ArticleGenome biology2009
Exploring the transcriptional landscape of plant circadian rhythms using genome tiling arrays.
Article in Genome biology, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 57 papers, 1 of them a synthesis that pooled it.
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Who cites it
57 citing papers in PubMed, 1 synthesis or guideline pooled it, 112 citations in OpenAlex.
- Antisense Transcription in Plants: A Systematic Review and an Update on cis-NATs of Sugarcane.International journal of molecular sciences · 2022Pooled it
- Regulatory links between the circadian clock and stress-induced biomolecular condensates.Npj biological timing and sleep · 2025Review
- Integrative analyses of long and short-read RNA sequencing reveal the spliced isoform regulatory network of seedling growth dynamics in upland cotton.Functional & integrative genomics · 2024Article
- Differential Response of MYB Transcription Factor Gene Transcripts to Circadian Rhythm in Tea Plants (International journal of molecular sciences · 2024Article
- Reciprocal regulation of flower induction by ELF3α and ELF3β generated via alternative promoter usage.The Plant cell · 2023Article
- The effects of different daily irradiance profiles on Arabidopsis growth, with special attention to the role of PsbS.Frontiers in plant science · 2023Article
- Phytochromes and Their Role in Diurnal Variations of ROS Metabolism and Plant Proteome.International journal of molecular sciences · 2022Article
- Emerging Data on the Diversity of Molecular Mechanisms Involving C/D snoRNAs.Non-coding RNA · 2021Review
- Regulation of flowering under short photoperiods based on transcriptomic and metabolomic analysis in Phaseolus vulgaris L.Molecular genetics and genomics : MGG · 2021Article
- Review
- Temporal Regulation of the Metabolome and Proteome in Photosynthetic and Photorespiratory Pathways Contributes to Maize Heterosis.The Plant cell · 2020Article
- A Natural Variant of miR397 Mediates a Feedback Loop in Circadian Rhythm.Plant physiology · 2020Article
- Interactive roles of chromatin regulation and circadian clock function in plants.Genome biology · 2019Review
- Beyond Transcription: Fine-Tuning of Circadian Timekeeping by Post-Transcriptional Regulation.Genes · 2018Review
- The Arabidopsis LDL1/2-HDA6 histone modification complex is functionally associated with CCA1/LHY in regulation of circadian clock genes.Nucleic acids research · 2018Article
- Under a New Light: Regulation of Light-Dependent Pathways by Non-coding RNAs.Frontiers in plant science · 2018Review
- Novel Stress-Inducible Antisense RNAs of Protein-Coding Loci Are Synthesized by RNA-Dependent RNA Polymerase.Plant physiology · 2017Article
- De novo transcriptome assembly reveals high transcriptional complexity in Pisum sativum axillary buds and shows rapid changes in expression of diurnally regulated genes.BMC genomics · 2017Article
- Light Regulation of Alternative Pre-mRNA Splicing in Plants.Photochemistry and photobiology · 2017Review
- Circadian Stress Regimes Affect the Circadian Clock and Cause Jasmonic Acid-Dependent Cell Death in Cytokinin-Deficient Arabidopsis Plants.The Plant cell · 2016Article
Corrections and comments
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Authors and funding
8 authors at 5 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundOrganisms are able to anticipate changes in the daily environment with an internal oscillator know as the circadian clock. Transcription is an important mechanism in maintaining these oscillations. Here we explore, using whole genome tiling arrays, the extent of rhythmic expression patterns genome-wide, with an unbiased analysis of coding and noncoding regions of the Arabidopsis genome.
resultsAs in previous studies, we detected a circadian rhythm for approximately 25% of the protein coding genes in the genome. With an unbiased interrogation of the genome, extensive rhythmic introns were detected predominantly in phase with adjacent rhythmic exons, creating a transcript that, if translated, would be expected to produce a truncated protein. In some cases, such as the MYB transcription factor AT2G20400, an intron was found to exhibit a circadian rhythm while the remainder of the transcript was otherwise arrhythmic. In addition to several known noncoding transcripts, including microRNA, trans-acting short interfering RNA, and small nucleolar RNA, greater than one thousand intergenic regions were detected as circadian clock regulated, many of which have no predicted function, either coding or noncoding. Nearly 7% of the protein coding genes produced rhythmic antisense transcripts, often for genes whose sense strand was not similarly rhythmic.
conclusionsThis study revealed widespread circadian clock regulation of the Arabidopsis genome extending well beyond the protein coding transcripts measured to date. This suggests a greater level of structural and temporal dynamics than previously known.
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