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Pacheco-Bernal I, Becerril-Pérez F, Bustamante-Zepeda M, González-Suárez M, Olmedo-Suárez MA, Hernández-Barrientos LR, Alarcón-Del-Carmen A, Escalante-Covarrubias Q, Mendoza-Viveros L, Hernández-Lemus E, León-Del-Río A, de la Rosa-Velázquez IA, Orozco-Solis R, Aguilar-Arnal L. Transitions in chromatin conformation shaped by fatty acids and the circadian clock underlie hepatic transcriptional reorganization in obese mice. Cell Mol Life Sci 2024; 81:309. [PMID: 39060446 PMCID: PMC11335233 DOI: 10.1007/s00018-024-05364-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 06/25/2024] [Accepted: 07/12/2024] [Indexed: 07/28/2024]
Abstract
The circadian clock system coordinates metabolic, physiological, and behavioral functions across a 24-h cycle, crucial for adapting to environmental changes. Disruptions in circadian rhythms contribute to major metabolic pathologies like obesity and Type 2 diabetes. Understanding the regulatory mechanisms governing circadian control is vital for identifying therapeutic targets. It is well characterized that chromatin remodeling and 3D structure at genome regulatory elements contributes to circadian transcriptional cycles; yet the impact of rhythmic chromatin topology in metabolic disease is largely unexplored. In this study, we explore how the spatial configuration of the genome adapts to diet, rewiring circadian transcription and contributing to dysfunctional metabolism. We describe daily fluctuations in chromatin contacts between distal regulatory elements of metabolic control genes in livers from lean and obese mice and identify specific lipid-responsive regions recruiting the clock molecular machinery. Interestingly, under high-fat feeding, a distinct interactome for the clock-controlled gene Dbp strategically promotes the expression of distal metabolic genes including Fgf21. Alongside, new chromatin loops between regulatory elements from genes involved in lipid metabolism control contribute to their transcriptional activation. These enhancers are responsive to lipids through CEBPβ, counteracting the circadian repressor REVERBa. Our findings highlight the intricate coupling of circadian gene expression to a dynamic nuclear environment under high-fat feeding, supporting a temporally regulated program of gene expression and transcriptional adaptation to diet.
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Affiliation(s)
- Ignacio Pacheco-Bernal
- Departamento de Biología Celular y Fisiología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico
| | - Fernando Becerril-Pérez
- Departamento de Biología Celular y Fisiología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico
| | - Marcia Bustamante-Zepeda
- Departamento de Biología Celular y Fisiología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico
| | - Mirna González-Suárez
- Departamento de Biología Celular y Fisiología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico
| | - Miguel A Olmedo-Suárez
- Departamento de Biología Celular y Fisiología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico
| | - Luis Ricardo Hernández-Barrientos
- Departamento de Biología Celular y Fisiología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico
| | - Alejandro Alarcón-Del-Carmen
- Departamento de Biología Celular y Fisiología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico
| | - Quetzalcoatl Escalante-Covarrubias
- Departamento de Biología Celular y Fisiología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico
| | - Lucía Mendoza-Viveros
- Departamento de Biología Celular y Fisiología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico
- Laboratorio de Cronobiología, Metabolismo y Envejecimiento, Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City, Mexico
- Centro de Investigacíon sobre el Envejecimiento, Centro de Investigación y de Estudios Avanzados (CIE-CINVESTAV), Mexico City, México
- Instituto Potosino de Investigación Científica y Tecnológica, San Luis Potosí, Mexico
| | - Enrique Hernández-Lemus
- Department of Computational Genomics, Centro de Ciencias de La Complejidad (C3), Instituto Nacional de Medicina Genómica (INMEGEN), Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Alfonso León-Del-Río
- Departamento de Medicina Genómica y Toxicología Ambiental, Programa Institucional de Cáncer de Mama, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico
| | - Inti A de la Rosa-Velázquez
- Genomics Laboratory, Red de Apoyo a la Investigación-CIC, Universidad Nacional Autónoma de México, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, 14080, Mexico City, Mexico
- Next Generation Sequencing Core Facility, Helmholtz Zentrum Muenchen, Ingolstaedter Landstr 1, 85754, Neuherberg, Germany
| | - Ricardo Orozco-Solis
- Laboratorio de Cronobiología, Metabolismo y Envejecimiento, Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City, Mexico
- Centro de Investigacíon sobre el Envejecimiento, Centro de Investigación y de Estudios Avanzados (CIE-CINVESTAV), Mexico City, México
| | - Lorena Aguilar-Arnal
- Departamento de Biología Celular y Fisiología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico.
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2
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Chen R, Zhang Z, Ma J, Liu B, Huang Z, Hu G, Huang J, Xu Y, Wang GZ. Circadian-driven tissue specificity is constrained under caloric restricted feeding conditions. Commun Biol 2024; 7:752. [PMID: 38902439 PMCID: PMC11190204 DOI: 10.1038/s42003-024-06421-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 06/06/2024] [Indexed: 06/22/2024] Open
Abstract
Tissue specificity is a fundamental property of an organ that affects numerous biological processes, including aging and longevity, and is regulated by the circadian clock. However, the distinction between circadian-affected tissue specificity and other tissue specificities remains poorly understood. Here, using multi-omics data on circadian rhythms in mice, we discovered that approximately 35% of tissue-specific genes are directly affected by circadian regulation. These circadian-affected tissue-specific genes have higher expression levels and are associated with metabolism in hepatocytes. They also exhibit specific features in long-reads sequencing data. Notably, these genes are associated with aging and longevity at both the gene level and at the network module level. The expression of these genes oscillates in response to caloric restricted feeding regimens, which have been demonstrated to promote longevity. In addition, aging and longevity genes are disrupted in various circadian disorders. Our study indicates that the modulation of circadian-affected tissue specificity is essential for understanding the circadian mechanisms that regulate aging and longevity at the genomic level.
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Affiliation(s)
- Renrui Chen
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Ziang Zhang
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Junjie Ma
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Bing Liu
- Collaborative Innovation Center for Brain Science, Department of Anatomy and Physiology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Zhengyun Huang
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and Cambridge-Su Genomic Resource Center, Medical School of Soochow University, Suzhou, Jiangsu, 215123, China
| | - Ganlu Hu
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China
| | - Ju Huang
- Collaborative Innovation Center for Brain Science, Department of Anatomy and Physiology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Ying Xu
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and Cambridge-Su Genomic Resource Center, Medical School of Soochow University, Suzhou, Jiangsu, 215123, China
| | - Guang-Zhong Wang
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China.
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3
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Zhang X, Procopio SB, Ding H, Semel MG, Schroder EA, Seward TS, Du P, Wu K, Johnson SR, Prabhat A, Schneider DJ, Stumpf IG, Rozmus ER, Huo Z, Delisle BP, Esser KA. New role for cardiomyocyte Bmal1 in the regulation of sex-specific heart transcriptomes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.18.590181. [PMID: 38659967 PMCID: PMC11042278 DOI: 10.1101/2024.04.18.590181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
It has been well established that cardiovascular diseases exhibit significant differences between sexes in both preclinical models and humans. In addition, there is growing recognition that disrupted circadian rhythms can contribute to the onset and progression of cardiovascular diseases. However little is known about sex differences between the cardiac circadian clock and circadian transcriptomes in mice. Here, we show that the the core clock genes are expressed in common in both sexes but the circadian transcriptome of the mouse heart is very sex-specific. Hearts from female mice expressed significantly more rhythmically expressed genes (REGs) than male hearts and the temporal pattern of REGs was distinctly different between sexes. We next used a cardiomyocyte-specific knock out of the core clock gene, Bmal1, to investigate its role in sex-specific gene expression in the heart. All sex differences in the circadian transcriptomes were significantly diminished with cardiomyocyte-specific loss of Bmal1. Surprisingly, loss of cardiomyocyte Bmal1 also resulted in a roughly 8-fold reduction in the number of all the differentially expressed genes between male and female hearts. We conclude that cardiomyocyte-specific Bmal1, and potentially the core clock mechanism, is vital in conferring sex-specific gene expression in the adult mouse heart.
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Affiliation(s)
- Xiping Zhang
- Department of Physiology and Aging, University of Florida, Gainesville FL, United States
- These authors contributed equally to this paper
| | - Spencer B. Procopio
- Department of Physiology and Aging, University of Florida, Gainesville FL, United States
- These authors contributed equally to this paper
| | - Haocheng Ding
- Department of Biostatics, University of Florida, Gainesville FL, United States
| | - Maya G. Semel
- Department of Physiology and Aging, University of Florida, Gainesville FL, United States
| | - Elizabeth A. Schroder
- Department of Physiology, University of Kentucky, Lexington, KY, United States
- Department of Internal Medicine, University of Kentucky, Lexington, KY, United States
| | - Tanya S. Seward
- Department of Physiology, University of Kentucky, Lexington, KY, United States
| | - Ping Du
- Department of Physiology and Aging, University of Florida, Gainesville FL, United States
| | - Kevin Wu
- Department of Physiology and Aging, University of Florida, Gainesville FL, United States
| | - Sidney R. Johnson
- Department of Physiology, University of Kentucky, Lexington, KY, United States
| | - Abhilash Prabhat
- Department of Physiology, University of Kentucky, Lexington, KY, United States
| | - David J. Schneider
- Department of Physiology, University of Kentucky, Lexington, KY, United States
| | - Isabel G Stumpf
- Department of Physiology, University of Kentucky, Lexington, KY, United States
| | - Ezekiel R Rozmus
- Department of Physiology, University of Kentucky, Lexington, KY, United States
| | - Zhiguang Huo
- Department of Biostatics, University of Florida, Gainesville FL, United States
| | - Brian P. Delisle
- Department of Physiology, University of Kentucky, Lexington, KY, United States
| | - Karyn A. Esser
- Department of Physiology and Aging, University of Florida, Gainesville FL, United States
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4
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Liu XL, Duan Z, Yu M, Liu X. Epigenetic control of circadian clocks by environmental signals. Trends Cell Biol 2024:S0962-8924(24)00028-X. [PMID: 38423855 DOI: 10.1016/j.tcb.2024.02.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 02/01/2024] [Accepted: 02/05/2024] [Indexed: 03/02/2024]
Abstract
Circadian clocks have evolved to enable organisms to respond to daily environmental changes. Maintaining a robust circadian rhythm under various perturbations and stresses is essential for the fitness of an organism. In the core circadian oscillator conserved in eukaryotes (from fungi to mammals), a negative feedback loop based on both transcription and translation drives circadian rhythms. The expression of circadian clock genes depends both on the binding of transcription activators at the promoter and on the chromatin state of the clock genes, and epigenetic modifications of chromatin are crucial for transcriptional regulation of circadian clock genes. Herein we review current knowledge of epigenetic regulation of circadian clock mechanisms and discuss how environmental cues can control clock gene expression by affecting chromatin states.
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Affiliation(s)
- Xiao-Lan Liu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Zeyu Duan
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Muqun Yu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xiao Liu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China; College of Life Sciences, University of the Chinese Academy of Sciences, Beijing, 100049, China.
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5
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Zhang C, Chen L, Sun L, Jin H, Ren K, Liu S, Qian Y, Li S, Li F, Zhu C, Zhao Y, Liu H, Liu Y. BMAL1 collaborates with CLOCK to directly promote DNA double-strand break repair and tumor chemoresistance. Oncogene 2023; 42:967-979. [PMID: 36725890 PMCID: PMC10038804 DOI: 10.1038/s41388-023-02603-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 01/17/2023] [Accepted: 01/19/2023] [Indexed: 02/03/2023]
Abstract
Accumulating evidence indicates a correlation between circadian dysfunction and genomic instability. However, whether the circadian machinery directly regulates DNA damage repair, especially in double-strand breaks (DSBs), remains poorly understood. Here, we report that in response to DSBs, BMAL1 is activated by ATM-mediated phosphorylation at S183. Phosphorylated BMAL1 is then localized to DNA damage sites, where it facilitates acetylase CLOCK to load in the chromatin, regulating the acetylation of histone H4 (H4Ac) at DSB sites. In this way, the BMAL1-CLOCK-H4Ac axis promotes the DNA end-resection to generate single-stranded DNA (ssDNA) and the subsequent homologous recombination (HR). BMAL1 deficient cells display defective HR, accumulation of unrepaired DSBs and genome instability. Accordingly, depletion of BMAL1 significantly enhances the sensitivity of adrenocortical carcinoma (ACC) to DNA damage-based therapy in vitro and in vivo. These findings uncover non-canonical function of BMAL1 and CLOCK in HR-mediated DSB repair, which may have an implication in cancer therapeutics.
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Affiliation(s)
- Canfeng Zhang
- The Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen, 518107, China.
| | - Liping Chen
- The Center for Medical Research, The First People's Hospital of Nanning City, Nanning, 530021, China
| | - Lu Sun
- The Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen, 518107, China
| | - Heping Jin
- MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510006, China
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, 510006, China
| | - Kai Ren
- The Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen, 518107, China
| | - Shiqi Liu
- MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510006, China
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, 510006, China
| | - Yongyu Qian
- MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510006, China
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, 510006, China
| | - Shupeng Li
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
| | - Fangping Li
- The Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen, 518107, China
| | - Chengming Zhu
- The Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen, 518107, China
| | - Yong Zhao
- MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510006, China
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, 510006, China
| | - Haiying Liu
- MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510006, China
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, 510006, China
| | - Yan Liu
- The Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen, 518107, China.
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6
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Deota S, Lin T, Chaix A, Williams A, Le H, Calligaro H, Ramasamy R, Huang L, Panda S. Diurnal transcriptome landscape of a multi-tissue response to time-restricted feeding in mammals. Cell Metab 2023; 35:150-165.e4. [PMID: 36599299 PMCID: PMC10026518 DOI: 10.1016/j.cmet.2022.12.006] [Citation(s) in RCA: 31] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 08/08/2022] [Accepted: 12/07/2022] [Indexed: 01/05/2023]
Abstract
Time-restricted feeding (TRF) is an emerging behavioral nutrition intervention that involves a daily cycle of feeding and fasting. In both animals and humans, TRF has pleiotropic health benefits that arise from multiple organ systems, yet the molecular basis of TRF-mediated benefits is not well understood. Here, we subjected mice to isocaloric ad libitum feeding (ALF) or TRF of a western diet and examined gene expression changes in samples taken from 22 organs and brain regions collected every 2 h over a 24-h period. We discovered that TRF profoundly impacts gene expression. Nearly 80% of all genes show differential expression or rhythmicity under TRF in at least one tissue. Functional annotation of these changes revealed tissue- and pathway-specific impacts of TRF. These findings and resources provide a critical foundation for future mechanistic studies and will help to guide human time-restricted eating (TRE) interventions to treat various disease conditions with or without pharmacotherapies.
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Affiliation(s)
- Shaunak Deota
- The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Terry Lin
- The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Amandine Chaix
- The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - April Williams
- The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Hiep Le
- The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Hugo Calligaro
- The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Ramesh Ramasamy
- The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Ling Huang
- The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Satchidananda Panda
- The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA.
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7
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Zhu B. Logic of the Temporal Compartmentalization of the Hepatic Metabolic Cycle. Physiology (Bethesda) 2022; 37:0. [PMID: 35658626 PMCID: PMC9394779 DOI: 10.1152/physiol.00003.2022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 05/05/2022] [Accepted: 05/28/2022] [Indexed: 12/25/2022] Open
Abstract
The mammalian liver must cope with various metabolic and physiological changes that normally recur every day and result primarily from rest-activity and fasting-feeding cycles. In this article, I present evidence supporting a temporal compartmentalization of rhythmic hepatic metabolic processes into four main clusters: regulation of energy homeostasis, maintenance of information integrity, immune response, and genetic information flow. I further review literatures and discuss how both the circadian and the newly discovered 12-h ultradian clock work together to regulate these four temporally separated processes in mouse liver, which, interestingly, is largely uncoupled from the liver zonation regulation.
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Affiliation(s)
- Bokai Zhu
- Aging Institute of UPMC, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
- Pittsburgh Liver Research Center, University of Pittsburgh, Pittsburgh, Pennsylvania
- Division of Endocrinology and Metabolism, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
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8
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Heywood HK, Gardner L, Knight MM, Lee DA. Oscillations of the circadian clock protein, BMAL-1, align to daily cycles of mechanical stimuli: a novel means to integrate biological time within predictive in vitro model systems. IN VITRO MODELS 2022; 1:405-412. [PMID: 36570670 PMCID: PMC9767245 DOI: 10.1007/s44164-022-00032-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 08/02/2022] [Accepted: 08/03/2022] [Indexed: 06/01/2023]
Abstract
PURPOSE In vivo, the circadian clock drives 24-h rhythms in human physiology. Isolated cells in vitro retain a functional clockwork but lack necessary timing cues resulting in the rapid loss of tissue-level circadian rhythms. This study tests the hypothesis that repeated daily mechanical stimulation acts as a timing cue for the circadian clockwork. The delineation and integration of circadian timing cues into predictive in vitro model systems, including organ-on-a-chip (OOAC) devices, represent a novel concept that introduces a key component of in vivo physiology into predictive in vitro model systems. METHODS Quiescent bovine chondrocytes were entrained for 3 days by daily 12-h bouts of cyclic biaxial tensile strain (10%, 0.33 Hz, Flexcell) before sampling during free-running conditions. The core clock protein, BMAL-1, was quantified from normalised Western Blot signal intensity and the temporal oscillations characterised by Cosinor linear fit with 24-h period. RESULTS Following entrainment, the cell-autonomous oscillations of the molecular clock protein, BMAL-1, exhibited circadian (24 h) periodicity (p < 0.001) which aligned to the diurnal mechanical stimuli. A 6-h phase shift in the mechanical entrainment protocol resulted in an equivalent shift of the circadian clockwork. Thus, repeated daily mechanical stimuli synchronised circadian rhythmicity of chondrocytes in vitro. CONCLUSION This work demonstrates that daily mechanical stimulation can act as a timing cue that is sufficient to entrain the peripheral circadian clock in vitro. This discovery may be exploited to induce and sustain circadian physiology within into predictive in vitro model systems, including OOAC systems. Integration of the circadian clock within these systems will enhance their potential to accurately recapitulate human diurnal physiology and hence augment their predictive value as drug testing platforms and as realistic models of human (patho)physiology. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s44164-022-00032-x.
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Affiliation(s)
- Hannah K. Heywood
- School of Engineering and Materials Science, Queen Mary University of London, London, UK
| | - Laurence Gardner
- Wirral University Teaching Hospital NHS Foundation Trust, Liverpool, UK
| | - Martin M. Knight
- School of Engineering and Materials Science, Queen Mary University of London, London, UK
| | - David A. Lee
- School of Engineering and Materials Science, Queen Mary University of London, London, UK
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9
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Stahlschmidt ZR. Flight capacity drives circadian patterns of metabolic rate and alters resource dynamics. JOURNAL OF EXPERIMENTAL ZOOLOGY PART A: ECOLOGICAL AND INTEGRATIVE PHYSIOLOGY 2022; 337:666-674. [PMID: 35438260 PMCID: PMC9324922 DOI: 10.1002/jez.2598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 03/31/2022] [Indexed: 11/29/2022]
Abstract
Animals must acquire, use, and allocate resources, and this balancing act may be influenced by the circadian clock and life‐history strategy. Field (Gryllus) crickets exhibit two distinct life‐history strategies during early adulthood—flight‐capable females invest in flight muscle at a cost to ovary mass, whereas flight‐incapable females instead invest solely into ovaries. In female Gryllus lineaticeps, I investigated the role of life‐history strategy in resource (food) acquisition and allocation, and in circadian patterns of energy use. Flight capacity increased the standard metabolic rate (SMR) due to greater late‐day SMR and flight‐capable crickets exhibited greater circadian rhythmicity in SMR. Flight‐capable crickets also ate less food and were less efficient at converting ingested food into body or ovary mass. Thus, investment into flight capacity reduced fecundity and the amount of resources available for allocation to other life‐history traits. Given the increasing uncertainty of food availability in many global regions, work in Gryllus may clarify the important roles of food and circadian patterns in life‐history evolution in a changing world. In a field cricket, investment into flight capacity (1) increased the circadian rhythmicity of resource use (standard metabolic rate), (2) reduced resource acquisition (food intake), and (3) reduced the efficiency by which ingested food was converted to reproductive tissue.
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10
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Seale K, Horvath S, Teschendorff A, Eynon N, Voisin S. Making sense of the ageing methylome. Nat Rev Genet 2022; 23:585-605. [PMID: 35501397 DOI: 10.1038/s41576-022-00477-6] [Citation(s) in RCA: 66] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/18/2022] [Indexed: 12/22/2022]
Abstract
Over time, the human DNA methylation landscape accrues substantial damage, which has been associated with a broad range of age-related diseases, including cardiovascular disease and cancer. Various age-related DNA methylation changes have been described, including at the level of individual CpGs, such as differential and variable methylation, and at the level of the whole methylome, including entropy and correlation networks. Here, we review these changes in the ageing methylome as well as the statistical tools that can be used to quantify them. We detail the evidence linking DNA methylation to ageing phenotypes and the longevity strategies aimed at altering both DNA methylation patterns and machinery to extend healthspan and lifespan. Lastly, we discuss theories on the mechanistic causes of epigenetic ageing.
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Affiliation(s)
- Kirsten Seale
- Institute for Health and Sport (iHeS), Victoria University, Footscray, Melbourne, Victoria, Australia
| | - Steve Horvath
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA.,Altos Labs, San Diego, CA, USA
| | - Andrew Teschendorff
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, China.,UCL Cancer Institute, University College London, London, UK
| | - Nir Eynon
- Institute for Health and Sport (iHeS), Victoria University, Footscray, Melbourne, Victoria, Australia.
| | - Sarah Voisin
- Institute for Health and Sport (iHeS), Victoria University, Footscray, Melbourne, Victoria, Australia.
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11
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Xu X, Yuan L, Yang X, Zhang X, Wang L, Xie Q. Circadian clock in plants: Linking timing to fitness. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2022; 64:792-811. [PMID: 35088570 DOI: 10.1111/jipb.13230] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 01/25/2022] [Indexed: 05/12/2023]
Abstract
Endogenous circadian clock integrates cyclic signals of environment and daily and seasonal behaviors of organisms to achieve spatiotemporal synchronization, which greatly improves genetic diversity and fitness of species. This review addresses recent studies on the plant circadian system in the field of chronobiology, covering topics on molecular mechanisms, internal and external Zeitgebers, and hierarchical regulation of physiological outputs. The architecture of the circadian clock involves the autoregulatory transcriptional feedback loops, post-translational modifications of core oscillators, and epigenetic modifications of DNA and histones. Here, light, temperature, humidity, and internal elemental nutrients are summarized to illustrate the sensitivity of the circadian clock to timing cues. In addition, the circadian clock runs cell-autonomously, driving independent circadian rhythms in various tissues. The core oscillators responds to each other with biochemical factors including calcium ions, mineral nutrients, photosynthetic products, and hormones. We describe clock components sequentially expressed during a 24-h day that regulate rhythmic growth, aging, immune response, and resistance to biotic and abiotic stresses. Notably, more data have suggested the circadian clock links chrono-culture to key agronomic traits in crops.
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Affiliation(s)
- Xiaodong Xu
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Li Yuan
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Xin Yang
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Xiao Zhang
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Lei Wang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China
| | - Qiguang Xie
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
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12
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Tartour K, Padmanabhan K. The Clock Takes Shape-24 h Dynamics in Genome Topology. Front Cell Dev Biol 2022; 9:799971. [PMID: 35047508 PMCID: PMC8762244 DOI: 10.3389/fcell.2021.799971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 12/14/2021] [Indexed: 11/20/2022] Open
Abstract
Circadian rhythms orchestrate organismal physiology and behavior in order to anticipate daily changes in the environment. Virtually all cells have an internal rhythm that is synchronized every day by Zeitgebers (environmental cues). The synchrony between clocks within the animal enables the fitness and the health of organisms. Conversely, disruption of rhythms is linked to a variety of disorders: aging, cancer, metabolic diseases, and psychological disorders among others. At the cellular level, mammalian circadian rhythms are built on several layers of complexity. The transcriptional-translational feedback loop (TTFL) was the first to be described in the 90s. Thereafter oscillations in epigenetic marks highlighted the role of chromatin state in organizing the TTFL. More recently, studies on the 3D organization of the genome suggest that genome topology could be yet another layer of control on cellular circadian rhythms. The dynamic nature of genome topology over a solar day implies that the 3D mammalian genome has to be considered in the fourth dimension-in time. Whether oscillations in genome topology are a consequence of 24 h gene-expression or a driver of transcriptional cycles remains an open question. All said and done, circadian clock-gated phenomena such as gene expression, DNA damage response, cell metabolism and animal behavior-go hand in hand with 24 h rhythms in genome topology.
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Affiliation(s)
- Kévin Tartour
- Institut de Genomique Fonctionnelle de Lyon, CNRS UMR 5242, Ecole Normale Supérieure de Lyon, Université Claude Bernard, Lyon, France
| | - Kiran Padmanabhan
- Institut de Genomique Fonctionnelle de Lyon, CNRS UMR 5242, Ecole Normale Supérieure de Lyon, Université Claude Bernard, Lyon, France
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13
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Aviram R, Adamovich Y, Asher G. Circadian Organelles: Rhythms at All Scales. Cells 2021; 10:2447. [PMID: 34572096 PMCID: PMC8469338 DOI: 10.3390/cells10092447] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Revised: 09/14/2021] [Accepted: 09/14/2021] [Indexed: 12/12/2022] Open
Abstract
Circadian clocks have evolved in most light-sensitive organisms, from unicellular organisms to mammals. Consequently, a myriad of biological functions exhibits circadian rhythmicity, from behavior to physiology, through tissue and cellular functions to subcellular processes. Circadian rhythms in intracellular organelles are an emerging and exciting research arena. We summarize herein the current literature for rhythmicity in major intracellular organelles in mammals. These include changes in the morphology, content, and functions of different intracellular organelles. While these data highlight the presence of rhythmicity in these organelles, a gap remains in our knowledge regarding the underlying molecular mechanisms and their functional significance. Finally, we discuss the importance and challenges faced by spatio-temporal studies on these organelles and speculate on the presence of oscillators in organelles and their potential mode of communication. As circadian biology has been and continues to be studied throughout temporal and spatial axes, circadian organelles appear to be the next frontier.
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Affiliation(s)
| | | | - Gad Asher
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel; (R.A.); (Y.A.)
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14
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Abstract
Epigenetics has enriched human disease studies by adding new interpretations to disease features that cannot be explained by genetic and environmental factors. However, identifying causal mechanisms of epigenetic origin has been challenging. New opportunities have risen from recent findings in intra-individual and cyclical epigenetic variation, which includes circadian epigenetic oscillations. Cytosine modifications display deterministic temporal rhythms, which may drive ageing and complex disease. Temporality in the epigenome, or the 'chrono' dimension, may help the integration of epigenetic, environmental and genetic disease studies, and reconcile several disparities stemming from the arbitrarily delimited research fields. The ultimate goal of chrono-epigenetics is to predict disease risk, age of onset and disease dynamics from within individual-specific temporal dynamics of epigenomes.
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15
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Wang L, Zhou A, Li J, Yang M, Bu F, Ge L, Chen L, Huang W. Circadian rhythms driving a fast-paced root clock implicate species-specific regulation in Medicago truncatula. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2021; 63:1537-1554. [PMID: 34009694 DOI: 10.1111/jipb.13138] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 05/13/2021] [Indexed: 06/12/2023]
Abstract
Plants have a hierarchical circadian structure comprising multiple tissue-specific oscillators that operate at different speeds and regulate the expression of distinct sets of genes in different organs. However, the identity of the genes differentially regulated by the circadian clock in different organs, such as roots, and how their oscillations create functional specialization remain unclear. Here, we profiled the diurnal and circadian landscapes of the shoots and roots of Medicago truncatula and identified the conserved regulatory sequences contributing to transcriptome oscillations in each organ. We found that the light-dark cycles strongly affect the global transcriptome oscillation in roots, and many clock genes oscillate only in shoots. Moreover, many key genes involved in nitrogen fixation are regulated by circadian rhythms. Surprisingly, the root clock runs faster than the shoot clock, which is contrary to the hierarchical circadian structure showing a slow-paced root clock in both detached and intact Arabidopsis thaliana (L.) Heynh. roots. Our result provides important clues about the species-specific circadian regulatory mechanism, which is often overlooked, and possibly coordinates the timing between shoots and roots independent of the current prevailing model.
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Affiliation(s)
- Liping Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Anqi Zhou
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Jing Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Mingkang Yang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Fan Bu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Liangfa Ge
- Department of Grassland Science, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Engineering Research Center for Grassland Science, Guangzhou, 510642, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University, Guangzhou, 510642, China
| | - Liang Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Wei Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
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16
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Grillault Laroche D, Curis E, Bellivier F, Nepost C, Gross G, Etain B, Marie-Claire C. Network of co-expressed circadian genes, childhood maltreatment and sleep quality in bipolar disorders. Chronobiol Int 2021; 38:986-993. [PMID: 33781139 DOI: 10.1080/07420528.2021.1903028] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Bipolar disorder (BD) is a chronic and burdensome psychiatric disease, characterized by variations in mood and energy. The literature has consistently demonstrated an association between BD and childhood maltreatment (CM), and genetic variants of circadian genes have been associated with an increased vulnerability to develop BD. In this context, environmental factors such as CM may also contribute to the susceptibility to BD through alterations in the functioning of the biological clock linked to modifications of expression of circadian genes. In this study, we explored the associations between childhood maltreatment, sleep quality, and the level of expression of a comprehensive set of circadian genes in lymphoblastoid cell lines from patients with BD. The sample consisted of 52 Caucasian euthymic patients with a diagnosis of BD type 1 or type 2. The exposure to CM was assessed with the Childhood Trauma Questionnaire (CTQ), and the sleep quality was assessed using the Pittsburgh Sleep Quality Index. We measured the expression of 18 circadian genes using quantitative RT-PCR: ARNTL2, BHLHE40, BHLHE41, CLOCK, CRY1, CRY2, CSNK1D, CSNK1E, DBP, GSK3B, NPAS2, NR1D1, PER1, PER2, PER3, PPARGC1A, RORA, and RORB. Gene expression networks were analyzed with the disjoint graphs method. Compared to the other investigated transcripts, PPARGC1A was the only one whose expression level was differentially affected in patients who have experienced CM and, more specifically, physical abuse. We observed no significant effects of the other CTQ subscores (emotional and sexual abuses, physical and emotional neglects), nor of the sleep quality on the network of circadian genes expression. Although requiring replication in larger cohorts, the result obtained here is consistent with the hypothesis of an influence of CM exposure on circadian systems and highlights the importance of PPARGC1A in these processes.
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Affiliation(s)
- D Grillault Laroche
- Université de Paris, INSERM UMR-S 1144, Paris, France
- Département de Psychiatrie et de Médecine Addictologique, Hôpitaux Lariboisière-Fernand Widal, GHU APHP.Nord - Université de Paris, Paris, France
| | - E Curis
- Laboratoire de Biomathématiques, Université de Paris, Paris, France
- Service de Biostatistique et Information Médicale, Paris, France
| | - F Bellivier
- Université de Paris, INSERM UMR-S 1144, Paris, France
- Département de Psychiatrie et de Médecine Addictologique, Hôpitaux Lariboisière-Fernand Widal, GHU APHP.Nord - Université de Paris, Paris, France
| | - C Nepost
- Université de Paris, INSERM UMR-S 1144, Paris, France
| | - G Gross
- Université de Paris, INSERM UMR-S 1144, Paris, France
- Pôle Hospitalo-Universitaire de Psychiatrie d'Adultes et d'Addictologie du Grand Nancy, Centre Psychothérapique de Nancy, Laxou, France
- Faculté de Médecine, Université de Lorraine, Vandoeuvre-lès-Nancy, France
| | - B Etain
- Université de Paris, INSERM UMR-S 1144, Paris, France
- Département de Psychiatrie et de Médecine Addictologique, Hôpitaux Lariboisière-Fernand Widal, GHU APHP.Nord - Université de Paris, Paris, France
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17
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Mosig RA, Kojima S. Timing without coding: How do long non-coding RNAs regulate circadian rhythms? Semin Cell Dev Biol 2021; 126:79-86. [PMID: 34116930 DOI: 10.1016/j.semcdb.2021.04.020] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 04/12/2021] [Accepted: 04/21/2021] [Indexed: 12/13/2022]
Abstract
Long non-coding RNAs (lncRNAs) are a new class of regulatory RNAs that play important roles in disease development and a variety of biological processes. Recent studies have underscored the importance of lncRNAs in the circadian clock system and demonstrated that lncRNAs regulate core clock genes and the core clock machinery in mammals. In this review, we provide an overview of our current understanding of how lncRNAs regulate the circadian clock without coding a protein. We also offer additional insights into the challenges in understanding the functions of lncRNAs and other unresolved questions in the field. We do not cover other regulatory ncRNAs even though they also play important roles; readers are highly encouraged to refer to other excellent reviews on this topic.
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Affiliation(s)
- Rebecca A Mosig
- Department of Biological Sciences, Fralin Life Sciences Institute, Virginia Tech 1015 Life Science Circle, Blacksburg, VA 24061, USA
| | - Shihoko Kojima
- Department of Biological Sciences, Fralin Life Sciences Institute, Virginia Tech 1015 Life Science Circle, Blacksburg, VA 24061, USA.
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18
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Furlan-Magaril M, Ando-Kuri M, Arzate-Mejía RG, Morf J, Cairns J, Román-Figueroa A, Tenorio-Hernández L, Poot-Hernández AC, Andrews S, Várnai C, Virk B, Wingett SW, Fraser P. The global and promoter-centric 3D genome organization temporally resolved during a circadian cycle. Genome Biol 2021; 22:162. [PMID: 34099014 PMCID: PMC8185950 DOI: 10.1186/s13059-021-02374-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 05/05/2021] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Circadian gene expression is essential for organisms to adjust their physiology and anticipate daily changes in the environment. The molecular mechanisms controlling circadian gene transcription are still under investigation. In particular, how chromatin conformation at different genomic scales and regulatory elements impact rhythmic gene expression has been poorly characterized. RESULTS Here we measure changes in the spatial chromatin conformation in mouse liver using genome-wide and promoter-capture Hi-C alongside daily oscillations in gene transcription. We find topologically associating domains harboring circadian genes that switch assignments between the transcriptionally active and inactive compartment at different hours of the day, while their boundaries stably maintain their structure over time. To study chromatin contacts of promoters at high resolution over time, we apply promoter capture Hi-C. We find circadian gene promoters displayed a maximal number of chromatin contacts at the time of their peak transcriptional output. Furthermore, circadian genes, as well as contacted and transcribed regulatory elements, reach maximal expression at the same timepoints. Anchor sites of circadian gene promoter loops are enriched in DNA binding sites for liver nuclear receptors and other transcription factors, some exclusively present in either rhythmic or stable contacts. Finally, by comparing the interaction profiles between core clock and output circadian genes, we show that core clock interactomes are more dynamic compared to output circadian genes. CONCLUSION Our results identify chromatin conformation dynamics at different scales that parallel oscillatory gene expression and characterize the repertoire of regulatory elements that control circadian gene transcription through rhythmic or stable chromatin configurations.
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Affiliation(s)
- Mayra Furlan-Magaril
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico.
| | - Masami Ando-Kuri
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, CB2 0RE, UK
| | - Rodrigo G Arzate-Mejía
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico
- Laboratory of Neuroepigenetics, Medical Faculty of the University of Zurich and Department of Health Science and Technology of the Swiss Federal Institute of Technology, Neuroscience Center Zurich, Zurich, Switzerland
| | - Jörg Morf
- Nuclear Dynamics Programme, The Babraham Institute, Cambridge, CB22 3AT, UK
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge, CB2 0AW, UK
| | - Jonathan Cairns
- Nuclear Dynamics Programme, The Babraham Institute, Cambridge, CB22 3AT, UK
| | - Abraham Román-Figueroa
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico
| | - Luis Tenorio-Hernández
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico
| | - A César Poot-Hernández
- Unidad de Bioinformática y Manejo de Información, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico
| | - Simon Andrews
- Bioinformatics Group, The Babraham Institute, Cambridge, CB22 3AT, UK
| | - Csilla Várnai
- Nuclear Dynamics Programme, The Babraham Institute, Cambridge, CB22 3AT, UK
- Centre for Computational Biology, University of Birmingham, Birmingham, B15 2FG, UK
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, B15 2SY, UK
| | - Boo Virk
- Bioinformatics Group, The Babraham Institute, Cambridge, CB22 3AT, UK
| | - Steven W Wingett
- Bioinformatics Group, The Babraham Institute, Cambridge, CB22 3AT, UK
- Cell Biology Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge, CB2 0QH, UK
| | - Peter Fraser
- Nuclear Dynamics Programme, The Babraham Institute, Cambridge, CB22 3AT, UK
- Department of Biological Science, Florida State University, Tallahassee, FL, USA
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19
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Manella G, Sabath E, Aviram R, Dandavate V, Ezagouri S, Golik M, Adamovich Y, Asher G. The liver-clock coordinates rhythmicity of peripheral tissues in response to feeding. Nat Metab 2021; 3:829-842. [PMID: 34059820 PMCID: PMC7611072 DOI: 10.1038/s42255-021-00395-7] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 04/23/2021] [Indexed: 02/04/2023]
Abstract
The mammalian circadian system consists of a central clock in the brain that synchronizes clocks in the peripheral tissues. Although the hierarchy between central and peripheral clocks is established, little is known regarding the specificity and functional organization of peripheral clocks. Here, we employ altered feeding paradigms in conjunction with liver-clock mutant mice to map disparities and interactions between peripheral rhythms. We find that peripheral clocks largely differ in their responses to feeding time. Disruption of the liver-clock, despite its prominent role in nutrient processing, does not affect the rhythmicity of clocks in other peripheral tissues. Yet, unexpectedly, liver-clock disruption strongly modulates the transcriptional rhythmicity of peripheral tissues, primarily on daytime feeding. Concomitantly, liver-clock mutant mice exhibit impaired glucose and lipid homeostasis, which are aggravated by daytime feeding. Overall, our findings suggest that, upon nutrient challenge, the liver-clock buffers the effect of feeding-related signals on rhythmicity of peripheral tissues, irrespective of their clocks.
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Affiliation(s)
- Gal Manella
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Elizabeth Sabath
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
- Department of Medicine, Institute for transformative molecular medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Rona Aviram
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Vaishnavi Dandavate
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Saar Ezagouri
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Marina Golik
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Yaarit Adamovich
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Gad Asher
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel.
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20
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Yi JS, Díaz NM, D'Souza S, Buhr ED. The molecular clockwork of mammalian cells. Semin Cell Dev Biol 2021; 126:87-96. [PMID: 33810978 DOI: 10.1016/j.semcdb.2021.03.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 03/15/2021] [Accepted: 03/17/2021] [Indexed: 12/20/2022]
Abstract
Most organisms contain self-sustained circadian clocks. These clocks can be synchronized by environmental stimuli, but can also oscillate indefinitely in isolation. In mammals this is true at the molecular level for the majority of cell types that have been examined. A core set of "clock genes" form a transcriptional/translational feedback loop (TTFL) which repeats with a period of approximately 24 h. The exact mechanism of the TTFL differs slightly in various cell types, but all involve similar family members of the core cohort of clock genes. The clock has many outputs which are unique for different tissues. Cells in diverse tissues will convert the timing signals provided by the TTFL into uniquely orchestrated transcriptional oscillations of many clock-controlled genes and cellular processes.
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Affiliation(s)
- Jonathan S Yi
- University of Washington, Dept. of Ophthalmology, 750 Republican St., Seattle, WA 98109, USA
| | - Nicolás M Díaz
- University of Washington, Dept. of Ophthalmology, 750 Republican St., Seattle, WA 98109, USA
| | - Shane D'Souza
- Center for Chronobiology, Abrahamson Pediatric Eye Institute, Division of Pediatric Ophthalmology, Cincinnati Children's Hospital, Cincinnati, OH 45229, USA
| | - Ethan D Buhr
- University of Washington, Dept. of Ophthalmology, 750 Republican St., Seattle, WA 98109, USA.
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21
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Phillips NE, Hugues A, Yeung J, Durandau E, Nicolas D, Naef F. The circadian oscillator analysed at the single-transcript level. Mol Syst Biol 2021; 17:e10135. [PMID: 33719202 PMCID: PMC7957410 DOI: 10.15252/msb.202010135] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 01/05/2021] [Accepted: 01/19/2021] [Indexed: 12/31/2022] Open
Abstract
The circadian clock is an endogenous and self-sustained oscillator that anticipates daily environmental cycles. While rhythmic gene expression of circadian genes is well-described in populations of cells, the single-cell mRNA dynamics of multiple core clock genes remain largely unknown. Here we use single-molecule fluorescence in situ hybridisation (smFISH) at multiple time points to measure pairs of core clock transcripts, Rev-erbα (Nr1d1), Cry1 and Bmal1, in mouse fibroblasts. The mean mRNA level oscillates over 24 h for all three genes, but mRNA numbers show considerable spread between cells. We develop a probabilistic model for multivariate mRNA counts using mixtures of negative binomials, which accounts for transcriptional bursting, circadian time and cell-to-cell heterogeneity, notably in cell size. Decomposing the mRNA variability into distinct noise sources shows that clock time contributes a small fraction of the total variability in mRNA number between cells. Thus, our results highlight the intrinsic biological challenges in estimating circadian phase from single-cell mRNA counts and suggest that circadian phase in single cells is encoded post-transcriptionally.
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Affiliation(s)
- Nicholas E Phillips
- Institute of BioengineeringSchool of Life SciencesEcole Polytechnique Fédérale de LausanneLausanneSwitzerland
| | - Alice Hugues
- Institute of BioengineeringSchool of Life SciencesEcole Polytechnique Fédérale de LausanneLausanneSwitzerland
- Master de BiologieÉcole Normale Supérieure de LyonUniversité Claude Bernard Lyon IUniversité de LyonLyonFrance
| | - Jake Yeung
- Institute of BioengineeringSchool of Life SciencesEcole Polytechnique Fédérale de LausanneLausanneSwitzerland
| | - Eric Durandau
- Institute of BioengineeringSchool of Life SciencesEcole Polytechnique Fédérale de LausanneLausanneSwitzerland
| | - Damien Nicolas
- Institute of BioengineeringSchool of Life SciencesEcole Polytechnique Fédérale de LausanneLausanneSwitzerland
| | - Felix Naef
- Institute of BioengineeringSchool of Life SciencesEcole Polytechnique Fédérale de LausanneLausanneSwitzerland
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22
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Mermet J, Yeung J, Naef F. Oscillating and stable genome topologies underlie hepatic physiological rhythms during the circadian cycle. PLoS Genet 2021; 17:e1009350. [PMID: 33524027 PMCID: PMC7877755 DOI: 10.1371/journal.pgen.1009350] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 02/11/2021] [Accepted: 01/08/2021] [Indexed: 01/08/2023] Open
Abstract
The circadian clock drives extensive temporal gene expression programs controlling daily changes in behavior and physiology. In mouse liver, transcription factors dynamics, chromatin modifications, and RNA Polymerase II (PolII) activity oscillate throughout the 24-hour (24h) day, regulating the rhythmic synthesis of thousands of transcripts. Also, 24h rhythms in gene promoter-enhancer chromatin looping accompany rhythmic mRNA synthesis. However, how chromatin organization impinges on temporal transcription and liver physiology remains unclear. Here, we applied time-resolved chromosome conformation capture (4C-seq) in livers of WT and arrhythmic Bmal1 knockout mice. In WT, we observed 24h oscillations in promoter-enhancer loops at multiple loci including the core-clock genes Period1, Period2 and Bmal1. In addition, we detected rhythmic PolII activity, chromatin modifications and transcription involving stable chromatin loops at clock-output gene promoters representing key liver function such as glucose metabolism and detoxification. Intriguingly, these contacts persisted in clock-impaired mice in which both PolII activity and chromatin marks no longer oscillated. Finally, we observed chromatin interaction hubs connecting neighbouring genes showing coherent transcription regulation across genotypes. Thus, both clock-controlled and clock-independent chromatin topology underlie rhythmic regulation of liver physiology.
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MESH Headings
- ARNTL Transcription Factors/genetics
- ARNTL Transcription Factors/metabolism
- Acetylation
- Animals
- CCCTC-Binding Factor/genetics
- CCCTC-Binding Factor/metabolism
- Chromatin/genetics
- Chromatin/metabolism
- Chromatin Immunoprecipitation Sequencing/methods
- Circadian Clocks/genetics
- Circadian Rhythm/genetics
- Gene Expression Regulation
- Genome/genetics
- Histones/metabolism
- Liver/metabolism
- Lysine/metabolism
- Mice, Inbred C57BL
- Mice, Knockout
- Nuclear Receptor Subfamily 1, Group D, Member 1/genetics
- Nuclear Receptor Subfamily 1, Group D, Member 1/metabolism
- Nuclear Receptor Subfamily 1, Group F, Member 3/genetics
- Nuclear Receptor Subfamily 1, Group F, Member 3/metabolism
- RNA Polymerase II/genetics
- RNA Polymerase II/metabolism
- RNA-Seq/methods
- Mice
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Affiliation(s)
- Jérôme Mermet
- The Institute of Bioengineering (IBI), School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Jake Yeung
- The Institute of Bioengineering (IBI), School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Felix Naef
- The Institute of Bioengineering (IBI), School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
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23
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Weger BD, Gobet C, David FPA, Atger F, Martin E, Phillips NE, Charpagne A, Weger M, Naef F, Gachon F. Systematic analysis of differential rhythmic liver gene expression mediated by the circadian clock and feeding rhythms. Proc Natl Acad Sci U S A 2021; 118:e2015803118. [PMID: 33452134 PMCID: PMC7826335 DOI: 10.1073/pnas.2015803118] [Citation(s) in RCA: 71] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The circadian clock and feeding rhythms are both important regulators of rhythmic gene expression in the liver. To further dissect the respective contributions of feeding and the clock, we analyzed differential rhythmicity of liver tissue samples across several conditions. We developed a statistical method tailored to compare rhythmic liver messenger RNA (mRNA) expression in mouse knockout models of multiple clock genes, as well as PARbZip output transcription factors (Hlf/Dbp/Tef). Mice were exposed to ad libitum or night-restricted feeding under regular light-dark cycles. During ad libitum feeding, genetic ablation of the core clock attenuated rhythmic-feeding patterns, which could be restored by the night-restricted feeding regimen. High-amplitude mRNA expression rhythms in wild-type livers were driven by the circadian clock, but rhythmic feeding also contributed to rhythmic gene expression, albeit with significantly lower amplitudes. We observed that Bmal1 and Cry1/2 knockouts differed in their residual rhythmic gene expression. Differences in mean expression levels between wild types and knockouts correlated with rhythmic gene expression in wild type. Surprisingly, in PARbZip knockout mice, the mean expression levels of PARbZip targets were more strongly impacted than their rhythms, potentially due to the rhythmic activity of the D-box-repressor NFIL3. Genes that lost rhythmicity in PARbZip knockouts were identified to be indirect targets. Our findings provide insights into the diurnal transcriptome in mouse liver as we identified the differential contributions of several core clock regulators. In addition, we gained more insights on the specific effects of the feeding-fasting cycle.
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Affiliation(s)
- Benjamin D Weger
- Société des Produits Nestlé, Nestlé Research, CH-1015 Lausanne, Switzerland
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia QLD-4072, Australia
| | - Cédric Gobet
- Société des Produits Nestlé, Nestlé Research, CH-1015 Lausanne, Switzerland
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Fabrice P A David
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
- Gene Expression Core Facility, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
- BioInformatics Competence Center, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Florian Atger
- Société des Produits Nestlé, Nestlé Research, CH-1015 Lausanne, Switzerland
- Department of Pharmacology and Toxicology, University of Lausanne, CH-1015 Lausanne, Switzerland
| | - Eva Martin
- Société des Produits Nestlé, Nestlé Research, CH-1015 Lausanne, Switzerland
| | - Nicholas E Phillips
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Aline Charpagne
- Société des Produits Nestlé, Nestlé Research, CH-1015 Lausanne, Switzerland
| | - Meltem Weger
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia QLD-4072, Australia
| | - Felix Naef
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland;
| | - Frédéric Gachon
- Société des Produits Nestlé, Nestlé Research, CH-1015 Lausanne, Switzerland;
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia QLD-4072, Australia
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24
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Droin C, Kholtei JE, Bahar Halpern K, Hurni C, Rozenberg M, Muvkadi S, Itzkovitz S, Naef F. Space-time logic of liver gene expression at sub-lobular scale. Nat Metab 2021; 3:43-58. [PMID: 33432202 PMCID: PMC7116850 DOI: 10.1038/s42255-020-00323-1] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 11/12/2020] [Indexed: 01/29/2023]
Abstract
The mammalian liver is a central hub for systemic metabolic homeostasis. Liver tissue is spatially structured, with hepatocytes operating in repeating lobules, and sub-lobule zones performing distinct functions. The liver is also subject to extensive temporal regulation, orchestrated by the interplay of the circadian clock, systemic signals and feeding rhythms. However, liver zonation has previously been analysed as a static phenomenon, and liver chronobiology has been analysed at tissue-level resolution. Here, we use single-cell RNA-seq to investigate the interplay between gene regulation in space and time. Using mixed-effect models of messenger RNA expression and smFISH validations, we find that many genes in the liver are both zonated and rhythmic, and most of them show multiplicative space-time effects. Such dually regulated genes cover not only key hepatic functions such as lipid, carbohydrate and amino acid metabolism, but also previously unassociated processes involving protein chaperones. Our data also suggest that rhythmic and localized expression of Wnt targets could be explained by rhythmically expressed Wnt ligands from non-parenchymal cells near the central vein. Core circadian clock genes are expressed in a non-zonated manner, indicating that the liver clock is robust to zonation. Together, our scRNA-seq analysis reveals how liver function is compartmentalized spatio-temporally at the sub-lobular scale.
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Affiliation(s)
- Colas Droin
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Jakob El Kholtei
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Keren Bahar Halpern
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Clémence Hurni
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Milena Rozenberg
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Sapir Muvkadi
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Shalev Itzkovitz
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel.
| | - Felix Naef
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.
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25
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Cox KH, Takahashi JS. Introduction to the Clock System. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1344:3-20. [PMID: 34773223 DOI: 10.1007/978-3-030-81147-1_1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Circadian (24-h) rhythms dictate almost everything we do, setting our clocks for specific times of sleeping and eating, as well as optimal times for many other basic functions. The physiological systems that coordinate circadian rhythms are intricate, but at their core, they all can be distilled down to cell-autonomous rhythms that are then synchronized within and among tissues. At first glance, these cell-autonomous rhythms may seem rather straight-forward, but years of research in the field has shown that they are strikingly complex, responding to many different external signals, often with remarkable tissue-specificity. To understand the cellular clock system, it is important to be familiar with the major players, which consist of pairs of proteins in a triad of transcriptional/translational feedback loops. In this chapter, we will go through each of the core protein pairs one-by-one, summarizing the literature as to their regulation and their broader impacts on circadian gene expression. We will conclude by briefly examining the human genetics literature, as well as providing perspectives on the future of the study of the molecular clock.
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Affiliation(s)
- Kimberly H Cox
- Department of Neuroscience and Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Joseph S Takahashi
- Department of Neuroscience and Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA. .,Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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26
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Abstract
The identification and characterization of rhythmically expressed mRNAs have been an active area of research over the past 20 years, as these mRNAs are believed to produce the daily rhythms in a wide range of biological processes. Circadian transcriptome studies have used mature mRNA as a primary readout and focused largely on rhythmic RNA synthesis as a regulatory mechanism underlying rhythmic mRNA expression. However, RNA synthesis, RNA degradation, or a combination of both must be rhythmic to drive rhythmic RNA profiles, and it is still unclear to what extent rhythmic synthesis leads to rhythmic RNA profiles. In addition, circadian RNA expression is also often tissue specific. Although a handful of genes cycle in all or most tissues, others are rhythmic only in certain tissues, even though the same core clock mechanism is believed to control the rhythmic RNA profiles in all tissues. This review focuses on the dynamics of rhythmic RNA synthesis and degradation and discusses how these steps collectively determine the rhythmicity, phase, and amplitude of RNA accumulation. In particular, we highlight a possible role of RNA degradation in driving tissue-specific RNA rhythms. By unifying findings from experimental and theoretical studies, we will provide a comprehensive overview of how rhythmic gene expression can be achieved and how each regulatory step contributes to tissue-specific circadian transcriptome output in mammals.
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Affiliation(s)
| | - Shihoko Kojima
- To whom all correspondence should be addressed: Shihoko Kojima, Department of Biological Sciences, Fralin Life Sciences Institute, Virginia Tech, 1015 Life Science Circle, Blacksburg, VA, 24061, USA; .
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27
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Li Y, Wang L, Yuan L, Song Y, Sun J, Jia Q, Xie Q, Xu X. Molecular investigation of organ-autonomous expression of Arabidopsis circadian oscillators. PLANT, CELL & ENVIRONMENT 2020; 43:1501-1512. [PMID: 32012302 DOI: 10.1111/pce.13739] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 01/27/2020] [Accepted: 01/28/2020] [Indexed: 06/10/2023]
Abstract
The circadian pacemaker in plants is a hierarchical multioscillator system that directs and maintains a 24-hr oscillation required for organism homeostasis and environmental fitness. Molecular clockwork within individual tissues and organs acts cell autonomously, showing differences in circadian expression of core oscillators and their target genes; there are functional dominance and coupling in the complex regulatory network. However, molecular characteristics of organ-specific clocks are still unknown. Here, we showed the detached shoot and root possess dynamic circadian protein-protein interactions between clock core components, periodicity in organs exhibits a difference. The period length difference between shoot and root was not remarkable in prr7-3 and prr7-3 prr9-1 mutants. In addition, the phase transition curve indicated that shoot and root clock respond differently to the resetting cues of ambient temperature. PRR9 and PRR7 compensate circadian period between 22°C and 28°C in shoot, not in root. The circadian rhythms of PRR9 or PRR7 transcript accumulation showed no difference at 22°C and 28°C in shoot, but differences were observed in root. In summary, our results reveal the specificity of dynamic circadian protein-protein interactions in organ-autonomous clocks and the critical roles of PRR9 and PRR7 in mechanisms regulating temperature compensation in aerial shoot system.
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Affiliation(s)
- Yue Li
- Key Laboratory of Molecular and Cell Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Lingbao Wang
- Key Laboratory of Molecular and Cell Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Li Yuan
- Key Laboratory of Molecular and Cell Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Yang Song
- Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, Kaifeng, China
| | - Junqiu Sun
- Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, Kaifeng, China
| | - Qian Jia
- Key Laboratory of Molecular and Cell Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Qiguang Xie
- Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, Kaifeng, China
| | - Xiaodong Xu
- Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, Kaifeng, China
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28
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Dantas LLDB, Almeida-Jesus FM, de Lima NO, Alves-Lima C, Nishiyama-Jr MY, Carneiro MS, Souza GM, Hotta CT. Rhythms of Transcription in Field-Grown Sugarcane Are Highly Organ Specific. Sci Rep 2020; 10:6565. [PMID: 32300143 PMCID: PMC7162945 DOI: 10.1038/s41598-020-63440-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2019] [Accepted: 03/25/2020] [Indexed: 12/29/2022] Open
Abstract
Circadian clocks improve plant fitness in a rhythmic environment. As each cell has its own circadian clock, we hypothesized that sets of cells with different functions would have distinct rhythmic behaviour. To test this, we investigated whether different organs in field-grown sugarcane follow the same rhythms in transcription. We assayed the transcriptomes of three organs during a day: leaf, a source organ; internodes 1 and 2, sink organs focused on cell division and elongation; and internode 5, a sink organ focused on sucrose storage. The leaf had twice as many rhythmic transcripts (>68%) as internodes, and the rhythmic transcriptomes of the internodes were more like each other than to those of the leaves. Among the transcripts expressed in all organs, only 7.4% showed the same rhythmic pattern. Surprisingly, the central oscillators of these organs - the networks that generate circadian rhythms - had similar dynamics, albeit with different amplitudes. The differences in rhythmic transcriptomes probably arise from amplitude differences in tissue-specific circadian clocks and different sensitivities to environmental cues, highlighted by the sampling under field conditions. The vast differences suggest that we must study tissue-specific circadian clocks in order to understand how the circadian clock increases the fitness of the whole plant.
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Affiliation(s)
- Luíza Lane de Barros Dantas
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, 05508-000, Brazil
- Max Planck Institute for Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
| | | | - Natalia Oliveira de Lima
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, 05508-000, Brazil
| | - Cícero Alves-Lima
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, 05508-000, Brazil
| | | | - Monalisa Sampaio Carneiro
- Departamento de Biotecnologia e Produção Vegetal e Animal, Centro de Ciências Agrárias, Universidade Federal de São Carlos, São Carlos, SP, 13600-970, Brazil
| | - Glaucia Mendes Souza
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, 05508-000, Brazil
| | - Carlos Takeshi Hotta
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, 05508-000, Brazil.
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29
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Abstract
Feeding schedules entrain circadian clocks in multiple brain regions and most peripheral organs and tissues, thereby synchronizing daily rhythms of foraging behavior and physiology with times of day when food is most likely to be found. Entrainment of peripheral clocks to mealtime is accomplished by multiple feeding-related signals, including absorbed nutrients and metabolic hormones, acting in parallel or in series in a tissue-specific fashion. Less is known about the signals that synchronize circadian clocks in the brain with feeding time, some of which are presumed to generate the circadian rhythms of food-anticipatory activity that emerge when food is restricted to a fixed daily mealtime. In this commentary, I consider the possibility that food-anticipatory activity rhythms are driven or entrained by circulating ghrelin, ketone bodies or insulin. While evidence supports the potential of these signals to participate in the induction or amount of food-anticipatory behavior, it falls short of establishing either a necessary or sufficient role or accounting for circadian properties of anticipatory rhythms. The availability of multiple, circulating signals by which circadian oscillators in many brain regions might entrain to mealtime has supported a view that food-anticipatory rhythms of behavior are mediated by a broadly distributed system of clocks. The evidence, however, does not rule out the possibility that multiple peripheral and central food-entrained oscillators and feeding-related signals converge on circadian oscillators in a defined location which ultimately set the phase and gate the expression of anticipatory activity rhythms. A candidate location is the dorsal striatum, a core component of the neural system which mediates reward, motivation and action and which contains circadian oscillators entrainable by food and dopaminergic drugs. Systemic metabolic signals, such as ghrelin, ketones and insulin, may participate in circadian food anticipation to the extent that they modulate dopamine afferents to circadian clocks in this area.
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Affiliation(s)
- Ralph E Mistlberger
- Department of Psychology, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A2S6, Canada
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30
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Cox KH, Takahashi JS. Circadian clock genes and the transcriptional architecture of the clock mechanism. J Mol Endocrinol 2019; 63:R93-R102. [PMID: 31557726 PMCID: PMC6872945 DOI: 10.1530/jme-19-0153] [Citation(s) in RCA: 228] [Impact Index Per Article: 45.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 09/26/2019] [Indexed: 12/12/2022]
Abstract
The mammalian circadian clock has evolved as an adaptation to the 24-h light/darkness cycle on earth. Maintaining cellular activities in synchrony with the activities of the organism (such as eating and sleeping) helps different tissue and organ systems coordinate and optimize their performance. The full extent of the mechanisms by which cells maintain the clock are still under investigation, but involve a core set of clock genes that regulate large networks of gene transcription both by direct transcriptional activation/repression as well as the recruitment of proteins that modify chromatin states more broadly.
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Affiliation(s)
- Kimberly H. Cox
- Department of Neuroscience, The University of Texas Southwestern Medical Center, Dallas, TX 75390-9111, USA
| | - Joseph S. Takahashi
- Department of Neuroscience, The University of Texas Southwestern Medical Center, Dallas, TX 75390-9111, USA
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390-9111, USA
- To whom correspondence should be addressed:
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31
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Brunet A, Forsberg F, Fan Q, Sæther T, Collas P. Nuclear Lamin B1 Interactions With Chromatin During the Circadian Cycle Are Uncoupled From Periodic Gene Expression. Front Genet 2019; 10:917. [PMID: 31632442 PMCID: PMC6785633 DOI: 10.3389/fgene.2019.00917] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 08/30/2019] [Indexed: 12/17/2022] Open
Abstract
Many mammalian genes exhibit circadian expression patterns concordant with periodic binding of transcription factors, chromatin modifications, and chromosomal interactions. Here we investigate whether chromatin periodically associates with nuclear lamins. Entrainment of the circadian clock is accompanied, in mouse liver, by a net gain of lamin B1–chromatin interactions genome-wide, after which the majority of lamina-associated domains (LADs) are conserved during the circadian cycle. By tailoring a bioinformatics pipeline designed to identify periodic gene expression patterns, we also observe hundreds of variable lamin B1–chromatin interactions among which oscillations occur at 64 LADs, affecting one or both LAD extremities or entire LADs. Only a small subset of these oscillations however exhibit highly significant 12, 18, 24, or 30 h periodicity. These periodic LADs display oscillation asynchrony between their 5′ and 3′ borders, and are uncoupled from periodic gene expression within or in the vicinity of these LADs. Periodic gene expression is also unrelated to variations in gene-to-nearest LAD distances detected during the circadian cycle. Accordingly, periodic genes, including central clock-control genes, are located megabases away from LADs throughout circadian time, suggesting stable residence in a transcriptionally permissive chromatin environment. We conclude that periodic LADs are not a dominant feature of variable lamin B1–chromatin interactions during the circadian cycle in mouse liver. Our results also suggest that periodic hepatic gene expression is not regulated by rhythmic chromatin associations with the nuclear lamina.
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Affiliation(s)
- Annaël Brunet
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Frida Forsberg
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Qiong Fan
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Thomas Sæther
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Philippe Collas
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Oslo, Norway.,Department of Immunology and Transfusion Medicine, Oslo University Hospital, Oslo, Norway
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