Arabidopsis clock model P2011.1.2 - PLM_71, version 1, SIMPLIFIED
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SUBMITTER: BioData SynthSys
PROVIDER: 389 | FAIRDOMHub | 2019-12-20
REPOSITORIES: FAIRDOMHub
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Project description:Flis2015 - Plant clock gene circuit
(P2011.1.2 PLM_71 ver 1)
This model is described in the article:
Defining the robust
behaviour of the plant clock gene circuit with absolute RNA
timeseries and open infrastructure.
Flis A, Fernández AP, Zielinski
T, Mengin V, Sulpice R, Stratford K, Hume A, Pokhilko A, Southern
MM, Seaton DD, McWatters HG, Stitt M, Halliday KJ, Millar
AJ.
Open Biol 2015 Oct; 5(10):
Abstract:
Our understanding of the complex, transcriptional feedback
loops in the circadian clock mechanism has depended upon
quantitative, timeseries data from disparate sources. We
measure clock gene RNA profiles in Arabidopsis thaliana
seedlings, grown with or without exogenous sucrose, or in
soil-grown plants and in wild-type and mutant backgrounds. The
RNA profiles were strikingly robust across the experimental
conditions, so current mathematical models are likely to be
broadly applicable in leaf tissue. In addition to providing
reference data, unexpected behaviours included co-expression of
PRR9 and ELF4, and regulation of PRR5 by GI. Absolute RNA
quantification revealed low levels of PRR9 transcripts (peak
approx. 50 copies cell(-1)) compared with other clock genes,
and threefold higher levels of LHY RNA (more than 1500 copies
cell(-1)) than of its close relative CCA1. The data are
disseminated from BioDare, an online repository for focused
timeseries data, which is expected to benefit mechanistic
modelling. One data subset successfully constrained clock gene
expression in a complex model, using publicly available
software on parallel computers, without expert tuning or
programming. We outline the empirical and mathematical
justification for data aggregation in understanding highly
interconnected, dynamic networks such as the clock, and the
observed design constraints on the resources required to make
this approach widely accessible.
cL_m_degr, param m1, modified to ensure light rate > dark rate.
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2024-09-02 | BIOMD0000000597 | BioModels
Project description:The plant circadian clock exerts a critical role in the regulation of multiple biological processes including responses to biotic and abiotic stresses. It is estimated that the clock regulates up to 80% of the transcriptome in Arabidopsis, thus understanding the molecular mechanisms that control this rhythmic transcriptome requires identification of the targets of each clock component. The Arabidopsis core clock is partially comprised of a transcriptional regulatory loop between the MYB domain containing transcription factors CIRCADIAN CLOCK ASSOCIATED1 (CCA1) and LATE ELONGATED HYPOCOTYL (LHY), and TIMING OF CAB EXPRESSION1 (TOC1). As a key component of the clock, CCA1 is able to initiate and set the phase of clock-controlled rhythms. CCA1 regulates the transcription of several genes by directly binding to the evening element (EE) motif primarily found in the promoters of evening expressed genes. Using a genome-wide approach we have identified direct targets of CCA1 in plants grown in constant (LL) and driven conditions (LD). These CCA1 targets are enriched for a myriad of biological processes and stress responses. While many of these target genes are evening phased and contain the EE in their promoter regions, a significant subset is morning phased and lack an EE. Furthermore, several CCA1 targets do not cycle in either LL or LD or both. Expression analysis in CCA1 overexpressing plants confirms CCA1 regulation of analyzed targets. Our results emphasize an expanded role for the circadian clock in regulation of key pathways in Arabidopsis, and provide a comprehensive and solid resource for future functional studies.
2015-07-26 | GSE70533 | GEO
Project description:We used the recently developed Excision Repair-sequencing (XR-seq) method to study genome-wide repair of UV-induced DNA damage in Arabidopsis. We found that the repair of cyclobutane pyrimidine dimers for a large fraction of the genome is controlled by the joint actions of the circadian clock and transcription by RNA polymerase II. Arabidopsis has a relatively compact genome, and a large fraction of the genes are controlled by the circadian clock. Our data on the interface of these two global regulatory systems reveal very strong repair preference of the transcribed strands of Arabidopsis genes, 10 to 30% of which are circadian time-dependent. Thus, throughout the day, Arabidopsis exhibits enormous dynamic range in repair to cope with exposure to sunlight.
2018-04-17 | GSE108932 | GEO
Project description:Plants are sessile organisms that have acquired highly plastic developmental strategies to adapt to the environment. Among these processes, the floral transition is essential to ensure reproductive success and is finely regulated by several internal and external genetic networks. The photoperiodic pathway, which controls the plant response to day length, is one of the most important pathways controlling flowering. In Arabidopsis photoperiodic flowering, CONSTANS (CO) is the central gene activating the expression of the florigen FLOWERING LOCUS T (FT) in the leaves at the end of a long day. CO expression is strongly regulated by the circadian clock. However, to date, no evidence has been reported regarding a feedback loop from the photoperiod pathway back to the circadian clock. Using transcriptional networks, we have identified relevant network motifs regulating the interplay between the circadian clock and the photoperiod pathway. Gene expression, chromatin immunoprecipitation experiments and phenotypic analysis allowed us to elucidate the role of CO over the circadian clock. Plants with altered CO expression showed a different internal clock period, measured by daily rhythmic movements in the leaves. We show that CO is able to activate key genes related to the circadian clock, such as CCA1, LHY, PRR5 and GI, at the end of a long day by binding to specific sites on their promoters. Moreover, a significant number of PRR5 repressed target genes are upregulated by CO, and this could explain the phase transition promoted by CO. The CO-PRR5 complex interacts with the bZIP transcription factor HY5 and helps to localize the complex in the promoters of clock genes. Our results indicate that there may be a feedback loop in which CO communicates back to the circadian clock, feeding seasonal information to the circadian system.
2024-01-01 | GSE222657 | GEO
Project description:Plants are sessile organisms that have acquired highly plastic developmental strategies to adapt to the environment. Among these processes, the floral transition is essential to ensure reproductive success and is finely regulated by several internal and external genetic networks. The photoperiodic pathway, which controls the plant response to day length, is one of the most important pathways controlling flowering. In Arabidopsis photoperiodic flowering, CONSTANS (CO) is the central gene activating the expression of the florigen FLOWERING LOCUS T (FT) in the leaves at the end of a long day. CO expression is strongly regulated by the circadian clock. However, to date, no evidence has been reported regarding a feedback loop from the photoperiod pathway back to the circadian clock. Using transcriptional networks, we have identified relevant network motifs regulating the interplay between the circadian clock and the photoperiod pathway. Gene expression, chromatin immunoprecipitation experiments and phenotypic analysis allowed us to elucidate the role of CO over the circadian clock. Plants with altered CO expression showed a different internal clock period, measured by daily rhythmic movements in the leaves. We show that CO is able to activate key genes related to the circadian clock, such as CCA1, LHY, PRR5 and GI, at the end of a long day by binding to specific sites on their promoters. Moreover, a significant number of PRR5 repressed target genes are upregulated by CO, and this could explain the phase transition promoted by CO. The CO-PRR5 complex interacts with the bZIP transcription factor HY5 and helps to localize the complex in the promoters of clock genes. Our results indicate that there may be a feedback loop in which CO communicates back to the circadian clock, feeding seasonal information to the circadian system.
2023-08-01 | GSE236178 | GEO
Project description:Purpose: Circadian clock in plants temporally coordinates biological processes throughout the day synchronizing gene expression with environmental changes. Here, we examined the genome-wide circadian and diurnal control of Arabidopsis transcriptome using high throughout RNA-seq approach. Methods: Transcriptional and posttranscritional profiles were identified and characterized for Arabidopsis seedlings grown under continuous light or long-day condition (16 h light/8 h dark) for one day (each condition has two biological replicates). Results: We show that rhythmic posttranscriptional regulation is also a significant factor for genome-wide profile of circadian plant transcriptome. Two major posttranscriptioal mechanisms alternative splicing (AS) and alternative polyadenylation (APA) show circadian rhythmicity, resulting from the oscillation in the genes invovled in AS and APA. Conclusions: Arabidopsis circadian clock not only controls the transcription of genes, but also affects their posttranscriptional regulation through regulating AS and APA.
2020-01-14 | GSE137732 | GEO
Project description:SBML L3V1 format model U2020.5 of the clock gene circuit in the plant Arabidopsis thaliana, inspired by the P2011 model, published in Pokhilko et al Mol Syst Biol 2012 (Biomodels BD000..0412). The U2019 version uses very similar interactions to P2011, where the combined LHY/CCA1 component indirectly activates the wave of PRR gene expression, whereas the U2020 version uses both indirect activation and inter-PRR repression. This .5 version has parameters scaled to yield absolute units for both RNAs and proteins (copy number per cell), whereas the .3 versions of each model are scaled to match only the absolute RNA level data (MODEL2212200002 is U2020.3, for example). SBML files were verified using COPASI software. The full process is described in Urquiza Garcia et al. Molecular Systems Biology, 2025.
2025-12-24 | MODEL2512170002 | BioModels
Project description:The plant circadian clock exerts a critical role in the regulation of multiple biological processes including responses to biotic and abiotic stresses. It is estimated that the clock regulates up to 80% of the transcriptome in Arabidopsis, thus understanding the molecular mechanisms that control this rhythmic transcriptome requires identification of the targets of each clock component. The Arabidopsis core clock is partially comprised of a transcriptional regulatory loop between the MYB domain containing transcription factors CIRCADIAN CLOCK ASSOCIATED1 (CCA1) and LATE ELONGATED HYPOCOTYL (LHY), and TIMING OF CAB EXPRESSION1 (TOC1). As a key component of the clock, CCA1 is able to initiate and set the phase of clock-controlled rhythms. CCA1 regulates the transcription of several genes by directly binding to the evening element (EE) motif primarily found in the promoters of evening expressed genes. Using a genome-wide approach we have identified direct targets of CCA1 in plants grown in constant (LL) and driven conditions (LD). These CCA1 targets are enriched for a myriad of biological processes and stress responses. While many of these target genes are evening phased and contain the EE in their promoter regions, a significant subset is morning phased and lack an EE. Furthermore, several CCA1 targets do not cycle in either LL or LD or both. Expression analysis in CCA1 overexpressing plants confirms CCA1 regulation of analyzed targets. Our results emphasize an expanded role for the circadian clock in regulation of key pathways in Arabidopsis, and provide a comprehensive and solid resource for future functional studies. ChIP-Seq of CCA1-GFP plants under control of the CCA1 promoter in continuous light and diel conditions
2015-07-26 | E-GEOD-70533 | biostudies-arrayexpress
Project description:This model of the clock gene circuit in the plant Arabidopsis thaliana is inspired by the P2011 model, published in Pokhilko et al Mol Syst Biol 2012. The U2019 version uses very similar interactions to P2011, where the combined LHY/CCA1 component indirectly activates the wave of PRR gene expression, whereas the U2020 version uses both indirect activation and inter-PRR repression. The .3 versions of each model are scaled to match the absolute RNA level data from the TiMet project, in Flis et al. 2015.
SBML files were verified using COPASI 4.24 (Build 197) software. The full process is described in Urquiza and Millar, In Silico Plants, 2021.
2022-12-21 | MODEL2212200001 | BioModels