ArticlePLoS genetics2008
Network discovery pipeline elucidates conserved time-of-day-specific cis-regulatory modules.
Article in PLoS genetics, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 280 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
280 citing papers in PubMed.
- SPIRAL: A versatile online single time-point circadian analysis platform for rice.Science advances · 2026Article
- Distinct processes contributing to post-submergence recovery determine leaf age-specific flood resilience in Arabidopsis.Plant physiology · 2026Article
- The Circadian Oscillator Affects Both Glutathione Homeostasis and Its Response to Salt Stress in Arabidopsis thaliana.Plant, cell & environment · 2026Article
- Photoperiodic patterns in miRNA-mRNA pairs and tRNA fragments revealed by time-course co-sequencing in Arabidopsis.PLoS genetics · 2026Article
- Vernalisation-induced changes to the Arabidopsis circadian clock require Polycomb Repressive Complex 2 and are FLC-independent.Plant & cell physiology · 2026Article
- Time- and space-resolved transcriptional regulation in Arabidopsis thaliana.Plant biology (Stuttgart, Germany) · 2026Article
- A PROMOTER::LUCIFERASE reporter system reveals key elements of the circadian regulation of Crassulacean acid metabolism (CAM) in Kalanchoë laxiflora Baker.The Plant journal : for cell and molecular biology · 2026Article
- Time after time: a quarter century of progress in plant circadian biology.Npj biological timing and sleep · 2026Review
- Circadian oscillations in chromatin accessibility systematically orchestrate rhythmic gene transcription in soybean.The Plant cell · 2026Article
- Molecular genetic examination of Circadian Clock Associated 1 gene (CCA1) in hexaploid wheat.BMC plant biology · 2026Article
- Constant Illumination Boosts Rice Immunity via the Nicotinamide Mononucleotide Signaling Pathway: A Mechanistic Exploration.Rice (New York, N.Y.) · 2026Article
- Rhythmic Mechanisms Governing CAM Photosynthesis inInternational journal of molecular sciences · 2026Article
- GEAR: an integrated atlas of gene expression dynamics in Arabidopsis thaliana.Nucleic acids research · 2026Article
- Photoperiod and Circadian Regulation in Plants: A Review of Insights from In Vitro Studies.Biology · 2025Review
- High resolution diel transcriptomes of autotetraploid potato reveal expression and sequence conservation among rhythmic genes.BMC genomics · 2025Article
- Targeted deletions of large syntenic regions inProceedings of the National Academy of Sciences of the United States of America · 2025Article
- Can a plant biologist fix a thermostat?The New phytologist · 2025Review
- Circadian gating: concepts, processes, and opportunities.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2025Review
- Exploring the metabolic daylength measurement system: implications for photoperiodic growth.The New phytologist · 2025Review
- Diurnal control of H3K27me1 deposition shapes expression of a subset of cell cycle and DNA damage response genes.The Plant journal : for cell and molecular biology · 2024Article
220 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
15 authors.
Funding
Abstract
Correct daily phasing of transcription confers an adaptive advantage to almost all organisms, including higher plants. In this study, we describe a hypothesis-driven network discovery pipeline that identifies biologically relevant patterns in genome-scale data. To demonstrate its utility, we analyzed a comprehensive matrix of time courses interrogating the nuclear transcriptome of Arabidopsis thaliana plants grown under different thermocycles, photocycles, and circadian conditions. We show that 89% of Arabidopsis transcripts cycle in at least one condition and that most genes have peak expression at a particular time of day, which shifts depending on the environment. Thermocycles alone can drive at least half of all transcripts critical for synchronizing internal processes such as cell cycle and protein synthesis. We identified at least three distinct transcription modules controlling phase-specific expression, including a new midnight specific module, PBX/TBX/SBX. We validated the network discovery pipeline, as well as the midnight specific module, by demonstrating that the PBX element was sufficient to drive diurnal and circadian condition-dependent expression. Moreover, we show that the three transcription modules are conserved across Arabidopsis, poplar, and rice. These results confirm the complex interplay between thermocycles, photocycles, and the circadian clock on the daily transcription program, and provide a comprehensive view of the conserved genomic targets for a transcriptional network key to successful adaptation.
Indexed as
Identifiers
What OpenQuestion holds
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.