These data further define the presence in Pharbitis of a clock system that is analogous to the Arabidopsis system, which co-exists and functions with the dusk-set system dedicated to the control of photoperiodic flowering.

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supporting

confidence: 68%

Differential effects of light-to-dark transitions on phase setting in circadian expression among clock-controlled genes in Pharbitis nil

Hayama

Mizoguchi

Coupland

2018

Plant Signaling & Behavior

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“…Effects of longterm Pi deficiency on various water-soluble metabolites involved in P and C metabolism were also examined. 13 C-NMR spectroscopy analysis showed a reduction in the concentration of fumarate, whereas glutamine and arginine increased in Pi-deficient plants (Fig. 1F).…”

Section: Resultsmentioning

confidence: 99%

“…For studying long-term effects of Pi deficiency, surface-sterilized seeds were sown in square (12 ϫ 12 cm) Petri dishes on Murashige and Skoog (MS)͞10 medium, 0.5% sucrose, 0.8% agar, and supplemented with either 500 M (Pϩ) or 5 M (PϪ) Pi; plants were grown vertically (12). Because some Arabidopsis genes are regulated by diurnal rhythm and circadian clocks (13), the roots and the leaves were harvested separately at the beginning and at the end of the photoperiod and pooled. Samples were rinsed with distilled water, blot-dried, and frozen in liquid nitrogen.…”

Section: Methodsmentioning

confidence: 99%

“…Metabolite analysis was performed by NMR as described (18) on leaf extracts from the plants grown in Petri dishes in a medium without sucrose for 20 days. The plants were enriched with 13 C in a growth chamber that allowed accurate regulation of the atmospheric gas composition and environmental parameters. The growth chamber conditions were: 10-h photoperiod with 100 mol⅐m Ϫ2 ⅐s Ϫ1 light, 22͞18°C day͞night temperature, and 90% humidity.…”

Section: Real-time Quantitative Rt-pcr (Qrt-pcr) and Northern Analysismentioning

confidence: 99%

“…We thank P. Auroy and P. Richaud for the analysis of ionic content; M. Pean, S. Boiry, and the GRAP team for plant growth and 13 …”

mentioning

confidence: 99%

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A genome-wide transcriptional analysis using Arabidopsis thaliana Affymetrix gene chips determined plant responses to phosphate deprivation

Misson

Raghothama

Jain

et al. 2005

Proc. Natl. Acad. Sci. U.S.A.

816

942

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Phosphorus, one of the essential elements for plants, is often a limiting nutrient because of its low availability and mobility in soils. Significant changes in plant morphology and biochemical processes are associated with phosphate (Pi) deficiency. However, the molecular bases of these responses to Pi deficiency are not thoroughly elucidated. Therefore, a comprehensive survey of global gene expression in response to Pi deprivation was done by using Arabidopsis thaliana whole genome Affymetrix gene chip (ATH1) to quantify the spatio-temporal variations in transcript abundance of 22,810 genes. The analysis revealed a coordinated induction and suppression of 612 and 254 Pi-responsive genes, respectively. The functional classification of some of these genes indicated their involvement in various metabolic pathways, ion transport, signal transduction, transcriptional regulation, and other processes related to growth and development. This study is a detailed analysis of Pi starvation-induced changes in gene expression of the entire genome of Arabidopsis correlated with biochemical processes. The results not only enhance our knowledge about molecular processes associated with Pi deficiency, but also facilitate the identification of key molecular determinants for improving Pi use by crop species.

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The ups and downs of daily life: Profiling circadian gene expression in Drosophila

Etter

Ramaswami

2002

BioEssays

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Circadian rhythms are responsible for 24-hour oscillations in diverse biological processes. While the central genes governing circadian pacemaker rhythmicity have largely been identified, clock-controlled output molecules responsible for regulating rhythmic behaviors remain largely unknown. Two recent reports from McDonald and Rosbash(1) and Claridge-Chang et al.2 address this issue. By identifying a large number of genes whose mRNA levels show circadian oscillations, the reports provide important new information on the biology of circadian rhythm. In addition, the reports illustrate both the power and limitations of microarray-based methods for profiling mRNA expression on a genomic scale.

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Microarray Analysis of Diurnal and Circadian-Regulated Genes in Arabidopsis

Cited by 72 publications

References 0 publications

Differential effects of light-to-dark transitions on phase setting in circadian expression among clock-controlled genes in Pharbitis nil

Differential effects of light-to-dark transitions on phase setting in circadian expression among clock-controlled genes in Pharbitis nil

A genome-wide transcriptional analysis using Arabidopsis thaliana Affymetrix gene chips determined plant responses to phosphate deprivation

The ups and downs of daily life: Profiling circadian gene expression in Drosophila

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