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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Various genetic interactions of GIGANTEA and EARLY FLOWERING 4 by a functional dominance during a day in Arabidopsis

ABSTRACT: Plants use their endogenous clock to regulate many physiological processes related to their survival and adaptability. GIGANTEA (GI), one of the clock proteins, contributes to the maintenance of circadian period length and amplitude and also regulates flowering time and hypocotyl growth in response to day length. In addition to GI, EARLY FLOWERING 4 (ELF4), another clock regulator, also contributes to these processes. However, little is known about the overall interactions between GI and ELF4 in Arabidopsis. In this study, we investigated the genetic interactions between GI and ELF4 in circadian output regulation. The results show that GI is dominant to ELF4 in flowering time determination, but ELF4 is dominant to GI in hypocotyl growth regulation. Moreover, GI and ELF4 have a synergistic effect on endogenous clock regulation. Further, gene expression profiling of gi-2, elf4, and gi-2 elf4 mutants confirmed that GI and ELF4 had differential dominant effects on circadian physiological outputs at dawn and dusk, respectively. This differential dominance of GI and ELF4 provides a potential means to achieve the diversity in the regulation of circadian physiological outputs including flowering time and hypocotyl growth. The genetic interactions between GI and ELF4 could be time-dependent functional dominance along a day, called temporal dominance hereafter. To test this hypothesis, we performed gene expression profiling of WT, gi-2, elf4 and gi elf4 plants at dawn (ZT1) and dusk (ZT16).

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Hee Jung Koo

PROVIDER: E-GEOD-32938 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Various genetic interactions of GIGANTEA and EARLY FLOWERING 4 by a functional dominance during a day in Arabidopsis

Project description:Plants use their endogenous clock to regulate many physiological processes related to their survival and adaptability. GIGANTEA (GI), one of the clock proteins, contributes to the maintenance of circadian period length and amplitude and also regulates flowering time and hypocotyl growth in response to day length. In addition to GI, EARLY FLOWERING 4 (ELF4), another clock regulator, also contributes to these processes. However, little is known about the overall interactions between GI and ELF4 in Arabidopsis. In this study, we investigated the genetic interactions between GI and ELF4 in circadian output regulation. The results show that GI is dominant to ELF4 in flowering time determination, but ELF4 is dominant to GI in hypocotyl growth regulation. Moreover, GI and ELF4 have a synergistic effect on endogenous clock regulation. Further, gene expression profiling of gi-2, elf4, and gi-2 elf4 mutants confirmed that GI and ELF4 had differential dominant effects on circadian physiological outputs at dawn and dusk, respectively. This differential dominance of GI and ELF4 provides a potential means to achieve the diversity in the regulation of circadian physiological outputs including flowering time and hypocotyl growth.

2012-07-01 | GSE32938 | GEO

Clock-dependent chromatin accessibility rhythms regulate circadian transcription

Project description:Chromatin organization plays a crucial role in gene regulation by controlling the accessibility of DNA to transcription machinery. While significant progress has been made in understanding the regulatory role of clock proteins in circadian rhythms, how chromatin organization affects circadian rhythms remains poorly understood. Here, we employed ATAC-seq (Assay for Transposase-Accessible Chromatin with Sequencing) on FAC-sorted Drosophila clock neurons to assess genome-wide chromatin accessibility at dawn and dusk over the circadian cycle. We observed significant oscillations in chromatin accessibility at promoter and enhancer regions of hundreds of genes, with enhanced accessibility either at dusk or dawn, which correlated with their peak transcriptional activity. Notably, genes with enhanced accessibility at dusk were enriched with E-box motifs, while those more accessible at dawn were enriched with VRI/PDP1-box motifs, indicating that they are regulated by the core circadian feedback loops, PER/CLK and VRI/PDP1, respectively. Further, we observed a complete loss of chromatin accessibility rhythms in per01 null mutants, with chromatin consistently accessible at both dawn and dusk, underscoring the critical role of Period protein in driving chromatin compaction during the repression phase at dawn. Together, this study demonstrates the significant role of chromatin organization in circadian regulation, revealing how the interplay between clock proteins and chromatin structure orchestrates the precise timing of biological processes throughout the day. This work further implies that variations in chromatin accessibility might play a central role in the generation of diverse circadian gene expression patterns in clock neurons.

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Transcription profiling of Arabidopsis wild-type and lwd1lwd2 double mutant to investigate the role of LWD1 and LWD2 in Arabidopsis photoperiod regulation

Project description:Transcriptome analysis has revealed a light-regulated WD (tryptophan and aspartate)-containing protein, LWD1. LWD1 and LWD2 share greater than 90% amino acid sequence homology. The lack of phenotype changes in the lwd1 or lwd2 single mutant implies that the proteins function redundantly. The lwd1lwd2 double mutant, however, has an early flowering phenotype under both long-day (LD) and short-day (SD) conditions. Functional complementation experiment revealed that LWDs are indeed responsible for the defect in photoperiod sensing in lwd1lwd2 double mutant plants. The expression of LWD1 exhibits a diurnal pattern and peaks before dawn. The period length of oscillator (CCA1, LHY, TOC1 and ELF4) and output (CCR2 and CAB2) genes in the lwd1lwd2 double mutant is significantly shorter than that in wild-type Arabidopsis under free running condition. Under entrainment conditions, the expression phase of oscillator (CCA1, LHY, TOC1 and ELF4) and output (GI, FKF1, CDF1, CO and FT) genes shifts ~3 hr forward in the lwd1lwd2 double mutant. Our data indicated that the early flowering phenotype in lwd1lwd2 plants is contributed by the significant phase shift of CO and, therefore, an increased expression of FT before dusk under SD conditions. Our data imply that LWD1/LWD2 proteins function in close proximity to the circadian oscillators for the regulation of photoperiod sensing. Experiment Overall Design: Two biological replicates were performed to examine the differential gene expression between wild-type and lwd1lwd2 double mutant. The plants were grown under 12 h L/ 12 h D for 31 days before harvesting their above ground tissues at ZT5-9.

2008-10-26 | E-GEOD-11762 | biostudies-arrayexpress

LWD1 and LWD2 in Arabidopsis photoperiod regulation

2008-10-08 | GSE11762 | GEO

The function of the GIGANTEA gene StGI.04 in potato: Uncovering a new function affecting the anthocyanin content of tuber skin

Project description:GIGANTEA (GI) is a plant-specific, circadian clock-regulated, nuclear protein with pleiotropic functions studied in many plant species. It is involved in flowering, circadian clock control, chloroplast biogenesis, carbohydrate metabolism, stress responses and synthesis of volatiles. In potato (Solanum tuberosum L.), however, only its role in tuber initiation is reported. Based on the findings in other plant species we hypothesized that the function of GI is not restricted to tuberization in potato. To test this hypothesis we repressed the expression of a GI gene, StGI.04 in the commercial potato cultivar ‘Désirée’ and investigated the effect of repression at morphological and transcriptome level. We found that, like GI in other plant species, StGI.04 influences the expression of the key genes of circadian clock, flowering, starch synthesis and stress responses. Furthermore, we detected a novel function of a GI gene in influencing the anthocyanin synthesis and skin colour of potato tubers.

2022-03-30 | GSE189956 | GEO

Circadian and diurnal expression data of Synechococcus

Project description:In the unicellular cyanobacterium, Synechococcus elongatus PCC 7942, essentially all promoter activities are under the control of the circadian clock in continuous light (LL) conditions. Here, we employed high-density oligonucleotide arrays to explore comprehensive profiles of genome-wide Synechococcus gene expression in wild type, kaiABC-null and kaiC-overexpressor strains under LL and continuous dark (DD) conditions. In the wild type strain more than 30% of transcripts significantly oscillated in a circadian fashion, peaking at subjective dawn and dusk. Such circadian control was nullified in kaiABC-null strains. Although KaiC has been proposed to globally repress gene expression, our analysis revealed that dawn expressing genes were upregulated by kaiC-overexpression, such that the clock was arrested at subjective dawn. Transfer of cells to continuous dark (DD) conditions from LL immediately suppressed expression of most of genes, while the clock keeps time even in the absence of transcriptional feedback. Thus, the Synechococcus genome seems primarily regulated by the light/dark cycles and dramatically modified by the protein-based circadian oscillator. Keywords: timecourse data (~48 hours under continuous light or darkness) from Synechococcus elongatus PCC 7942 (wild type, kaiABC-null, and inducible kaiC-overexpressor) strains

2009-08-01 | GSE14225 | GEO

The Evening Complex Establishes Repressive Chromatin Domains via H2A.Z-Nucleosome Deposition in Arabidopsis

Project description:The Evening Complex (EC) is a core component of the circadian clock, which represses target gene expression at the end of the day and integrates temperature information in order to coordinate environmental and endogenous signals. Despite its importance, the mechanism of EC function remains unknown. Here we show that the EC recruits repressive chromatin domains to regulate the evening transcriptome. The EC component EARLY FLOWERING 3 (ELF3) directly interacts with a protein from the Swi2/Snf2-Related 1 (SWR1) complex to control deposition of H2A.Z-nucleosomes at the EC target genes. The SWR1 components display a circadian oscillation in gene expression with a peak at dusk, suggesting that the circadian clock controls the expression and function of SWR1. In turn, SWR1 is required for the circadian clockwork as defects in SWR1 activity alters morning-expressed genes. The EC-SWR1 complex binds to the promoters of the core clock genes PSEUDORESPONSE REGULATOR 7 (PRR7) and PRR9 and catalyzes H2A.Z deposition coincident with their repression at dusk. This provides a mechanism by which the circadian clock temporally establishes repressive chromatin domains to shape oscillatory gene expression around dusk.

2020-01-22 | GSE109101 | GEO

Global Mapping at the Core of the Arabidopsis Circadian Clock Defines the Network Structure of the Oscillator

Project description:In many organisms, the circadian clock is composed of functionally coupled morning and evening oscillators that regulate the bouts of dawn and dusk activity. In Arabidopsis, oscillator coupling relies on a core loop in which the evening oscillator component TOC1 was proposed to activate a subset of morning-expressed oscillator genes. Our systems-biological approach overturns the current view of the Arabidopsis circadian clock showing that TOC1 does not function as an activator but as a timely-controlled general repressor of morning and evening oscillator components. Repression occurs through rhythmic binding to the promoters of all oscillator genes, suggesting a previously unexpected direct connection between the morning and evening loops.

2012-03-08 | GSE35952 | GEO

Function of CK2-alpha in a minimal circadian system

Project description:Casein Kinase 2 (CK2) is an evolutionarily conserved kinase protein that phosphorylates a plethora of cellular target protein involved in processes including DNA repair, cell cycle control, and circadian rhythms. CK2 is functionally conserved across all eukaryotes, although the substrate proteins identified in targeted experiments on a diverse range of complex tissues are often different. A growing interest exists to identify conserved, core signalling principles essential to eukaryotic life. To efficiently study generic roles of CK2 in the cellular circadian clock, we used a minimal eukaryotic model organism (Ostreococcus tauri). Overexpression of CK2 leads to a slow circadian rhythm, verifying functional conservation of CK2 in cellular timekeeping. CK2 activity contributes more strongly to the clock around dusk than around dawn, and analysis of the phospho-proteome at this time revealed a strong overrepresentation of potential CK2 sites. Large changes to the phospho-proteome are reported here upon overexpression of CK2, identifying a set of CK2-responsive phospho-sites. To identify more CK2-specific phosphorylation events, the phospho-proteome of cells treated with CK2 inhibitor were analysed and compared to the overexpression lines. We thus report a full inventory of the CK2-responsive phospho-proteome to inform studies into CK2 activity in the circadian clock of more complex tissues, as science moves to understand and modulate cellular circadian rhythms to help us negate the negative effects of shiftwork or cross-continental travel.

2015-08-11 | PXD000975 | Pride

GIGANTEA recruits deubiquitylases, UBP12 and UBP13, to regulate accumulation of the ZTL photoreceptor complex

Project description:ZEILUPE (ZTL), a blue light photoreceptor with E3 ubiquitin ligase activity, communicates end-of-day light conditions to the circadian clock. To function properly, ZTL protein must accumulate but not destablilize target clock transcription factors before dusk, while in the dark ZTL mediates degradation of target proteins. It is not clear how ZTL can accumulate to high levels in the ligh while its targets remain stable. Two deubiquitylating enzymes, UBIQUITIN-SPECIFIC PROTEASE 12 and UBIQUITIN-SPECIFIC PROTEASE 13 (UBP12 and UBP13), which regulate colock period and protein ubiquitylation in a manner opposite to ZTL, were shown to associate with the ZTL protein complex. Here we demonstrate that the ZTL light-dependent interacting partner GIGANTEA (GI), recruites UBP12 and UBP13 to the ZTL photoreceptor complex.

2019-08-22 | PXD014636 | Pride

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