ArticleGenome research2018
Transcription factor activity rhythms and tissue-specific chromatin interactions explain circadian gene expression across organs.
Article in Genome research, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 74 papers.
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Who cites it
74 citing papers in PubMed.
- Role of the circadian rhythm in squamous cell carcinoma: From molecular mechanism to therapy (Review).Molecular medicine reports · 2026Review
- CLOCK/BMAL1 interactome uncovers homeodomain factors as tissue regulators.Nature cell biology · 2026Article
- Nonlinearities and Switch-Like Behavior in Gene Expression: From Genetics to Biochemistry and Back.FASEB journal : official publication of the Federation of American Societies for Experimental Biology · 2026Review
- Chrono-atlas of cell-type specific daily gene expression rhythms in the regenerating colon.Nature communications · 2026Article
- Circadian rhythm: The hidden "puppet master" behind musculoskeletal disorders.Journal of orthopaedic translation · 2026Review
- D-Box Binding Protein (DBP) as a Circadian Output Regulator: Molecular Mechanisms, Tissue-Specific Functions, and Disease Relevance.International journal of molecular sciences · 2026Review
- ARNTL deregulation promotes ovarian cancer progression and metastasis by activating cancer-associated fibroblasts.Journal of ovarian research · 2026Article
- Epigenetic Regulation of Higher-Order Chromatin Structure (HOCS) and Its Implication in Human Diseases.Cancers · 2026Review
- Circadian clock and cancer.Military Medical Research · 2026Review
- Perturbation of the circadian clock in chronic diseases involving organ fibrosis.The Journal of clinical investigation · 2025Review
- The metabolic significance of peripheral tissue clocks.Communications biology · 2025Review
- A guide to studying 3D genome structure and dynamics in the kidney.Nature reviews. Nephrology · 2025Review
- Twelve-hour ultradian rhythmic reprogramming of gene expression in the human ovary during aging.Journal of assisted reproduction and genetics · 2025Article
- Intermittent fasting shifts the diurnal transcriptome atlas of transcription factors.Molecular and cellular biochemistry · 2025Article
- Diminished circadian and ultradian rhythms of human brain activity in pathological tissue in vivo.Nature communications · 2024Article
- Transitions in chromatin conformation shaped by fatty acids and the circadian clock underlie hepatic transcriptional reorganization in obese mice.Cellular and molecular life sciences : CMLS · 2024Article
- Circadian-driven tissue specificity is constrained under caloric restricted feeding conditions.Communications biology · 2024Article
- Timeless noncoding DNA contains cell-type preferential enhancers important for proper Drosophila circadian regulation.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Coordination of rhythmic RNA synthesis and degradation orchestrates 24- and 12-h RNA expression patterns in mouse fibroblasts.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- TimeTeller: A tool to probe the circadian clock as a multigene dynamical system.PLoS computational biology · 2024Article
14 more citing papers are in PubMed but not listed here.
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Temporal control of physiology requires the interplay between gene networks involved in daily timekeeping and tissue function across different organs. How the circadian clock interweaves with tissue-specific transcriptional programs is poorly understood. Here, we dissected temporal and tissue-specific regulation at multiple gene regulatory layers by examining mouse tissues with an intact or disrupted clock over time. Integrated analysis uncovered two distinct regulatory modes underlying tissue-specific rhythms: tissue-specific oscillations in transcription factor (TF) activity, which were linked to feeding-fasting cycles in liver and sodium homeostasis in kidney; and colocalized binding of clock and tissue-specific transcription factors at distal enhancers. Chromosome conformation capture (4C-seq) in liver and kidney identified liver-specific chromatin loops that recruited clock-bound enhancers to promoters to regulate liver-specific transcriptional rhythms. Furthermore, this looping was remarkably promoter-specific on the scale of less than 10 kilobases (kb). Enhancers can contact a rhythmic promoter while looping out nearby nonrhythmic alternative promoters, confining rhythmic enhancer activity to specific promoters. These findings suggest that chromatin folding enables the clock to regulate rhythmic transcription of specific promoters to output temporal transcriptional programs tailored to different tissues.
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