ArticlePLoS computational biology2015
Integrative analysis of circadian transcriptome and metabolic network reveals the role of de novo purine synthesis in circadian control of cell cycle.
Article in PLoS computational biology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 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
22 citing papers in PubMed, 34 citations in OpenAlex.
- Lysosome-related organelles orchestrate guanine crystal formation in pigment cells.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Tuned by time: the role of circadian rhythms in metabolic energy sensing and chronotherapy.Annals of medicine · 2025Review
- Genetic control over biogenic crystal morphogenesis in zebrafish.Nature chemical biology · 2025Article
- Altered Metabolism during the Dark Period in Drosophila Short Sleep Mutants.Journal of proteome research · 2024Article
- Inhibition of Expression of the Circadian Clock GeneInternational journal of molecular sciences · 2023Article
- Impact of Negative Feedbacks on De Novo Pyrimidines Biosynthesis inInternational journal of molecular sciences · 2023Article
- A highly conserved zebrafish IMPDH retinal isoform produces the majority of guanine and forms dynamic protein filaments in photoreceptor cells.The Journal of biological chemistry · 2022Article
- Circadian and Sleep Metabolomics Across Species.Journal of molecular biology · 2020Review
- Establishment of the circadian metabolic phenotype strategy in spontaneously hypertensive rats: a dynamic metabolomics study.Journal of translational medicine · 2020Article
- Feeding Entrainment of the Zebrafish Circadian Clock Is Regulated by the Glucocorticoid Receptor.Cells · 2019Article
- Toxicogenomic analysis of publicly available transcriptomic data can predict food, drugs, and chemical-induced asthma.Pharmacogenomics and personalized medicine · 2019Article
- Circadian- and Light-driven Metabolic Rhythms in Drosophila melanogaster.Journal of biological rhythms · 2018Article
- Article
- Clock1a affects mesoderm development and primitive hematopoiesis by regulating Nodal-Smad3 signaling in the zebrafish embryo.The Journal of biological chemistry · 2017Article
- Trans-omics approaches used to characterise fish nutritional biorhythms in leopard coral grouper (Plectropomus leopardus).Scientific reports · 2017Article
- Inhibition of expression of the circadian clock gene Period causes metabolic abnormalities including repression of glycometabolism in Bombyx mori cells.Scientific reports · 2017Article
- Clock Regulation of Metabolites Reveals Coupling between Transcription and Metabolism.Cell metabolism · 2017Article
- Article
- Extensive Regulation of Diurnal Transcription and Metabolism by Glucocorticoids.PLoS genetics · 2016Article
- Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Metabolism is the major output of the circadian clock in many organisms. We developed a computational method to integrate both circadian gene expression and metabolic network. Applying this method to zebrafish circadian transcriptome, we have identified large clusters of metabolic genes containing mostly genes in purine and pyrimidine metabolism in the metabolic network showing similar circadian phases. Our metabolomics analysis found that the level of inosine 5'-monophosphate (IMP), an intermediate metabolite in de novo purine synthesis, showed significant circadian oscillation in larval zebrafish. We focused on IMP dehydrogenase (impdh), a rate-limiting enzyme in de novo purine synthesis, with three circadian oscillating gene homologs: impdh1a, impdh1b and impdh2. Functional analysis revealed that impdh2 contributes to the daily rhythm of S phase in the cell cycle while impdh1a contributes to ocular development and pigment synthesis. The three zebrafish homologs of impdh are likely regulated by different circadian transcription factors. We propose that the circadian regulation of de novo purine synthesis that supplies crucial building blocks for DNA replication is an important mechanism conferring circadian rhythmicity on the cell cycle. Our method is widely applicable to study the impact of circadian transcriptome on metabolism in complex organisms.
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.