Absolute units for proteins in Arabidopsis clock models up to U2020.5

The dataset presents mathematical models of the gene regulatory network of the circadian clock, in the plant Arabidopsis thaliana. The work will be published as Urquiza-Garcia, Molina, Halliday and Millar, title "Abundant clock proteins point to missing molecular regulation in the plant circadian clock", in Molecular Systems Biology, 2025.

Starting from the U2019.3 and U2020.3 models, this project rescales parameters to match protein levels that were predicted using a simple model from the TiMet ...

Submitter: Andrew Millar

Studies: Construction of NanoLUC-tagged plants, Estimating DNA-binding affinities for Arabidopsis proteins, Measuring absolute levels of clock proteins with calibrated NanoLUC assays, Predicting absolute levels of clock proteins with a simple model, Recalibrating the clock models for absolute protein levels, to create mo..., Reproducibility documentation

Assays: Clock protein number determination with NanoLUC calibration, Clock proteins NanoLUC fusion raw data, Gatway maps of genomic regions of clock genes, In vivo bioluminescence of clock protein-NanoLUC fusions: example experi..., Jupyter notebook Predicting Protein Numbers, Propagating scaling factors into model parameters for U2019.4->U2019.5 a..., Protein level time series, Python packages, Reproducibility tool set, Selection of complemented transgenic lines, TiMet RNA timeseries data, promoter binding affinity calculations on the genome based on PBMs and E...

Circadian period analysis

Luciferase reporter gene assay for circadian period of seedlings in constant light, for Col0 (WT) and prr7prr9, with and without exogenous gibberellins (GA). Supplementary Figure 11f in Chew et al., _in Silico _Plants.

Raw and processed data, together with circadian period analysis and summary statistics, are available from BioDare.ed.ac.uk: choose https://biodare.ed.ac.uk/experiment ("Browse Public Resources" on the Login screen), then you can link to https://biodare.ed.ac.uk/robust/ShowExperiment.action?experimentId=3838, ...

Submitter: Andrew Millar

Assay type: Transcriptional reporter gene

Technology type: Imaging

Investigation: Prediction and analysis of phenotypes in the Ar...

Study: Test of FMv2, study Gibberellins 1

framework model v1_5

Model associated with the following:

Hannah A Kinmonth-Schultz, Melissa J S MacEwen, Daniel D Seaton, Andrew J Millar, Takato Imaizumi, Soo-Hyung Kim, An explanatory model of temperature influence on flowering through whole-plant accumulation of FLOWERING LOCUS T in Arabidopsis thaliana, in silico Plants, Volume 1, Issue 1, 2019, diz006, https://doi.org/10.1093/insilicoplants/diz006

Creator: Hannah Kinmonth-Schultz

Submitter: Hannah Kinmonth-Schultz

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Framework Model v2

Framework Model for Arabidopsis vegetative growth, version 2 (FMv2), as described in Chew et al. bioRxiv 2017 (https://doi.org/10.1101/105437; please see linked Article file).

The FMv2 model record on FAIRDOMHub has the following versions, which represent the same FMv2 model: Version 1 is an archive of the github repository of MATLAB code for the Framework Model v2, downloaded from https://github.com/danielseaton/frameworkmodel on 06/02/17. This version was not licensed for further use and was ...

Creators: Daniel Seaton, Yin Hoon Chew, Andrew Millar

Submitter: Daniel Seaton

External Link
The Arabidopsis Framework Model version 2 predicts the organism-level effects of circadian clock gene mis-regulation

Abstract (Expand)

Predicting a multicellular organism’s phenotype quantitatively from its genotype is challenging, as genetic effects must propagate across scales. Circadian clocks are intracellular regulators that … control temporal gene expression patterns and hence metabolism, physiology and behaviour. Here we explain and predict canonical phenotypes of circadian timing in a multicellular, model organism. We used diverse metabolic and physiological data to combine and extend mathematical models of rhythmic gene expression, photoperiod-dependent flowering, elongation growth and starch metabolism within a Framework Model for the vegetative growth of Arabidopsis thaliana, sharing the model and data files in a structured, public resource. The calibrated model predicted the effect of altered circadian timing upon each particular phenotype in clock-mutant plants under standard laboratory conditions. Altered night-time metabolism of stored starch accounted for most of the decrease in whole-plant biomass, as previously proposed. Mobilization of a secondary store of malate and fumarate was also mis-regulated, accounting for any remaining biomass defect. The three candidate mechanisms tested did not explain this organic acid accumulation. Our results link genotype through specific processes to higher-level phenotypes, formalizing our understanding of a subtle, pleiotropic syndrome at the whole-organism level, and validating the systems approach to understand complex traits starting from intracellular circuits.

Authors: Yin Hoon Chew, Daniel D Seaton, Virginie Mengin, Anna Flis, Sam T Mugford, Gavin M George, Michael Moulin, Alastair Hume, Samuel C Zeeman, Teresa B Fitzpatrick, Alison M Smith, Mark Stitt, Andrew J Millar

Date Published: 1st Jul 2022

Publication Type: Journal

The Arabidopsis Framework Model version 2 predicts the organism-level effects of circadian clock gene mis-regulation

Abstract (Expand)

Predicting a multicellular organism’s phenotype quantitatively from its genotype is challenging, as genetic effects must propagate across scales. Circadian clocks are intracellular regulators that … control temporal gene expression patterns and hence metabolism, physiology and behaviour. Here we explain and predict canonical phenotypes of circadian timing in a multicellular, model organism. We used diverse metabolic and physiological data to combine and extend mathematical models of rhythmic gene expression, photoperiod-dependent flowering, elongation growth and starch metabolism within a Framework Model for the vegetative growth of Arabidopsis thaliana, sharing the model and data files in a structured, public resource. The calibrated model predicted the effect of altered circadian timing upon each particular phenotype in clock-mutant plants under standard laboratory conditions. Altered night-time metabolism of stored starch accounted for most of the decrease in whole-plant biomass, as previously proposed. Mobilisation of a secondary store of malate and fumarate was also mis-regulated, accounting for any remaining biomass defect. We test three candidate mechanisms for the accumulation of these organic acids. Our results link genotype through specific processes to higher-level phenotypes, formalising our understanding of a subtle, pleiotropic syndrome at the whole-organism level, and validating the systems approach to understand complex traits starting from intracellular circuits. This work updates the first biorXiv version, February 2017,with an expanded description and additional analysis of the same core data sets and the same FMv2 model, summary tables and supporting, follow-on data from three further studies with further collaborators. This biorXiv revision constitutes the second version of this report.

Authors: Yin Hoon Chew, Daniel D. Seaton, Virginie Mengin, Anna Flis, Sam T. Mugford, Gavin M. George, Michael Moulin, Alastair Hume, Samuel C. Zeeman, Teresa B. Fitzpatrick, Alison M. Smith, Mark Stitt, Andrew J. Millar

Date Published: 6th Feb 2017

Publication Type: Tech report

Pictures of Arabidopsis plants growing outside in Edinburgh

ZIP file of Andrew Millar's pictures showing the growth location and setup on 8th June 2016, for plants that were later harvested at the summer solstice in 2016. Location was at the South edge of King's Buildings campus, outside the shelter belt of trees (so they did not shade the plot). The plot is surrounded by access fencing that also cuts some of the wind, established by UoE greenhouse staff led by Dr. Sophie Haupt. The plants were set up and grown by Sarah Hodge, under a light shade of 4 ...

Creators: Andrew Millar, Sarah Hodge

Submitter: Andrew Millar

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