The Plant Circadian Oscillator

McClung, C. Robertson

doi:10.3390/biology8010014

Cited by 132 publications

(138 citation statements)

References 158 publications

(207 reference statements)

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“…The plant circadian clock entrained by environmental stimuli coordinates biological processes on a daily basis and enables proper growth and development (1)(2)(3). The circadian oscillator consists of multiple interlocked transcriptional feedback loops, formed by the sequential induction of core-clock genes acting as reciprocal transcriptional repressors throughout the day (4). Through this regulatory system, about 30% of genes exhibit circadian oscillation in Arabidopsis thaliana based on microarray analyses (5).…”

Section: Introductionmentioning

confidence: 99%

The circadian clock shapes the Arabidopsis transcriptome by regulating alternative splicing and alternative polyadenylation

Yang

Sancar

et al. 2020

Journal of Biological Chemistry

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The circadian clock in plants temporally coordinates biological processes throughout the day, synchronizing gene expression with diurnal environmental changes. Circadian oscillator proteins are known to regulate the expression of clock-controlled plant genes by controlling their transcription. Here, using a high-throughput RNA-Seq approach, we examined genome-wide circadian and diurnal control of the Arabidopsis transcriptome, finding that the oscillation patterns of different transcripts of multitranscript genes can exhibit substantial differences and demonstrating that the circadian clock affects posttranscriptional regulation. In parallel, we found that two major posttranscriptional mechanisms, alternative splicing (AS; especially intron retention) and alternative polyadenylation (APA), display circadian rhythmicity resulting from oscillation in the genes involved in AS and APA. Moreover, AS-related genes exhibited rhythmic AS and APA regulation, adding another layer of complexity to circadian regulation of gene expression. We conclude that the Arabidopsis circadian clock not only controls transcription of genes but also affects their posttranscriptional regulation by influencing alternative splicing and alternative polyadenylation.

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Section: Introductionmentioning

confidence: 99%

The circadian clock shapes the Arabidopsis transcriptome by regulating alternative splicing and alternative polyadenylation

Yang

Sancar

et al. 2020

Journal of Biological Chemistry

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“…4C). Among the list of 49 TFs, six are part of the core circadian clock (ELF3, ELF4, PRR9, PRR7, PRR5, and TOC1), and a seventh, RVE1, integrates the circadian clock and auxin pathways (37,38). Based on the predicted targets of these TFs in the GENIE3 model, there are 11,559 B. rapa and 3387 Arabidopsis genes regulated by these 49 TFs, providing further support for the retention and novel innovation of the circadian network in B. rapa.…”

Section: Do Retained Multi-copy Circadian Regulated Genes Exhibit Genmentioning

confidence: 99%

Expansion of the circadian transcriptome inBrassica rapaand genome-wide diversification of paralog expression patterns

Greenham

Sartor

Zorich

et al. 2020

Preprint

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An important challenge of crop improvement strategies is assigning function to paralogs in polyploid crops. Gene expression is one method for determining the activity of paralogs; however, the majority of transcript abundance data represents a static point that does not consider the spatial and temporal dynamics of the transcriptome. Studies in Arabidopsis have estimated up to 90% of the transcriptome to be under diel or circadian control depending on the condition. As a result, time of day effects on the transcriptome have major implications on how we characterize gene activity. In this study, we aimed to resolve the circadian transcriptome in the polyploid crop Brassica rapa and explore the fate of multicopy orthologs of Arabidopsis circadian regulated genes. We performed a high-resolution time course study with 2 h sampling density to capture the genes under circadian control. Strikingly, more than two-thirds of expressed genes exhibited rhythmicity indicative of circadian regulation. To compare the expression patterns of paralogous genes, we developed a program in R called DiPALM (Differential Pattern Analysis by Linear Models) that analyzes time course data to identify transcripts with significant pattern differences. Using DiPALM, we identified genome-wide divergence of expression patterns among retained paralogs. Cross-comparison with a previously generated diel drought experiment in B. rapa revealed evidence for differential drought response for these diverging paralog pairs. Using gene regulatory network models we compared transcription factor targets between B. rapa and Arabidopsis circadian networks to reveal additional evidence for divergence in expression between B. rapa paralogs that may be driven in part by variation in conserved non coding sequences. These findings provide new insight into the rapid expansion and divergence of the transcriptional network in a polyploid crop and offer a new method for assessing paralog activity at the transcript level.SignificanceThe circadian regulation of the transcriptome leads to time of day changes in gene expression that coordinates environmental conditions with physiological responses. Brassica rapa, a morphologically diverse crop species, has undergone whole genome triplication since diverging from Arabidopsis resulting in an expansion of gene copy number. To examine how this expansion has influenced the circadian transcriptome we developed a new method for comparing gene expression patterns. This method facilitated the discovery of genome-wide expansion of expression patterns for genes present in multiple copies and divergence in temporal abiotic stress response. We find support for conserved sequences outside the gene body contributing to these expression pattern differences and ultimately generating new connections in the gene regulatory network.

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“…The daily rotation of the Earth generates approximately 24‐hr cycles of light and temperature. To coordinate their internal physiological responses to match the predicted external environment, most eukaryotic and some prokaryotic organisms have evolved a molecular timekeeping mechanism termed a circadian clock (Cohen & Golden, ; McClung, ; Takahashi, ). In plants, the circadian clock controls a diverse array of processes including photosynthesis, thermomorphogenesis, hormone signalling, the response to biotic and abiotic stress, and flowering time (Sanchez & Kay, ).…”

Section: Introductionmentioning

confidence: 99%

“…The evening complex composed of EARLY FLOWERING3, ELF4, and LUX ARRYTHMO (LUX) represses the expression of PRR9 and PRR7 from dusk, whereas TOC1 and PRR5 are degraded in the evening through their interaction with ZEITLUPE (ZTL) and GIGANTEA (GI; Herrero et al, , Kim et al, , Kolmos et al, , Nusinow et al, ). For a detailed discussion of the plant circadian oscillator, we point readers to recent reviews (McClung, ; Ronald & Davis, ).…”

Section: Introductionmentioning

confidence: 99%

Focusing on the nuclear and subnuclear dynamics of light and circadian signalling

Ronald

Davis

2019

Plant Cell & Environment

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Circadian clocks provide organisms the ability to synchronize their internal physiological responses with the external environment. This process, termed entrainment, occurs through the perception of internal and external stimuli. As with other organisms, in plants, the perception of light is a critical for the entrainment and sustainment of circadian rhythms. Red, blue, far-red, and UV-B light are perceived by the oscillator through the activity of photoreceptors. Four classes of photoreceptors signal to the oscillator: phytochromes, cryptochromes, UVR8, and LOV-KELCH domain proteins.In most cases, these photoreceptors localize to the nucleus in response to light and can associate to subnuclear structures to initiate downstream signalling. In this review, we will highlight the recent advances made in understanding the mechanisms facilitating the nuclear and subnuclear localization of photoreceptors and the role these subnuclear bodies have in photoreceptor signalling, including to the oscillator.We will also highlight recent progress that has been made in understanding the regulation of the nuclear and subnuclear localization of components of the plant circadian clock.

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The Plant Circadian Oscillator

Cited by 132 publications

References 158 publications

The circadian clock shapes the Arabidopsis transcriptome by regulating alternative splicing and alternative polyadenylation

The circadian clock shapes the Arabidopsis transcriptome by regulating alternative splicing and alternative polyadenylation

Expansion of the circadian transcriptome inBrassica rapaand genome-wide diversification of paralog expression patterns

Focusing on the nuclear and subnuclear dynamics of light and circadian signalling

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