ArticleProceedings of the National Academy of Sciences of the United States of America2015
Genome-wide identification of CCA1 targets uncovers an expanded clock network in Arabidopsis.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 146 papers.
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Who cites it
146 citing papers in PubMed, 283 citations in OpenAlex.
- CCRG1 Acts as a Downstream Effector of the Clock Proteins CCA1 and LHY to Coordinate Growth, Flowering, and Senescence.Plant, cell & environment · 2026Article
- The Circadian Clock Regulates Receptor-Mediated Immune Responses to a Herbivore-Associated Molecular Pattern.Plant, cell & environment · 2026Article
- Time- and space-resolved transcriptional regulation in Arabidopsis thaliana.Plant biology (Stuttgart, Germany) · 2026Article
- Genome-Wide Characterization and Seasonal-Circadian Expression Analysis of CCT Family Genes inGenes · 2026Article
- The core clock transcription factor TOC1 binds directly to defence gene promoters regulating immunity in Arabidopsis.Communications biology · 2026Article
- Review
- RrLHY regulates arginine biosynthesis by activating RrNAGS1 in Rosa roxburghii fruit.Plant cell reports · 2026Article
- Cis-regulatory elements co-opting core circadian clock regulator CCA1 underlie enhanced expression of HMA4 for metal hyperaccumulation in Arabidopsis halleri.Plant communications · 2025Article
- Temperature compensation of the Arabidopsis circadian clock.Npj biological timing and sleep · 2025Review
- Antioxidant properties of dihydroxy B-ring flavonoids modulate circadian amplitude inLife science alliance · 2025Article
- Fine-tuning wheat development for the winter to spring transition.Plant communications · 2025Article
- A circadian morning complex modulates far-red light signaling in Arabidopsis.Nature communications · 2025Article
- TOC1 phosphorylation disproportionally enhances chromatin binding at rhythmic gene promoters.Science advances · 2025Article
- Transcriptional activation and repression in the plant circadian clock: Revisiting core oscillator feedback loops and output pathways.Plant communications · 2025Review
- Machine learning models highlight environmental and genetic factors associated with the Arabidopsis circadian clock.Nature communications · 2025Article
- Stable and dynamic gene expression patterns over diurnal and developmental timescales in Arabidopsis thaliana.The New phytologist · 2025Article
- The core morning clock component CCA1 enhances UPR target gene expression to facilitate ER stress recovery.Plant communications · 2025Article
- Abundant clock proteins point to missing molecular regulation in the plant circadian clock.Molecular systems biology · 2025Article
- Thaumatin-like GeneInternational journal of molecular sciences · 2025Article
- Research progress on delayed flowering under short-day condition inFrontiers in plant science · 2025Review
86 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
6 authors at 4 institutions in 1 country.
Funding
Abstract
The circadian clock in Arabidopsis exerts a critical role in timing multiple biological processes and stress responses through the regulation of up to 80% of the transcriptome. As a key component of the clock, the Myb-like transcription factor CIRCADIAN CLOCK ASSOCIATED1 (CCA1) is able to initiate and set the phase of clock-controlled rhythms and has been shown to regulate gene expression by binding directly to the evening element (EE) motif found in target gene promoters. However, the precise molecular mechanisms underlying clock regulation of the rhythmic transcriptome, specifically how clock components connect to clock output pathways, is poorly understood. In this study, using ChIP followed by deep sequencing of CCA1 in constant light (LL) and diel (LD) conditions, more than 1,000 genomic regions occupied by CCA1 were identified. CCA1 targets are enriched for a myriad of biological processes and stress responses, providing direct links to clock-controlled pathways and suggesting that CCA1 plays an important role in regulating a large subset of the rhythmic transcriptome. Although many of these target genes are evening expressed and contain the EE motif, a significant subset is morning phased and enriched for previously unrecognized motifs associated with CCA1 function. Furthermore, this work revealed several CCA1 targets that do not cycle in either LL or LD conditions. Together, our results emphasize an expanded role for the clock in regulating a diverse category of genes and key pathways in Arabidopsis and provide a comprehensive resource for future functional studies.
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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.