ArticleOpen biology2015
Defining the robust behaviour of the plant clock gene circuit with absolute RNA timeseries and open infrastructure.
Article in Open biology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
19 citing papers in PubMed, 44 citations in OpenAlex.
- Practical RNA-Seq with Spike-Ins: A Bench-to-Bioinformatics Guide.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Genome-scale transcriptome augmentation during Arabidopsis thaliana photomorphogenesis.Nature communications · 2025Article
- Abundant clock proteins point to missing molecular regulation in the plant circadian clock.Molecular systems biology · 2025Article
- Rising rates of starch degradation during daytime and trehalose 6-phosphate optimize carbon availability.Plant physiology · 2022Article
- Fillable and unfillable gaps in plant transcriptome under field and controlled environments.Plant, cell & environment · 2022Article
- The circadian clock mutant lhy cca1 elf3 paces starch mobilization to dawn despite severely disrupted circadian clock function.Plant physiology · 2022Article
- Characterization of the Heat-Stable Proteome during Seed Germination in Arabidopsis with Special Focus on LEA Proteins.International journal of molecular sciences · 2021Article
- Diurnal dynamics of the Arabidopsis rosette proteome and phosphoproteome.Plant, cell & environment · 2021Article
- A mobile ELF4 delivers circadian temperature information from shoots to roots.Nature plants · 2020Article
- Response of the Circadian Clock and Diel Starch Turnover to One Day of Low Light or Low COPlant physiology · 2019Article
- Time-resolved interaction proteomics of the GIGANTEA protein under diurnal cycles in Arabidopsis.FEBS letters · 2019Article
- Luciferase-Based Screen for Post-translational Control Factors in the Regulation of the Pseudo-Response Regulator PRR7.Frontiers in plant science · 2019Article
- Response of Arabidopsis primary metabolism and circadian clock to low night temperature in a natural light environment.Journal of experimental botany · 2018Article
- Feedback regulation by trehalose 6-phosphate slows down starch mobilization below the rate that would exhaust starch reserves at dawn in Arabidopsis leaves.Plant direct · 2018Article
- Waveforms of molecular oscillations reveal circadian timekeeping mechanisms.Communications biology · 2018Article
- Circadian, Carbon, and Light Control of Expansion Growth and Leaf Movement.Plant physiology · 2017Article
- Light Controls Cytokinin Signaling via Transcriptional Regulation of Constitutively Active Sensor Histidine Kinase CKI1.Plant physiology · 2017Article
- Parallel analysis ofOpen biology · 2017Article
- Approximate Bayesian inference in semi-mechanistic models.Statistics and computing · 2017Article
Corrections and comments
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Authors and funding
14 authors at 4 institutions in 2 countries.
Funding
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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.