T2011 Ostreococcus clock, TOC1 degr D - PLM_90, version 1, SUBMITTED
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ABSTRACT:
SUBMITTER: BioData SynthSys
PROVIDER: 523 | FAIRDOMHub | 2019-01-10
REPOSITORIES: FAIRDOMHub
Similar Datasets
Project description:To gain insights into the mechanisms of TOC1 function in the Arabidopsis circadian clock we performed transcriptional profiling of Wild-Type (WT) and and TOC1 overexpressor plants (TOC1-ox).
2009-09-09 | GSE18007 | GEO
Project description:To gain insights into the mechanisms of TOC1 function in the Arabidopsis circadian clock we performed transcriptional profiling of Wild-Type (WT) and and TOC1 mutant plants (toc1-2) under constant light conditions for two days.
2009-09-09 | GSE18001 | GEO
Project description:The first described feedback loop of the Arabidopsis circadian clock is based on reciprocal regulation between TOC1 and CCA1/LHY. CCA1 and LHY are MYB transcription factors that bind directly to the TOC1 promoter to negatively regulate its expression. Conversely, the activity of TOC1 has remained less well characterized. Genetic data supports that TOC1 is necessary for the reactivation of CCA1/LHY, but there is little description of its biochemical function. Here we show that TOC1 occupies specific genomic regions in the CCA1 and LHY promoters. Purified TOC1 binds directly to DNA through its CCT domain, which is similar to known DNA binding domains. Chemical induction and transient overexpression of TOC1 in Arabidopsis seedlings cause repression of CCA1/LHY expression demonstrating that TOC1 can repress direct targets, and mutation or deletion of the CCT domain prevents this repression showing that DNA binding is necessary for TOC1 action. Furthermore, we use the Gal4/UAS system in Arabidopsis to show that TOC1 acts as a general transcriptional repressor, and that repression activity is in the Pseudoreceiver (PR) domain of the protein. To identify the genes regulated by TOC1 on a genomic scale, we couple TOC1 chemical induction with microarray analysis and identify new potential TOC1 targets and output pathways. Together these results define the biochemical action of the core clock protein TOC1 and refine our perspective on how plant clocks function. Keywords: Expression profiling by array
2012-01-15 | GSE34897 | GEO
Project description:To gain insights into the mechanisms of TOC1 function in the Arabidopsis circadian clock we performed transcriptional profiling of Wild-Type (WT) and and TOC1 overexpressor plants (TOC1-ox). Experiment Overall Design: Comparisons of WT and TOC1-ox. Three biological replicates synchronized under 12-hour light:12-hour dark (LD) cycles for 12 days. Samples were collected at Zeitgeber Time 15 (ZT15).
2009-09-18 | E-GEOD-18007 | biostudies-arrayexpress
Project description:To gain insights into the mechanisms of TOC1 function in the Arabidopsis circadian clock we performed transcriptional profiling of Wild-Type (WT) and and TOC1 mutant plants (toc1-2) under constant light conditions for two days. Comparisons of WT and toc1-2. Two biological replicates each per array. Two Arabidopsis Oligonucleotide Microarrays (two-color Cy3 and Cy5). synchronized under 12-hour light:12-hour dark (LD) cycles for 10 days followed by two days under constant light conditions. Samples were collected at circadian time 16 (CT16).
2010-05-05 | E-GEOD-18001 | biostudies-arrayexpress
Project description:The first described feedback loop of the Arabidopsis circadian clock is based on reciprocal regulation between TOC1 and CCA1/LHY. CCA1 and LHY are MYB transcription factors that bind directly to the TOC1 promoter to negatively regulate its expression. Conversely, the activity of TOC1 has remained less well characterized. Genetic data supports that TOC1 is necessary for the reactivation of CCA1/LHY, but there is little description of its biochemical function. Here we show that TOC1 occupies specific genomic regions in the CCA1 and LHY promoters. Purified TOC1 binds directly to DNA through its CCT domain, which is similar to known DNA binding domains. Chemical induction and transient overexpression of TOC1 in Arabidopsis seedlings cause repression of CCA1/LHY expression demonstrating that TOC1 can repress direct targets, and mutation or deletion of the CCT domain prevents this repression showing that DNA binding is necessary for TOC1 action. Furthermore, we use the Gal4/UAS system in Arabidopsis to show that TOC1 acts as a general transcriptional repressor, and that repression activity is in the Pseudoreceiver (PR) domain of the protein. To identify the genes regulated by TOC1 on a genomic scale, we couple TOC1 chemical induction with microarray analysis and identify new potential TOC1 targets and output pathways. Together these results define the biochemical action of the core clock protein TOC1 and refine our perspective on how plant clocks function. Keywords: Expression profiling by array wild type (Col-0) and ALC::TOC1 were sown on Murashige-Skoog with 0.8% agar, stratified for 48 hours and grown in12:12 light:dark (LD) for 12 days and either left in LD or transferred to constant light (LL) and then grown for one more day before the start of the experiment. Tissue was submerged in Murashige-Skoog media supplemented with 2.5% ethanol or no ethanol (mock) and with 20mM MG132 for 3 hours and harvested at ZT1. Three replicates each of the seedlings were collected and frozen in liquid nitrogen.
2012-01-15 | E-GEOD-34897 | biostudies-arrayexpress
Project description:Pokhilko2013 - TOC1 signalling in Arabidopsis
circadian clock
In this model, Pokhilko
et al. has incorporated the negative transcriptional
regulations of the core clock genes by TOC1 and the up-regulation
of TOC1 expression by ABA signalling, to their previous model
BIOMD0000000412
This model is described in the article:
Modelling the widespread
effects of TOC1 signalling on the plant circadian clock and its
outputs.
Pokhilko A, Mas P, Millar AJ.
BMC Syst Biol 2013; 7: 23
Abstract:
BACKGROUND: 24-hour biological clocks are intimately
connected to the cellular signalling network, which complicates
the analysis of clock mechanisms. The transcriptional regulator
TOC1 (TIMING OF CAB EXPRESSION 1) is a founding component of
the gene circuit in the plant circadian clock. Recent results
show that TOC1 suppresses transcription of multiple target
genes within the clock circuit, far beyond its
previously-described regulation of the morning transcription
factors LHY (LATE ELONGATED HYPOCOTYL) and CCA1 (CIRCADIAN
CLOCK ASSOCIATED 1). It is unclear how this pervasive effect of
TOC1 affects the dynamics of the clock and its outputs. TOC1
also appears to function in a nested feedback loop that
includes signalling by the plant hormone Abscisic Acid (ABA),
which is upregulated by abiotic stresses, such as drought. ABA
treatments both alter TOC1 levels and affect the clock's timing
behaviour. Conversely, the clock rhythmically modulates
physiological processes induced by ABA, such as the closing of
stomata in the leaf epidermis. In order to understand the
dynamics of the clock and its outputs under changing
environmental conditions, the reciprocal interactions between
the clock and other signalling pathways must be integrated.
RESULTS: We extended the mathematical model of the plant clock
gene circuit by incorporating the repression of multiple clock
genes by TOC1, observed experimentally. The revised model more
accurately matches the data on the clock's molecular profiles
and timing behaviour, explaining the clock's responses in TOC1
over-expression and toc1 mutant plants. A simplified
representation of ABA signalling allowed us to investigate the
interactions of ABA and circadian pathways. Increased ABA
levels lengthen the free-running period of the clock,
consistent with the experimental data. Adding stomatal closure
to the model, as a key ABA- and clock-regulated downstream
process allowed to describe TOC1 effects on the rhythmic gating
of stomatal closure. CONCLUSIONS: The integrated model of the
circadian clock circuit and ABA-regulated environmental sensing
allowed us to explain multiple experimental observations on the
timing and stomatal responses to genetic and environmental
perturbations. These results crystallise a new role of TOC1 as
an environmental sensor, which both affects the pace of the
central oscillator and modulates the kinetics of downstream
processes.
This model is hosted on
BioModels Database
and identified by:
BIOMD0000000445.
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2024-09-02 | BIOMD0000000445 | BioModels
Project description:The circadian clock is comprised of proteins that form negative feedback loops, which regulate the timing of global gene expression in a coordinated 24 hour cycle. As a result, the plant circadian clock is responsible for regulating numerous physiological processes central to growth and survival. To date, most plant circadian clock studies have relied on diurnal transcriptome changes to elucidate molecular connections between the circadian clock and observable phenotypes in wild-type plants. Here, we have combined high-throughput RNA-sequencing and mass spectrometry to comparatively characterize the lhycca1, prr7prr9, gi and toc1 circadian clock mutant rosette transcriptome and proteome at the end-of-day and end-of-night.
2018-01-02 | PXD004763 | Pride
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. Examination of TOC1 genome-wide binding using TOC1 Minigene (TMG) seedlings expressing the genomic fragment of TOC1 fused to the Yellow Fluorescent Protein in a toc1-2 mutant background (TMG-YFP/toc1-2 seedlings) grown under LD cycles (12h light:12h dark).
2012-03-08 | E-GEOD-35952 | biostudies-arrayexpress
Project description:Ostreococcus tauri infected with the virus OtV5 over 10 hours
2012-01-15 | E-MEXP-3520 | biostudies-arrayexpress