Circadian Control of Global Gene Expression Patterns

Doherty, Colleen J.; Kay, Steve A.

doi:10.1146/annurev-genet-102209-163432

Cited by 270 publications

(234 citation statements)

References 143 publications

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“…Our study revealed a positive feedback loop consisting of LWD1 and PRR9 in the Arabidopsis circadian clock (Figure 9). Positive and negative feedback loops exist in the circadian clock of many model organisms (for review, see Doherty and Kay, 2010). Negative feedback loops can contribute to the clock's function in building the 24-h oscillation.…”

Section: Discussion Lwd1 and Prr9 Constitute A Positive Feedback Loopmentioning

confidence: 99%

LIGHT-REGULATED WD1 and PSEUDO-RESPONSE REGULATOR9 Form a Positive Feedback Regulatory Loop in the Arabidopsis Circadian Clock

et al. 2011

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In Arabidopsis thaliana, central circadian clock genes constitute several feedback loops. These interlocking loops generate an ;24-h oscillation that enables plants to anticipate the daily diurnal environment. The identification of additional clock proteins can help dissect the complex nature of the circadian clock. Previously, LIGHT-REGULATED WD1 (LWD1) and LWD2 were identified as two clock proteins regulating circadian period length and photoperiodic flowering. Here, we systematically studied the function of LWD1/2 in the Arabidopsis circadian clock. Analysis of the lwd1 lwd2 double mutant revealed that LWD1/ 2 plays dual functions in the light input pathway and the regulation of the central oscillator. Promoter:luciferase fusion studies showed that activities of LWD1/2 promoters are rhythmic and depend on functional PSEUDO-RESPONSE REGULATOR9 (PRR9) and PRR7. LWD1/2 is also needed for the expression of PRR9, PRR7, and PRR5. LWD1 is preferentially localized within the nucleus and associates with promoters of PRR9, PRR5, and TOC1 in vivo. Our results support the existence of a positive feedback loop within the Arabidopsis circadian clock. Further mechanistic studies of this positive feedback loop and its regulatory effects on the other clock components will further elucidate the complex nature of the Arabidopsis circadian clock.

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Section: Discussion Lwd1 and Prr9 Constitute A Positive Feedback Loopmentioning

confidence: 99%

LIGHT-REGULATED WD1 and PSEUDO-RESPONSE REGULATOR9 Form a Positive Feedback Regulatory Loop in the Arabidopsis Circadian Clock

et al. 2011

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“…Researchers have devised and evaluated many methods (see a short list in Doherty and Kay, 2010), each with strengths and weaknesses (e.g. Deckard et al, 2013;Wu et al, 2014).…”

Section: Introductionmentioning

confidence: 99%

MetaCycle: an integrated R package to evaluate periodicity in large scale data

et al. 2016

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Summary: Detecting periodicity in large scale data remains a challenge. While efforts have been made to identify best of breed algorithms, relatively little research has gone into integrating these methods in a generalizable method. Here, we present MetaCycle, an R package that incorporates ARSER, JTK_CYCLE and Lomb-Scargle to conveniently evaluate periodicity in time-series data. MetaCycle has two functions, meta2d and meta3d, designed to analyze two-dimensional and three-dimensional time-series datasets, respectively. Meta2d implements N-version programming concepts using a suite of algorithms and integrating their results. Availability and implementation: MetaCycle package is available on the CRAN repository (https:// cran.r-project

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“…The circadian clockwork allows plants to anticipate environmental changes and adapt their activity to the most appropriate time of day (18). In Arabidopsis thaliana, the core of the oscillator is composed of morning-and evening-expressed components that regulate their expression in a highly complex network of interconnections (19). The transcription factors CCA1 (CIRCADIAN CLOCK ASSOCIATED 1) (20), LHY (LATE ELONGATED HYPOCOTYL) (21), and the PSEUDO-RESPONSE REGU-LATOR (PRR) proteins (PRR9, -7, and -5) (22) have peak phases of expression during the day, whereas TOC1 (TIMING OF CAB EXPRESSION 1 or PRR1) (23,24), GI (GIGANTEA) (25,26), and the members of the Evening Complex (EC) (27), all have evening peak-phase oscillations.…”

mentioning

confidence: 99%

Ordered changes in histone modifications at the core of the Arabidopsis circadian clock

Malapeira

Khaitová

Más

2012

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

122

147

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Circadian clock function in Arabidopsis thaliana relies on a complex network of reciprocal regulations among oscillator components. Here, we demonstrate that chromatin remodeling is a prevalent regulatory mechanism at the core of the clock. The peak-to-trough circadian oscillation is paralleled by the sequential accumulation of H3 acetylation (H3K56ac, K9ac), H3K4 trimethylation (H3K4me3), and H3K4me2. Inhibition of acetylation and H3K4me3 abolishes oscillator gene expression, indicating that both marks are essential for gene activation. Mechanistically, blocking H3K4me3 leads to increased clock-repressor binding, suggesting that H3K4me3 functions as a transition mark modulating the progression from activation to repression. The histone methyltransferase SET DOMAIN GROUP 2/ARABIDOPSIS TRITHORAX RELATED 3 (SDG2/ATXR3) might contribute directly or indirectly to this regulation because oscillator gene expression, H3K4me3 accumulation, and repressor binding are altered in plants misexpressing SDG2/ATXR3. Despite divergences in oscillator components, a chromatin-dependent mechanism of clock gene activation appears to be common to both plant and mammal circadian systems.

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Circadian Control of Global Gene Expression Patterns

Cited by 270 publications

References 143 publications

LIGHT-REGULATED WD1 and PSEUDO-RESPONSE REGULATOR9 Form a Positive Feedback Regulatory Loop in the Arabidopsis Circadian Clock

LIGHT-REGULATED WD1 and PSEUDO-RESPONSE REGULATOR9 Form a Positive Feedback Regulatory Loop in the Arabidopsis Circadian Clock

MetaCycle: an integrated R package to evaluate periodicity in large scale data

Ordered changes in histone modifications at the core of the Arabidopsis circadian clock

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