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Deng L, Gao B, Zhao L, Zhang Y, Zhang Q, Guo M, Yang Y, Wang S, Xie L, Lou H, Ma M, Zhang W, Cao Z, Zhang Q, McClung CR, Li G, Li X. Diurnal RNAPII-tethered chromatin interactions are associated with rhythmic gene expression in rice. Genome Biol 2022; 23:7. [PMID: 34991658 PMCID: PMC8734370 DOI: 10.1186/s13059-021-02594-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 12/29/2021] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND The daily cycling of plant physiological processes is speculated to arise from the coordinated rhythms of gene expression. However, the dynamics of diurnal 3D genome architecture and their potential functions underlying the rhythmic gene expression remain unclear. RESULTS Here, we reveal the genome-wide rhythmic occupancy of RNA polymerase II (RNAPII), which precedes mRNA accumulation by approximately 2 h. Rhythmic RNAPII binding dynamically correlates with RNAPII-mediated chromatin architecture remodeling at the genomic level of chromatin interactions, spatial clusters, and chromatin connectivity maps, which are associated with the circadian rhythm of gene expression. Rhythmically expressed genes within the same peak phases of expression are preferentially tethered by RNAPII for coordinated transcription. RNAPII-associated chromatin spatial clusters (CSCs) show high plasticity during the circadian cycle, and rhythmically expressed genes in the morning phase and non-rhythmically expressed genes in the evening phase tend to be enriched in RNAPII-associated CSCs to orchestrate expression. Core circadian clock genes are associated with RNAPII-mediated highly connected chromatin connectivity networks in the morning in contrast to the scattered, sporadic spatial chromatin connectivity in the evening; this indicates that they are transcribed within physical proximity to each other during the AM circadian window and are located in discrete "transcriptional factory" foci in the evening, linking chromatin architecture to coordinated transcription outputs. CONCLUSION Our findings uncover fundamental diurnal genome folding principles in plants and reveal a distinct higher-order chromosome organization that is crucial for coordinating diurnal dynamics of transcriptional regulation.
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Affiliation(s)
- Li Deng
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, 1 Shizishan Street, Hongshan District, Wuhan, 430070, Hubei, China
| | - Baibai Gao
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, 1 Shizishan Street, Hongshan District, Wuhan, 430070, Hubei, China
| | - Lun Zhao
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, 1 Shizishan Street, Hongshan District, Wuhan, 430070, Hubei, China
| | - Ying Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, 1 Shizishan Street, Hongshan District, Wuhan, 430070, Hubei, China
| | - Qing Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, 1 Shizishan Street, Hongshan District, Wuhan, 430070, Hubei, China
| | - Minrong Guo
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, 1 Shizishan Street, Hongshan District, Wuhan, 430070, Hubei, China
| | - Yongqing Yang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, 1 Shizishan Street, Hongshan District, Wuhan, 430070, Hubei, China
| | - Shuangqi Wang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, 1 Shizishan Street, Hongshan District, Wuhan, 430070, Hubei, China
| | - Liang Xie
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, 1 Shizishan Street, Hongshan District, Wuhan, 430070, Hubei, China
| | - Hao Lou
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, 1 Shizishan Street, Hongshan District, Wuhan, 430070, Hubei, China
| | - Meng Ma
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, 1 Shizishan Street, Hongshan District, Wuhan, 430070, Hubei, China
| | - Wei Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, 1 Shizishan Street, Hongshan District, Wuhan, 430070, Hubei, China
| | - Zhilin Cao
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, 1 Shizishan Street, Hongshan District, Wuhan, 430070, Hubei, China
- Department of Resources and Environment, Henan University of Engineering, 1 Xianghe Road, Longhu Town, Zhengzhou, 451191, Henan, China
| | - Qinghua Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, 1 Shizishan Street, Hongshan District, Wuhan, 430070, Hubei, China
| | - C Robertson McClung
- Department of Biological Sciences, Dartmouth College, Hanover, NH, 03755, USA
| | - Guoliang Li
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, 1 Shizishan Street, Hongshan District, Wuhan, 430070, Hubei, China
- Agricultural Bioinformatics Key Laboratory of Hubei Province and Hubei Engineering Technology Research Center of Agricultural Big Data, 3D Genomics Research Center, Huazhong Agricultural University, 1 Shizishan Street, Hongshan District, Wuhan, 430070, Hubei, China
| | - Xingwang Li
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, 1 Shizishan Street, Hongshan District, Wuhan, 430070, Hubei, China.
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Delisle BP, George AL, Nerbonne JM, Bass JT, Ripplinger CM, Jain MK, Hermanstyne TO, Young ME, Kannankeril PJ, Duffy JF, Goldhaber JI, Hall MH, Somers VK, Smolensky MH, Garnett CE, Anafi RC, Scheer FA, Shivkumar K, Shea SA, Balijepalli RC. Understanding Circadian Mechanisms of Sudden Cardiac Death: A Report From the National Heart, Lung, and Blood Institute Workshop, Part 1: Basic and Translational Aspects. Circ Arrhythm Electrophysiol 2021; 14:e010181. [PMID: 34719240 PMCID: PMC8815462 DOI: 10.1161/circep.121.010181] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Sudden cardiac death (SCD), the unexpected death due to acquired or genetic cardiovascular disease, follows distinct 24-hour patterns in occurrence. These 24-hour patterns likely reflect daily changes in arrhythmogenic triggers and the myocardial substrate caused by day/night rhythms in behavior, the environment, and endogenous circadian mechanisms. To better address fundamental questions regarding the circadian mechanisms, the National Heart, Lung, and Blood Institute convened a workshop, Understanding Circadian Mechanisms of Sudden Cardiac Death. We present a 2-part report of findings from this workshop. Part 1 summarizes the workshop and serves to identify research gaps and opportunities in the areas of basic and translational research. Among the gaps was the lack of standardization in animal studies for reporting environmental conditions (eg, timing of experiments relative to the light dark cycle or animal housing temperatures) that can impair rigor and reproducibility. Workshop participants also pointed to uncertainty regarding the importance of maintaining normal circadian rhythmic synchrony and the potential pathological impact of desynchrony on SCD risk. One related question raised was whether circadian mechanisms can be targeted to reduce SCD risk. Finally, the experts underscored the need for studies aimed at determining the physiological importance of circadian clocks in the many different cell types important to normal heart function and SCD. Addressing these gaps could lead to new therapeutic approaches/molecular targets that can mitigate the risk of SCD not only at certain times but over the entire 24-hour period.
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Affiliation(s)
| | - Alfred L. George
- Department of Pharmacology, Northwestern University, Feinberg School of Medicine, Chicago, IL
| | - Jeanne M. Nerbonne
- Departments of Medicine, Cardiovascular Division, and Developmental Biology, Washington University School of Medicine, St. Louis, MO
| | - Joseph T. Bass
- Department of Medicine, Northwestern University, Feinberg School of Medicine, Chicago, IL
| | | | - Mukesh K. Jain
- Department of Medicine, Case Western Reserve University, Cleveland, OH
| | - Tracey O. Hermanstyne
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO
| | - Martin E. Young
- Department of Medicine, University of Alabama, Birmingham, AL
| | | | | | | | - Martica H. Hall
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA
| | | | | | | | - Ron C. Anafi
- Department of Medicine and Center for Sleep and Circadian Neurobiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | | | - Kalyanam Shivkumar
- Departement of Medicine, David Greffen School of Medicine at UCLA, Los Angeles, CA
| | - Steven A. Shea
- Oregon Institute of Occupational Health Sciences, Oregon Health and Science University, Portland, OR
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Ruberto AA, Gréchez-Cassiau A, Guérin S, Martin L, Revel JS, Mehiri M, Subramaniam M, Delaunay F, Teboul M. KLF10 integrates circadian timing and sugar signaling to coordinate hepatic metabolism. eLife 2021; 10:65574. [PMID: 34402428 PMCID: PMC8410083 DOI: 10.7554/elife.65574] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 08/15/2021] [Indexed: 12/13/2022] Open
Abstract
The mammalian circadian timing system and metabolism are highly interconnected, and disruption of this coupling is associated with negative health outcomes. Krüppel-like factors (KLFs) are transcription factors that govern metabolic homeostasis in various organs. Many KLFs show a circadian expression in the liver. Here, we show that the loss of the clock-controlled KLF10 in hepatocytes results in extensive reprogramming of the mouse liver circadian transcriptome, which in turn alters the temporal coordination of pathways associated with energy metabolism. We also show that glucose and fructose induce Klf10, which helps mitigate glucose intolerance and hepatic steatosis in mice challenged with a sugar beverage. Functional genomics further reveal that KLF10 target genes are primarily involved in central carbon metabolism. Together, these findings show that in the liver KLF10 integrates circadian timing and sugar metabolism-related signaling, and serves as a transcriptional brake that protects against the deleterious effects of increased sugar consumption.
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Affiliation(s)
| | | | - Sophie Guérin
- Université Côte d'Azur, CNRS, Inserm, iBV, Nice, France
| | - Luc Martin
- Université Côte d'Azur, CNRS, Inserm, iBV, Nice, France
| | - Johana S Revel
- Université Côte d'Azur, CNRS, Institut de Chimie de Nice, Nice, France
| | - Mohamed Mehiri
- Université Côte d'Azur, CNRS, Institut de Chimie de Nice, Nice, France
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Dibner C. The importance of being rhythmic: Living in harmony with your body clocks. Acta Physiol (Oxf) 2020; 228:e13281. [PMID: 30980501 DOI: 10.1111/apha.13281] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 04/05/2019] [Accepted: 04/08/2019] [Indexed: 02/06/2023]
Abstract
Circadian rhythms have developed in all light-sensitive organisms, including humans, as a fundamental anticipatory mechanism that enables proactive adaptation to environmental changes. The circadian system is organized in a highly hierarchical manner, with clocks operative in most cells of the body ensuring the temporal coordination of physiological processes. Circadian misalignment, stemming from modern life style, draws increasing attention due to its tight association with the development of metabolic, cardiovascular, inflammatory and mental diseases as well as cancer. This review highlights recent findings emphasizing the role of the circadian system in the temporal orchestration of physiology, with a particular focus on implications of circadian misalignment in human pathologies.
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Affiliation(s)
- Charna Dibner
- Division of Endocrinology, Diabetes, Hypertension and Nutrition, Department of Medicine University Hospital of Geneva Geneva Switzerland
- Department of Cell Physiology and Metabolism, Faculty of Medicine University of Geneva Geneva Switzerland
- Diabetes Center, Faculty of Medicine University of Geneva Geneva Switzerland
- Institute of Genetics and Genomics in Geneva (iGE3) Geneva Switzerland
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Nakao A. Clockwork allergy: How the circadian clock underpins allergic reactions. J Allergy Clin Immunol 2019; 142:1021-1031. [PMID: 30293559 DOI: 10.1016/j.jaci.2018.08.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 08/19/2018] [Accepted: 08/21/2018] [Indexed: 12/22/2022]
Abstract
Allergic disease is characterized by marked day-night changes in the clinical symptoms and laboratory parameters of allergy. Recent reports suggest that the circadian clock, which drives a biological rhythm with a periodicity of approximately 24 hours in behavior and physiology, underpins a time of day-dependent variation in allergic reactions. New studies also suggest that disruption of clock activity not only influences temporal variation but can also enhance the severity of allergic reactions and even increase susceptibility to allergic disease. These findings suggest that the circadian clock is a potent regulator of allergic reactions that plays more than a simple circadian timekeeping role in allergy. A better understanding of these processes will provide new insight into previously unknown aspects of the biology of allergies and can lead to the application of clock modifiers to treat allergic disease. Finally, this area of research provides a novel opportunity to consider how modern lifestyles in the developed world are changing the clinical manifestations of allergy as our society quickly transforms into a circadian rhythm-disrupted society in which sleeping, working, and eating habits are out of sync with endogenous circadian rhythmicity. Such findings might reveal lifestyle interventions that enable us to better control allergic disease.
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Affiliation(s)
- Atsuhito Nakao
- Department of Immunology, Faculty of Medicine, University of Yamanashi, Yamanashi, Japan; Atopy Research Center, Juntendo University School of Medicine, Tokyo, Japan.
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