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Gillen AE, Fu R, Riemondy KA, Jager J, Fang B, Lazar MA, Martin SL. Liver Transcriptome Dynamics During Hibernation Are Shaped by a Shifting Balance Between Transcription and RNA Stability. Front Physiol 2021; 12:662132. [PMID: 34093224 PMCID: PMC8176218 DOI: 10.3389/fphys.2021.662132] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 04/26/2021] [Indexed: 12/12/2022] Open
Abstract
Hibernators dramatically lower metabolism to save energy while fasting for months. Prolonged fasting challenges metabolic homeostasis, yet small-bodied hibernators emerge each spring ready to resume all aspects of active life, including immediate reproduction. The liver is the body’s metabolic hub, processing and detoxifying macromolecules to provide essential fuels to brain, muscle and other organs throughout the body. Here we quantify changes in liver gene expression across several distinct physiological states of hibernation in 13-lined ground squirrels, using RNA-seq to measure the steady-state transcriptome and GRO-seq to measure transcription for the first time in a hibernator. Our data capture key timepoints in both the seasonal and torpor-arousal cycles of hibernation. Strong positive correlation between transcription and the transcriptome indicates that transcriptional control dominates the known seasonal reprogramming of metabolic gene expression in liver for hibernation. During the torpor-arousal cycle, however, discordance develops between transcription and the steady-state transcriptome by at least two mechanisms: 1) although not transcribed during torpor, some transcripts are unusually stable across the torpor bout; and 2) unexpectedly, on some genes, our data suggest continuing, slow elongation with a failure to terminate transcription across the torpor bout. While the steady-state RNAs corresponding to these read through transcripts did not increase during torpor, they did increase shortly after rewarming despite their simultaneously low transcription. Both of these mechanisms would assure the immediate availability of functional transcripts upon rewarming. Integration of transcriptional, post-transcriptional and RNA stability control mechanisms, all demonstrated in these data, likely initiate a serial gene expression program across the short euthermic period that restores the tissue and prepares the animal for the next bout of torpor.
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Affiliation(s)
- Austin E Gillen
- RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, CO, United States
| | - Rui Fu
- RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, CO, United States
| | - Kent A Riemondy
- RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, CO, United States
| | - Jennifer Jager
- Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, and The Institute for Diabetes, Obesity and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States.,Division of Endocrinology, Diabetes, and Metabolism, Department of Genetics, and The Institute for Diabetes, Obesity and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Bin Fang
- Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, and The Institute for Diabetes, Obesity and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States.,Division of Endocrinology, Diabetes, and Metabolism, Department of Genetics, and The Institute for Diabetes, Obesity and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Mitchell A Lazar
- Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, and The Institute for Diabetes, Obesity and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States.,Division of Endocrinology, Diabetes, and Metabolism, Department of Genetics, and The Institute for Diabetes, Obesity and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Sandra L Martin
- RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, CO, United States.,Department of Cell and Developmental Biology, University of Colorado School of Medicine, Aurora, CO, United States
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52
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Natural antisense transcript of Period2, Per2AS, regulates the amplitude of the mouse circadian clock. Genes Dev 2021; 35:899-913. [PMID: 34016691 PMCID: PMC8168560 DOI: 10.1101/gad.343541.120] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 04/26/2021] [Indexed: 12/20/2022]
Abstract
In mammals, a set of core clock genes form transcription-translation feedback loops to generate circadian oscillations. We and others recently identified a novel transcript at the Period2 (Per2) locus that is transcribed from the antisense strand of Per2 This transcript, Per2AS, is expressed rhythmically and antiphasic to Per2 mRNA, leading to our hypothesis that Per2AS and Per2 mutually inhibit each other's expression and form a double negative feedback loop. By perturbing the expression of Per2AS, we found that Per2AS transcription, but not transcript, represses Per2 However, Per2 does not repress Per2AS, as Per2 knockdown led to a decrease in the Per2AS level, indicating that Per2AS forms a single negative feedback loop with Per2 and maintains the level of Per2 within the oscillatory range. Per2AS also regulates the amplitude of the circadian clock, and this function cannot be solely explained through its interaction with Per2, as Per2 knockdown does not recapitulate the phenotypes of Per2AS perturbation. Overall, our data indicate that Per2AS is an important regulatory molecule in the mammalian circadian clock machinery. Our work also supports the idea that antisense transcripts of core clock genes constitute a common feature of circadian clocks, as they are found in other organisms.
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Abulmeaty MMA, Almajwal AM, Alnumair KS, Razak S, Hasan MM, Fawzy A, Farraj AI, Abudawood M, Aljuraiban GS. Effect of Long-Term Continuous Light Exposure and Western Diet on Adropin Expression, Lipid Metabolism, and Energy Homeostasis in Rats. BIOLOGY 2021; 10:biology10050413. [PMID: 34066943 PMCID: PMC8148543 DOI: 10.3390/biology10050413] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 04/30/2021] [Accepted: 05/01/2021] [Indexed: 12/15/2022]
Abstract
Long-term continuous light exposure (CL) and western diet (WD) effects on Adropin expression, RORα, and Rev-erb-α nuclear receptors and energy homeostasis were studied in rats. Thirty-two male Wistar rats (250-290 g) were enrolled for 3 months in the following groups (n = 8/group): (a) Normal control group (NC), (b) CL group, (c) WD group, and (d) CL + WD group. Then, indirect calorimetry and food intake (FI) were measured. Finally, Adropin, hormone-sensitive lipase (HSL), adipocyte triglyceride lipase (ATGL), and free fatty acids (FFA) were measured. Additionally, the histopathology and gene expression of Enho, RORα, and Rev-erb-α genes were done. The CL alone elevated the Adropin plasma level and gene expression, increased RORα expression, and decreased the Rev-erb-α nuclear receptor expression mainly in the liver and kidney. Besides, CL increased the total energy expenditure (TEE) and decreased the respiratory quotient. WD alone or in combination with the CL reversed gene expression of Enho, RORα, and Rev-erb-α. Combined CL and WD increased the TEE, reduced the food intake, increased the ATGL, and reduced the Adropin level in addition to widespread degenerative changes in the liver, spleen, and renal tissues. The deleterious effects of CL and WD on energy homeostasis may include Adropin with the involvement of the RORα and Rev-erb-α nuclear receptors.
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Affiliation(s)
- Mahmoud Mustafa Ali Abulmeaty
- Department of Community Health Sciences, College of Applied Medical Sciences, King Saud University, Riyadh 11362, Saudi Arabia; (A.M.A.); (K.S.A.); (S.R.); (G.S.A.)
- Department of Medical Physiology, School of Medicine, Zagazig University, Zagazig 44519, Egypt;
- Correspondence: ; Tel.: +966-54-815-5983
| | - Ali Madi Almajwal
- Department of Community Health Sciences, College of Applied Medical Sciences, King Saud University, Riyadh 11362, Saudi Arabia; (A.M.A.); (K.S.A.); (S.R.); (G.S.A.)
| | - Khalid S. Alnumair
- Department of Community Health Sciences, College of Applied Medical Sciences, King Saud University, Riyadh 11362, Saudi Arabia; (A.M.A.); (K.S.A.); (S.R.); (G.S.A.)
| | - Suhail Razak
- Department of Community Health Sciences, College of Applied Medical Sciences, King Saud University, Riyadh 11362, Saudi Arabia; (A.M.A.); (K.S.A.); (S.R.); (G.S.A.)
| | - Mai Mohammed Hasan
- Department of Medical Physiology, School of Medicine, Zagazig University, Zagazig 44519, Egypt;
| | - Amal Fawzy
- Department of Medical Biochemistry, School of Medicine, Zagazig University, Zagazig 44519, Egypt;
| | - Abdullah Ibrahim Farraj
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Saud University, Riyadh 11362, Saudi Arabia; (A.I.F.); (M.A.)
| | - Manal Abudawood
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Saud University, Riyadh 11362, Saudi Arabia; (A.I.F.); (M.A.)
| | - Ghadeer S. Aljuraiban
- Department of Community Health Sciences, College of Applied Medical Sciences, King Saud University, Riyadh 11362, Saudi Arabia; (A.M.A.); (K.S.A.); (S.R.); (G.S.A.)
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54
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Fu X, Liu JS, Li P. Stopping the Clock on Seizures! Trends Neurosci 2021; 44:422-423. [PMID: 33965214 DOI: 10.1016/j.tins.2021.04.002] [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: 03/30/2021] [Accepted: 04/12/2021] [Indexed: 10/21/2022]
Abstract
A recent paper by Zhang et al. shows that REV-ERBα, a negative regulator of the circadian molecular clock, is pro-convulsant through its action on GABA signaling. The findings support the role of the circadian molecular clock in epilepsy and suggest REV-ERBα as a potential therapeutic target for the management of seizures.
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Affiliation(s)
- Xiaoqin Fu
- The Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, 325000, China
| | - Judy S Liu
- Department of Neurology, Brown University, Providence, RI 02903, USA; Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI 02903, USA.
| | - Peijun Li
- The Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, 325000, China.
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55
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Abruzzi KC, Gobet C, Naef F, Rosbash M. Comment on "Circadian rhythms in the absence of the clock gene Bmal1". Science 2021; 372:372/6539/eabf0922. [PMID: 33859000 DOI: 10.1126/science.abf0922] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 03/05/2021] [Indexed: 01/13/2023]
Abstract
Ray et al (Reports, 14 February 2020, p. 800) recently claimed temperature-compensated, free-running mRNA oscillations in Bmal1 -/- liver slices and skin fibroblasts. We reanalyzed these data and found far fewer reproducible mRNA oscillations in this genotype. We also note errors and potentially inappropriate analyses.
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Affiliation(s)
| | - Cédric Gobet
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Felix Naef
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland.
| | - Michael Rosbash
- Howard Hughes Medical Institute, Brandeis University, Waltham, MA, USA.
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56
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Wang Y, Mao Y, Zhao Y, Yi X, Ding G, Yu C, Sheng J, Liu X, Meng Y, Huang H. Early-life undernutrition induces enhancer RNA remodeling in mice liver. Epigenetics Chromatin 2021; 14:18. [PMID: 33789751 PMCID: PMC8011416 DOI: 10.1186/s13072-021-00392-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Accepted: 03/19/2021] [Indexed: 01/10/2023] Open
Abstract
Background Maternal protein restriction diet (PRD) increases the risk of metabolic dysfunction in adulthood, the mechanisms during the early life of offspring are still poorly understood. Apart from genetic factors, epigenetic mechanisms are crucial to offer phenotypic plasticity in response to environmental situations and transmission. Enhancer-associated noncoding RNAs (eRNAs) transcription serves as a robust indicator of enhancer activation, and have potential roles in mediating enhancer functions and gene transcription. Results Using global run-on sequencing (GRO-seq) of nascent RNA including eRNA and total RNA sequencing data, we show that early-life undernutrition causes remodeling of enhancer activity in mouse liver. Differentially expressed nascent active genes were enriched in metabolic pathways. Besides, our work detected a large number of high confidence enhancers based on eRNA transcription at the ages of 4 weeks and 7 weeks, respectively. Importantly, except for ~ 1000 remodeling enhancers, the early-life undernutrition induced instability of enhancer activity which decreased in 4 weeks and increased in adulthood. eRNA transcription mainly contributes to the regulation of some important metabolic enzymes, suggesting a link between metabolic dysfunction and enhancer transcriptional control. We discovered a novel eRNA that is positively correlated to the expression of circadian gene Cry1 with increased binding of epigenetic cofactor p300. Conclusions Our study reveals novel insights into mechanisms of metabolic dysfunction. Enhancer activity in early life acts on metabolism-associated genes, leading to the increased susceptibility of metabolic disorders. Supplementary Information The online version contains supplementary material available at 10.1186/s13072-021-00392-w.
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Affiliation(s)
- Yinyu Wang
- The International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yiting Mao
- The International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yiran Zhao
- The International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xianfu Yi
- School of Biomedical Engineering and Technology, Tianjin Medical University, Tianjin, China
| | - Guolian Ding
- The International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Key Laboratory of Embryo Original Disease, Shanghai, China.,Institute of Embryo-Fetal Original Adult Disease Affiliated To Shanghai, Jiao Tong University School of Medicine, Shanghai, China
| | - Chuanjin Yu
- The International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Key Laboratory of Embryo Original Disease, Shanghai, China.,Institute of Embryo-Fetal Original Adult Disease Affiliated To Shanghai, Jiao Tong University School of Medicine, Shanghai, China
| | - Jianzhong Sheng
- Shanghai Key Laboratory of Embryo Original Disease, Shanghai, China.,Department of Pathology and Pathophysiology, School of Medicine, Zhejiang University, Hangzhou, China
| | - Xinmei Liu
- The International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Key Laboratory of Embryo Original Disease, Shanghai, China.,Institute of Embryo-Fetal Original Adult Disease Affiliated To Shanghai, Jiao Tong University School of Medicine, Shanghai, China
| | - Yicong Meng
- The International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China. .,Shanghai Key Laboratory of Embryo Original Disease, Shanghai, China. .,Institute of Embryo-Fetal Original Adult Disease Affiliated To Shanghai, Jiao Tong University School of Medicine, Shanghai, China.
| | - Hefeng Huang
- The International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China. .,Shanghai Key Laboratory of Embryo Original Disease, Shanghai, China. .,Institute of Embryo-Fetal Original Adult Disease Affiliated To Shanghai, Jiao Tong University School of Medicine, Shanghai, China.
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57
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Woller A, Gonze D. Circadian Misalignment and Metabolic Disorders: A Story of Twisted Clocks. BIOLOGY 2021; 10:biology10030207. [PMID: 33801795 PMCID: PMC8001388 DOI: 10.3390/biology10030207] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 03/01/2021] [Accepted: 03/02/2021] [Indexed: 01/18/2023]
Abstract
Simple Summary In mammals, many physiological processes follow a 24 h rhythmic pattern. These rhythms are governed by a complex network of circadian clocks, which perceives external time cues (notably light and nutrients) and adjusts the timing of metabolic and physiological functions to allow a proper adaptation of the organism to the daily changes in the environmental conditions. Circadian rhythms originate at the cellular level through a transcriptional–translational regulatory network involving a handful of clock genes. In this review, we show how adverse effects caused by ill-timed feeding or jet lag can lead to a dysregulation of this genetic clockwork, which in turn results in altered metabolic regulation and possibly in diseases. We also show how computational modeling can complement experimental observations to understand the design of the clockwork and the onset of metabolic disorders. Abstract Biological clocks are cell-autonomous oscillators that can be entrained by periodic environmental cues. This allows organisms to anticipate predictable daily environmental changes and, thereby, to partition physiological processes into appropriate phases with respect to these changing external conditions. Nowadays our 24/7 society challenges this delicate equilibrium. Indeed, many studies suggest that perturbations such as chronic jet lag, ill-timed eating patterns, or shift work increase the susceptibility to cardiometabolic disorders, diabetes, and cancers. However the underlying mechanisms are still poorly understood. A deeper understanding of this complex, dynamic system requires a global holistic approach for which mathematical modeling can be highly beneficial. In this review, we summarize several experimental works pertaining to the effect of adverse conditions on clock gene expression and on physiology, and we show how computational models can bring interesting insights into the links between circadian misalignment and metabolic diseases.
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Affiliation(s)
- Aurore Woller
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel;
| | - Didier Gonze
- Unité de Chronobiologie Théorique, Faculté des Sciences CP 231, Université Libre de Bruxelles, Bvd du Triomphe, 1050 Bruxelles, Belgium
- Correspondence:
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58
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Affiliation(s)
- Ravi Allada
- From the Department of Neurobiology, Northwestern University, Evanston (R.A.), and the Department of Medicine, Division of Endocrinology, Metabolism, and Molecular Medicine, Feinberg School of Medicine, Northwestern University, Chicago (J.B.) - both in Illinois
| | - Joseph Bass
- From the Department of Neurobiology, Northwestern University, Evanston (R.A.), and the Department of Medicine, Division of Endocrinology, Metabolism, and Molecular Medicine, Feinberg School of Medicine, Northwestern University, Chicago (J.B.) - both in Illinois
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59
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Zheng Z, Nakamura K, Gershbaum S, Wang X, Thomas S, Bessler M, Schrope B, Krikhely A, Liu RM, Ozcan L, López JA, Tabas I. Interacting hepatic PAI-1/tPA gene regulatory pathways influence impaired fibrinolysis severity in obesity. J Clin Invest 2021; 130:4348-4359. [PMID: 32657780 PMCID: PMC7410057 DOI: 10.1172/jci135919] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 05/13/2020] [Indexed: 12/13/2022] Open
Abstract
Fibrinolysis is initiated by tissue-type plasminogen activator (tPA) and inhibited by plasminogen activator inhibitor 1 (PAI-1). In obese humans, plasma PAI-1 and tPA proteins are increased, but PAI-1 dominates, leading to reduced fibrinolysis and thrombosis. To understand tPA–PAI-1 regulation in obesity, we focused on hepatocytes, a functionally important source of tPA and PAI-1 that sense obesity-induced metabolic stress. We showed that obese mice, like humans, had reduced fibrinolysis and increased plasma PAI-1 and tPA, due largely to their increased hepatocyte expression. A decrease in the PAI-1 (SERPINE1) gene corepressor Rev-Erbα increased PAI-1, which then increased the tPA gene PLAT via a PAI-1/LRP1/PKA/p-CREB1 pathway. This pathway was partially counterbalanced by increased DACH1, a PLAT-negative regulator. We focused on the PAI-1/PLAT pathway, which mitigates the reduction in fibrinolysis in obesity. Thus, silencing hepatocyte PAI-1, CREB1, or tPA in obese mice lowered plasma tPA and further impaired fibrinolysis. The PAI-1/PLAT pathway was present in primary human hepatocytes, and associations among PAI-1, tPA, and PLAT in livers from obese and lean humans were consistent with these findings. Knowledge of PAI-1 and tPA regulation in hepatocytes in obesity may suggest therapeutic strategies for improving fibrinolysis and lowering the risk of thrombosis in this setting.
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Affiliation(s)
- Ze Zheng
- Department of Medicine, Columbia University Irving Medical Center, New York, New York, USA
| | - Keiko Nakamura
- Department of Medicine, Columbia University Irving Medical Center, New York, New York, USA.,Graduate School of Medicine and.,Faculty of Medicine, University of Tokyo, Tokyo, Japan
| | - Shana Gershbaum
- Department of Medicine, Columbia University Irving Medical Center, New York, New York, USA.,Neuroscience and Behavior Department, Barnard College, New York, New York, USA
| | - Xiaobo Wang
- Department of Medicine, Columbia University Irving Medical Center, New York, New York, USA
| | - Sherry Thomas
- Department of Medicine, Columbia University Irving Medical Center, New York, New York, USA
| | - Marc Bessler
- Department of Surgery, Columbia University Irving Medical Center, New York, New York, USA
| | - Beth Schrope
- Department of Surgery, Columbia University Irving Medical Center, New York, New York, USA
| | - Abraham Krikhely
- Department of Surgery, Columbia University Irving Medical Center, New York, New York, USA
| | - Rui-Ming Liu
- Division of Pulmonary Allergy, and Critical Care Medicine, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Lale Ozcan
- Department of Medicine, Columbia University Irving Medical Center, New York, New York, USA
| | - José A López
- Department of Medicine, University of Washington, Seattle, Washington, USA.,Bloodworks Research Institute, Seattle, Washington, USA
| | - Ira Tabas
- Department of Medicine, Columbia University Irving Medical Center, New York, New York, USA.,Department of Physiology and.,Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, New York, USA
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60
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Abstract
The circadian clock controls several aspects of mammalian physiology and orchestrates the daily oscillations of biological processes and behavior. Our circadian rhythms are driven by an endogenous central clock in the brain that synchronizes with clocks in peripheral tissues, thereby regulating our immune system and the severity of infections. These rhythms affect the pharmacokinetics and efficacy of therapeutic agents and vaccines. The core circadian regulatory circuits and clock-regulated host pathways provide fertile ground to identify novel antiviral therapies. An increased understanding of the role circadian systems play in regulating virus infection and the host response to the virus will inform our clinical management of these diseases. This review provides an overview of the experimental and clinical evidence reporting on the interplay between the circadian clock and viral infections, highlighting the importance of virus-clock research.
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Affiliation(s)
- Helene Borrmann
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | | | - Xiaodong Zhuang
- Xiaodong Zhuang, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7FZ, UK; e-mail:
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61
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Revealing the hidden reality of the mammalian 12-h ultradian rhythms. Cell Mol Life Sci 2021; 78:3127-3140. [PMID: 33449146 DOI: 10.1007/s00018-020-03730-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 11/18/2020] [Accepted: 12/04/2020] [Indexed: 12/29/2022]
Abstract
Biological oscillations often cycle at different harmonics of the 24-h circadian rhythms, a phenomenon we coined "Musica Universalis" in 2017. Like the circadian rhythm, the 12-h oscillation is also evolutionarily conserved, robust, and has recently gained new traction in the field of chronobiology. Originally thought to be regulated by the circadian clock and/or environmental cues, recent new evidences support the notion that the majority of 12-h rhythms are regulated by a distinct and cell-autonomous pacemaker that includes the unfolded protein response (UPR) transcription factor spliced form of XBP1 (XBP1s). 12-h cycle of XBP1s level in turn transcriptionally generates robust 12-h rhythms of gene expression enriched in the central dogma information flow (CEDIF) pathway. Given the regulatory and functional separation of the 12-h and circadian clocks, in this review, we will focus our attention on the mammalian 12-h pacemaker, and discuss our current understanding of its prevalence, evolutionary origin, regulation, and functional roles in both physiological and pathological processes.
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The circadian cryptochrome, CRY1, is a pro-tumorigenic factor that rhythmically modulates DNA repair. Nat Commun 2021; 12:401. [PMID: 33452241 PMCID: PMC7810852 DOI: 10.1038/s41467-020-20513-5] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 12/03/2020] [Indexed: 01/01/2023] Open
Abstract
Mechanisms regulating DNA repair processes remain incompletely defined. Here, the circadian factor CRY1, an evolutionally conserved transcriptional coregulator, is identified as a tumor specific regulator of DNA repair. Key findings demonstrate that CRY1 expression is androgen-responsive and associates with poor outcome in prostate cancer. Functional studies and first-in-field mapping of the CRY1 cistrome and transcriptome reveal that CRY1 regulates DNA repair and the G2/M transition. DNA damage stabilizes CRY1 in cancer (in vitro, in vivo, and human tumors ex vivo), which proves critical for efficient DNA repair. Further mechanistic investigation shows that stabilized CRY1 temporally regulates expression of genes required for homologous recombination. Collectively, these findings reveal that CRY1 is hormone-induced in tumors, is further stabilized by genomic insult, and promotes DNA repair and cell survival through temporal transcriptional regulation. These studies identify the circadian factor CRY1 as pro-tumorigenic and nominate CRY1 as a new therapeutic target. Cryptochrome 1 (CRY1) is a transcriptional coregulator associated with the circadian clock. Here the authors reveal that CRY1 is hormone-regulated, stabilized by genomic insult, and promotes DNA repair and cell survival through temporal transcriptional regulation.
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63
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Morris H, Gonçalves CF, Dudek M, Hoyland J, Meng QJ. Tissue physiology revolving around the clock: circadian rhythms as exemplified by the intervertebral disc. Ann Rheum Dis 2021; 80:828-839. [PMID: 33397731 DOI: 10.1136/annrheumdis-2020-219515] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 12/15/2020] [Accepted: 12/16/2020] [Indexed: 01/07/2023]
Abstract
Circadian clocks in the brain and peripheral tissues temporally coordinate local physiology to align with the 24 hours rhythmic environment through light/darkness, rest/activity and feeding/fasting cycles. Circadian disruptions (during ageing, shift work and jet-lag) have been proposed as a risk factor for degeneration and disease of tissues, including the musculoskeletal system. The intervertebral disc (IVD) in the spine separates the bony vertebrae and permits movement of the spinal column. IVD degeneration is highly prevalent among the ageing population and is a leading cause of lower back pain. The IVD is known to experience diurnal changes in loading patterns driven by the circadian rhythm in rest/activity cycles. In recent years, emerging evidence indicates the existence of molecular circadian clocks within the IVD, disruption to which accelerates tissue ageing and predispose animals to IVD degeneration. The cell-intrinsic circadian clocks in the IVD control key aspects of physiology and pathophysiology by rhythmically regulating the expression of ~3.5% of the IVD transcriptome, allowing cells to cope with the drastic biomechanical and chemical changes that occur throughout the day. Indeed, epidemiological studies on long-term shift workers have shown an increased incidence of lower back pain. In this review, we summarise recent findings of circadian rhythms in health and disease, with the IVD as an exemplar tissue system. We focus on rhythmic IVD functions and discuss implications of utilising biological timing mechanisms to improve tissue health and mitigate degeneration. These findings may have broader implications in chronic rheumatic conditions, given the recent findings of musculoskeletal circadian clocks.
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Affiliation(s)
- Honor Morris
- Wellcome Centre for Cell Matrix Research, University of Manchester, Manchester, UK.,Division of Cell Matrix Biology and Regenerative Medicine, School of Biological Sciences, University of Manchester, Manchester, UK
| | - Cátia F Gonçalves
- Wellcome Centre for Cell Matrix Research, University of Manchester, Manchester, UK.,Division of Cell Matrix Biology and Regenerative Medicine, School of Biological Sciences, University of Manchester, Manchester, UK
| | - Michal Dudek
- Wellcome Centre for Cell Matrix Research, University of Manchester, Manchester, UK.,Division of Cell Matrix Biology and Regenerative Medicine, School of Biological Sciences, University of Manchester, Manchester, UK
| | - Judith Hoyland
- Division of Cell Matrix Biology and Regenerative Medicine, School of Biological Sciences, University of Manchester, Manchester, UK .,NIHR Manchester Musculoskeletal Biomedical Research Centre, Manchester University, NHS Foundation Trust, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
| | - Qing-Jun Meng
- Wellcome Centre for Cell Matrix Research, University of Manchester, Manchester, UK .,Division of Cell Matrix Biology and Regenerative Medicine, School of Biological Sciences, University of Manchester, Manchester, UK
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64
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Fang B, Guan D, Lazar MA. Using GRO-Seq to Measure Circadian Transcription and Discover Circadian Enhancers. Methods Mol Biol 2021; 2130:127-148. [PMID: 33284441 DOI: 10.1007/978-1-0716-0381-9_10] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Circadian gene transcription transmits timing information and drives cyclic physiological processes across various tissues. Recent studies indicate that oscillating enhancer activity is a major driving force of rhythmic gene transcription. Functional circadian enhancers can be identified in an unbiased manner by correlation with the rhythms of nearby gene transcription.Global run-on sequencing (GRO-seq) measures nascent transcription of both pre-mRNAs and enhancer RNAs (eRNAs) at a genome-wide level, making it a unique tool for unraveling complex gene regulation mechanisms in vivo. Here, we describe a comprehensive protocol, ranging from wet lab to in silico analysis, for detecting and quantifying circadian transcription of genes and eRNAs. Moreover, using gene-eRNA correlation, we detail the steps necessary to identify functional enhancers and transcription factors (TFs) that control circadian gene expression in vivo. While we use mouse liver as an example, this protocol is applicable for multiple tissues.
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Affiliation(s)
- Bin Fang
- Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA.,The Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA.,Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Dongyin Guan
- Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Mitchell A Lazar
- Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA. .,The Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA.
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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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66
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Xiao Y, Kim M, Lazar MA. Nuclear receptors and transcriptional regulation in non-alcoholic fatty liver disease. Mol Metab 2020; 50:101119. [PMID: 33220489 PMCID: PMC8324695 DOI: 10.1016/j.molmet.2020.101119] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 11/13/2020] [Accepted: 11/16/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND As a result of a sedentary lifestyle and excess food consumption in modern society, non-alcoholic fatty liver disease (NAFLD) characterized by fat accumulation in the liver is becoming a major disease burden. Non-alcoholic steatohepatitis (NASH) is an advanced form of NAFLD characterized by inflammation and fibrosis that can lead to hepatocellular carcinoma and liver failure. Nuclear receptors (NRs) are a family of ligand-regulated transcription factors that closely control multiple aspects of metabolism. Their transcriptional activity is modulated by various ligands, including hormones and lipids. NRs serve as potential pharmacological targets for NAFLD/NASH and other metabolic diseases. SCOPE OF REVIEW In this review, we provide a comprehensive overview of NRs that have been studied in the context of NAFLD/NASH with a focus on their transcriptional regulation, function in preclinical models, and studies of their clinical utility. MAJOR CONCLUSIONS The transcriptional regulation of NRs is context-dependent. During the dynamic progression of NAFLD/NASH, NRs play diverse roles in multiple organs and different cell types in the liver, which highlights the necessity of targeting NRs in a stage-specific and cell-type-specific manner to enhance the efficacy and safety of treatment methods.
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Affiliation(s)
- Yang Xiao
- Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Mindy Kim
- Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Mitchell A Lazar
- Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA.
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67
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Abstract
Circadian rhythms govern a large array of physiological and metabolic functions. Perturbations of the daily cycle have been linked to elevated risk of developing cancer as well as poor prognosis in patients with cancer. Also, expression of core clock genes or proteins is remarkably attenuated particularly in tumours of a higher stage or that are more aggressive, possibly linking the circadian clock to cellular differentiation. Emerging evidence indicates that metabolic control by the circadian clock underpins specific hallmarks of cancer metabolism. Indeed, to support cell proliferation and biomass production, the clock may direct metabolic processes of cancer cells in concert with non-clock transcription factors to control how nutrients and metabolites are utilized in a time-specific manner. We hypothesize that the metabolic switch between differentiation or stemness of cancer may be coupled to the molecular clockwork. Moreover, circadian rhythms of host organisms appear to dictate tumour growth and proliferation. This Review outlines recent discoveries of the interplay between circadian rhythms, proliferative metabolism and cancer, highlighting potential opportunities in the development of future therapeutic strategies.
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Affiliation(s)
- Kenichiro Kinouchi
- Center for Epigenetics and Metabolism, U1233 INSERM, Department of Biological Chemistry, University of California, Irvine, CA, USA.
- Department of Endocrinology, Metabolism, and Nephrology, School of Medicine, Keio University, Tokyo, Japan.
| | - Paolo Sassone-Corsi
- Center for Epigenetics and Metabolism, U1233 INSERM, Department of Biological Chemistry, University of California, Irvine, CA, USA.
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68
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Hu H, Chen Z, Ji L, Wang Y, Yang M, Lai R, Zhong Y, Zhang X, Wang L. ARID1A-dependent permissive chromatin accessibility licenses estrogen-receptor signaling to regulate circadian rhythms genes in endometrial cancer. Cancer Lett 2020; 492:162-173. [PMID: 32858102 DOI: 10.1016/j.canlet.2020.08.034] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 08/10/2020] [Accepted: 08/21/2020] [Indexed: 01/22/2023]
Abstract
Estrogen receptor α (ER) acts as an oncogenic signal in endometrial endometrioid carcinoma. ER binding activity largely depends on chromatin remodeling and recruitment of transcription factors to estrogen response elements. A deeper understanding of these regulatory mechanisms may uncover therapeutic targets for ER-dependent endometrial cancers. We show that estrogen induces accessible chromatin and ER binding at a subset of enhancers, which form higher-order super enhancers that are vital for ER signaling. ER positively correlates with active enhancers in primary tumors, and tumors were effectively classified into molecular subtypes with chromatin accessibility dynamics and ER-dependent gene signature. ARID1A binds within ER-bound enhancers and regulates ER-dependent transcription. Knockdown of ARID1A or fulvestrant treatment profoundly affects the gene-expression program, and inhibits cell growth phenotype by affecting the chromatin environment. Importantly, we found dysregulated expression of circadian rhythms genes by estrogen in cancer cells and in primary tumors. Knockdown of ARID1A reduces the chromatin accessibility and ER binding at enhancers of the circadian gene ARNTL and BHLHE41, leading to a decreased expression of these genes. Altogether, we uncover a critical role for ARID1A in ER signaling and therapeutic target in ER-positive endometrial cancer.
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Affiliation(s)
- Hanyang Hu
- Department of Histology and Embryology, School of Basic Medical Sciences, Wuhan University, Wuhan, 430071, Hubei Province, China
| | - Zhiguo Chen
- Department of Histology and Embryology, School of Basic Medical Sciences, Wuhan University, Wuhan, 430071, Hubei Province, China; Department of Human Anatomy, Basic Medical Sciences of Xinxiang Medical University, Xinxiang, 453003, Henan Province, China
| | - Lulu Ji
- Department of Histology and Embryology, School of Basic Medical Sciences, Wuhan University, Wuhan, 430071, Hubei Province, China
| | - Yanling Wang
- Department of Histology and Embryology, School of Basic Medical Sciences, Wuhan University, Wuhan, 430071, Hubei Province, China
| | - Mengzhen Yang
- Department of Histology and Embryology, School of Basic Medical Sciences, Wuhan University, Wuhan, 430071, Hubei Province, China
| | - Rujie Lai
- Department of Histology and Embryology, School of Basic Medical Sciences, Wuhan University, Wuhan, 430071, Hubei Province, China
| | - Yu Zhong
- Department of Histology and Embryology, School of Basic Medical Sciences, Wuhan University, Wuhan, 430071, Hubei Province, China
| | - Xiaoli Zhang
- Department of Obstetrics and Gynecology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, Hubei Province, China
| | - Lin Wang
- Department of Histology and Embryology, School of Basic Medical Sciences, Wuhan University, Wuhan, 430071, Hubei Province, China; Hubei Provincial Key Laboratory of Developmentally Originated Disease, Wuhan, 430071, Hubei Province, China.
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69
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Gao WK, Shu YY, Ye J, Pan XL. Circadian clock and liver energy metabolism. Shijie Huaren Xiaohua Zazhi 2020; 28:1025-1035. [DOI: 10.11569/wcjd.v28.i20.1025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Circadian rhythm, generated by the circadian clock, is an internal rhythm that the body evolved to adapt to the diurnal changes in the external environment. Under its influence, mammals have distinct feeding and fasting cycles, which cause rhythmic changes in nutrient supply and demand. In recent years, many studies have shown that biorhythms are closely related to body metabolism. The liver, as the metabolism center of the body, is affected by circadian rhythm. However, with the acceleration of the pace of modern life and the change of life styles, the body's original rhythm is disrupted, resulting in a significant increase in the incidence of liver related metabolic diseases. Meanwhile, the disorder of circadian rhythm can also promote the occurrence and development of these diseases, and affect their prognosis and outcome. This paper reviews the relationship between the function of liver clock genes and the metabolism of liver glucose, lipids, bile acids, protein, etc.
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Affiliation(s)
- Wen-Kang Gao
- Division of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, Hubei Province, China
| | - Yan-Yun Shu
- Division of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, Hubei Province, China
| | - Jin Ye
- Division of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, Hubei Province, China
| | - Xiao-Li Pan
- Division of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, Hubei Province, China
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70
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Kim YH, Lazar MA. Transcriptional Control of Circadian Rhythms and Metabolism: A Matter of Time and Space. Endocr Rev 2020; 41:5835826. [PMID: 32392281 PMCID: PMC7334005 DOI: 10.1210/endrev/bnaa014] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 05/04/2020] [Indexed: 02/07/2023]
Abstract
All biological processes, living organisms, and ecosystems have evolved with the Sun that confers a 24-hour periodicity to life on Earth. Circadian rhythms arose from evolutionary needs to maximize daily organismal fitness by enabling organisms to mount anticipatory and adaptive responses to recurrent light-dark cycles and associated environmental changes. The clock is a conserved feature in nearly all forms of life, ranging from prokaryotes to virtually every cell of multicellular eukaryotes. The mammalian clock comprises transcription factors interlocked in negative feedback loops, which generate circadian expression of genes that coordinate rhythmic physiology. In this review, we highlight previous and recent studies that have advanced our understanding of the transcriptional architecture of the mammalian clock, with a specific focus on epigenetic mechanisms, transcriptomics, and 3-dimensional chromatin architecture. In addition, we discuss reciprocal ways in which the clock and metabolism regulate each other to generate metabolic rhythms. We also highlight implications of circadian biology in human health, ranging from genetic and environment disruptions of the clock to novel therapeutic opportunities for circadian medicine. Finally, we explore remaining fundamental questions and future challenges to advancing the field forward.
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Affiliation(s)
- Yong Hoon Kim
- Institute for Diabetes, Obesity, and Metabolism, and Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Mitchell A Lazar
- Institute for Diabetes, Obesity, and Metabolism, and Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
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71
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Mukherji A, Dachraoui M, Baumert TF. Perturbation of the circadian clock and pathogenesis of NAFLD. Metabolism 2020; 111S:154337. [PMID: 32795560 PMCID: PMC7613429 DOI: 10.1016/j.metabol.2020.154337] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 07/24/2020] [Accepted: 07/26/2020] [Indexed: 12/12/2022]
Abstract
All living organisms including humans, experience changes in the light exposure generated by the Earth's rotation. In anticipation of this unavoidable geo-physical variability, and to generate an appropriate biochemical response, species of many phyla, including mammals have evolved a nearly 24-hour endogenous timing device known as the circadian clock (CC), which is self-sustained, cell autonomous and is present in every cell type. At the heart of the 'clock' functioning resides the CC-oscillator, an elegantly designed transcriptional-translational feedback system. Notably, the core components of the CC-oscillator not only drive daily rhythmicity of their own synthesis, but also generate circadian phase-specific variability in the expression levels of thousands of target genes through transcriptional, post-transcriptional and post-translational mechanisms. Thereby, this 'clock'-system provides proper chronological coordination in the functioning of cells, tissues and organs. The CC governs many physiologically critical functions. Among these functions, the key role of the CC in maintaining metabolic homeostasis deserves special emphasis. Indeed, the several features of the modern lifestyle (e.g. travel-induced jet lag, rotating shift work, energy-dense food) which, force disruption of circadian rhythms have recently emerged as a major driver to global health problems like obesity, cardiovascular disease and metabolic liver disease such as non-alcoholic fatty liver disease (NAFLD). Here we review, the CC-dependent pathways in different tissues which play critical roles in mediating several critical metabolic functions under physiological conditions and discuss their impact for the development of metabolic disease with a focus on the liver.
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Affiliation(s)
- Atish Mukherji
- Université de Strasbourg, Inserm, Institut de Recherche sur les Maladies Virales et Hépatiques INSERM, UMR_S 1110, Strasbourg, France.
| | - Mayssa Dachraoui
- Université de Strasbourg, Inserm, Institut de Recherche sur les Maladies Virales et Hépatiques INSERM, UMR_S 1110, Strasbourg, France
| | - Thomas F Baumert
- Université de Strasbourg, Inserm, Institut de Recherche sur les Maladies Virales et Hépatiques INSERM, UMR_S 1110, Strasbourg, France; Pôle Hépato-Digestif, Institut Hospitalo-Universitaire, Hôpitaux Universitaires de Strasbourg, Strasbourg, France.
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72
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eRNAs and Superenhancer lncRNAs Are Functional in Human Prostate Cancer. DISEASE MARKERS 2020; 2020:8847986. [PMID: 33029258 PMCID: PMC7532396 DOI: 10.1155/2020/8847986] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 07/27/2020] [Accepted: 08/14/2020] [Indexed: 01/06/2023]
Abstract
Prostate cancer (PCa) is one of the most commonly diagnosed cancers in males worldwide. lncRNAs (long noncoding RNAs) play a significant role in the occurrence and development of PCa. eRNAs (enhancer RNAs) and SE-lncRNAs (superenhancer lncRNAs) are important elements of lncRNAs, but the role of eRNAs and SE-lncRNAs in PCa remains largely unclear. In this work, we identified 681 eRNAs and 292 SE-lncRNAs that were expressed differentially in PCa using a microarray. We also found that eRNAs transcribed from active open chromatin had significantly higher expression than those from active closed chromatin, and SE-lncRNAs had a little higher expression than eRNAs. Next, we constructed a transcriptional regulation network that eRNA-related enhancer and the target genes shared the same TF-binding motifs. Further, we investigated whether CTCF played a role in mediating the transcriptional regulation network. eRNAs, especially those that regulate androgen response genes, may be candidates for prognostic biomarkers and therapy targets. Our work provides a new perspective for developing medical treatments and therapies for prostate cancer.
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73
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Dichotomous engagement of HDAC3 activity governs inflammatory responses. Nature 2020; 584:286-290. [PMID: 32760002 PMCID: PMC7725280 DOI: 10.1038/s41586-020-2576-2] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 05/12/2020] [Indexed: 12/14/2022]
Abstract
The histone deacetylases (HDACs) are a superfamily of chromatin-modifying enzymes that silence transcription through the modification of histones. Among them, HDAC3 is unique in that interaction with nuclear receptor corepressors 1 and 2 (NCoR1/2) is required to engage its catalytic activity1-3. However, global loss of HDAC3 also results in the repression of transcription, the mechanism of which is currently unclear4-8. Here we report that, during the activation of macrophages by lipopolysaccharides, HDAC3 is recruited to activating transcription factor 2 (ATF2)-bound sites without NCoR1/2 and activates the expression of inflammatory genes through a non-canonical mechanism. By contrast, the deacetylase activity of HDAC3 is selectively engaged at ATF3-bound sites that suppress Toll-like receptor signalling. Loss of HDAC3 in macrophages safeguards mice from lethal exposure to lipopolysaccharides, but this protection is not conferred upon genetic or pharmacological abolition of the catalytic activity of HDAC3. Our findings show that HDAC3 is a dichotomous transcriptional activator and repressor, with a non-canonical deacetylase-independent function that is vital for the innate immune system.
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74
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Marcheva B, Perelis M, Weidemann BJ, Taguchi A, Lin H, Omura C, Kobayashi Y, Newman MV, Wyatt EJ, McNally EM, Fox JEM, Hong H, Shankar A, Wheeler EC, Ramsey KM, MacDonald PE, Yeo GW, Bass J. A role for alternative splicing in circadian control of exocytosis and glucose homeostasis. Genes Dev 2020; 34:1089-1105. [PMID: 32616519 PMCID: PMC7397853 DOI: 10.1101/gad.338178.120] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 06/10/2020] [Indexed: 11/24/2022]
Abstract
The circadian clock is encoded by a negative transcriptional feedback loop that coordinates physiology and behavior through molecular programs that remain incompletely understood. Here, we reveal rhythmic genome-wide alternative splicing (AS) of pre-mRNAs encoding regulators of peptidergic secretion within pancreatic β cells that are perturbed in Clock-/- and Bmal1-/- β-cell lines. We show that the RNA-binding protein THRAP3 (thyroid hormone receptor-associated protein 3) regulates circadian clock-dependent AS by binding to exons at coding sequences flanking exons that are more frequently skipped in clock mutant β cells, including transcripts encoding Cask (calcium/calmodulin-dependent serine protein kinase) and Madd (MAP kinase-activating death domain). Depletion of THRAP3 restores expression of the long isoforms of Cask and Madd, and mimicking exon skipping in these transcripts through antisense oligonucleotide delivery in wild-type islets reduces glucose-stimulated insulin secretion. Finally, we identify shared networks of alternatively spliced exocytic genes from islets of rodent models of diet-induced obesity that significantly overlap with clock mutants. Our results establish a role for pre-mRNA alternative splicing in β-cell function across the sleep/wake cycle.
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Affiliation(s)
- Biliana Marcheva
- Department of Medicine, Division of Endocrinology, Metabolism, and Molecular Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
| | - Mark Perelis
- Department of Medicine, Division of Endocrinology, Metabolism, and Molecular Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, California 92093, USA
| | - Benjamin J Weidemann
- Department of Medicine, Division of Endocrinology, Metabolism, and Molecular Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
| | - Akihiko Taguchi
- Department of Medicine, Division of Endocrinology, Metabolism, and Molecular Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
| | - Haopeng Lin
- Department of Pharmacology, Alberta Diabetes Institute, University of Alberta, Edmonton, Alberta T6G 2E1, Canada
| | - Chiaki Omura
- Department of Medicine, Division of Endocrinology, Metabolism, and Molecular Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
| | - Yumiko Kobayashi
- Department of Medicine, Division of Endocrinology, Metabolism, and Molecular Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
| | - Marsha V Newman
- Department of Medicine, Division of Endocrinology, Metabolism, and Molecular Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
| | - Eugene J Wyatt
- Center for Genetic Medicine, Northwestern University, Chicago, Illinois 60611, USA
| | - Elizabeth M McNally
- Center for Genetic Medicine, Northwestern University, Chicago, Illinois 60611, USA
| | - Jocelyn E Manning Fox
- Department of Pharmacology, Alberta Diabetes Institute, University of Alberta, Edmonton, Alberta T6G 2E1, Canada
| | - Heekyung Hong
- Department of Medicine, Division of Endocrinology, Metabolism, and Molecular Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
| | - Archana Shankar
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, California 92093, USA
| | - Emily C Wheeler
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, California 92093, USA
| | - Kathryn Moynihan Ramsey
- Department of Medicine, Division of Endocrinology, Metabolism, and Molecular Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
| | - Patrick E MacDonald
- Department of Pharmacology, Alberta Diabetes Institute, University of Alberta, Edmonton, Alberta T6G 2E1, Canada
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, California 92093, USA
| | - Joseph Bass
- Department of Medicine, Division of Endocrinology, Metabolism, and Molecular Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
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75
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Pourcet B, Duez H. Circadian Control of Inflammasome Pathways: Implications for Circadian Medicine. Front Immunol 2020; 11:1630. [PMID: 32849554 PMCID: PMC7410924 DOI: 10.3389/fimmu.2020.01630] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 06/18/2020] [Indexed: 12/25/2022] Open
Abstract
The innate immune system senses “non-self” molecules derived from pathogens (PAMPs) as well as endogenous damage-associated molecular patterns (DAMPs) and promotes sterile inflammation that is necessary for injury resolution, tissue repair/regeneration, and homeostasis. The NOD-, LRR- and pyrin domain containing protein 3 (NLRP3) is an innate immune signaling complex whose assembly and activation can be triggered by various signals ranging from microbial molecules to ATP or the abnormal accumulation of crystals, thus leading to IL-1β and IL-18 maturation and secretion. Deregulation of the NLRP3 signaling cascade is associated with numerous inflammatory and metabolic diseases including rheumatoid arthritis, gout, atherosclerosis or type 2 diabetes. Interestingly, the circadian clock controls numerous inflammatory processes while clock disruption leads to or exacerbates inflammation. Recently, the biological clock was demonstrated to control NLRP3 expression and activation, thereby controlling IL-1β and IL-18 secretion in diverse tissues and immune cells, particularly macrophages. Circadian oscillations of NLRP3 signaling is lost in models of clock disruption, contributing to the development of peritonitis, hepatitis, or colitis. Sterile inflammation is also an important driver of atherosclerosis, and targeting the production of IL-1β has proven to be a promising approach for atherosclerosis management in humans. Interestingly, the extent of injury after fulminant hepatitis or myocardial infarction is time-of-day dependent under the control of the clock, and chronotherapy represents a promising approach for the management of pathologies involving deregulation of NLRP3 signaling.
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Affiliation(s)
- Benoit Pourcet
- University of Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1011-EGID, Lille, France
| | - Hélène Duez
- University of Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1011-EGID, Lille, France
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76
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Wang Q, Robinette ML, Billon C, Collins PL, Bando JK, Fachi JL, Sécca C, Porter SI, Saini A, Gilfillan S, Solt LA, Musiek ES, Oltz EM, Burris TP, Colonna M. Circadian rhythm-dependent and circadian rhythm-independent impacts of the molecular clock on type 3 innate lymphoid cells. Sci Immunol 2020; 4:4/40/eaay7501. [PMID: 31586012 DOI: 10.1126/sciimmunol.aay7501] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 08/29/2019] [Indexed: 11/02/2022]
Abstract
Many gut functions are attuned to circadian rhythm. Intestinal group 3 innate lymphoid cells (ILC3s) include NKp46+ and NKp46- subsets, which are RORγt dependent and provide mucosal defense through secretion of interleukin-22 (IL-22) and IL-17. Because ILC3s highly express some key circadian clock genes, we investigated whether ILC3s are also attuned to circadian rhythm. We noted circadian oscillations in the expression of clock and cytokine genes, such as REV-ERBα, IL-22, and IL-17, whereas acute disruption of the circadian rhythm affected cytokine secretion by ILC3s. Because of prominent and rhythmic expression of REV-ERBα in ILC3s, we also investigated the impact of constitutive deletion of REV-ERBα, which has been previously shown to inhibit the expression of a RORγt repressor, NFIL3, while also directly antagonizing DNA binding of RORγt. Development of the NKp46+ ILC3 subset was markedly impaired, with reduced cell numbers, RORγt expression, and IL-22 production in REV-ERBα-deficient mice. The NKp46- ILC3 subsets developed normally, potentially due to compensatory expression of other clock genes, but IL-17 secretion paradoxically increased, probably because RORγt was not antagonized by REV-ERBα. We conclude that ILC3s are attuned to circadian rhythm, but clock regulator REV-ERBα also has circadian-independent impacts on ILC3 development and functions due to its roles in the regulation of RORγt.
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Affiliation(s)
- Qianli Wang
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Michelle L Robinette
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Cyrielle Billon
- Center for Clinical Pharmacology, Washington University School of Medicine and St. Louis College of Pharmacy, St. Louis, MO 63110, USA
| | - Patrick L Collins
- Department of Microbial Infection and Immunity, Ohio State University College of Medicine, Columbus, OH 43210, USA
| | - Jennifer K Bando
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - José Luís Fachi
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA.,Laboratory of Immunoinflammation, Department of Genetics, Evolution, Microbiology, and Immunology, Institute of Biology, University of Campinas, Campinas, SP 13083-862, Brazil
| | - Cristiane Sécca
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Sofia I Porter
- Department of Microbial Infection and Immunity, Ohio State University College of Medicine, Columbus, OH 43210, USA
| | - Ankita Saini
- Department of Microbial Infection and Immunity, Ohio State University College of Medicine, Columbus, OH 43210, USA
| | - Susan Gilfillan
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Laura A Solt
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Erik S Musiek
- Hope Center for Neurological Disorders, Department of Neurology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Eugene M Oltz
- Department of Microbial Infection and Immunity, Ohio State University College of Medicine, Columbus, OH 43210, USA
| | - Thomas P Burris
- Center for Clinical Pharmacology, Washington University School of Medicine and St. Louis College of Pharmacy, St. Louis, MO 63110, USA
| | - Marco Colonna
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA.
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77
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Matthews BJ, Waxman DJ. Impact of 3D genome organization, guided by cohesin and CTCF looping, on sex-biased chromatin interactions and gene expression in mouse liver. Epigenetics Chromatin 2020; 13:30. [PMID: 32680543 PMCID: PMC7368777 DOI: 10.1186/s13072-020-00350-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 07/03/2020] [Indexed: 12/13/2022] Open
Abstract
Several thousand sex-differential distal enhancers have been identified in mouse liver; however, their links to sex-biased genes and the impact of any sex-differences in nuclear organization and chromatin interactions are unknown. To address these issues, we first characterized 1847 mouse liver genomic regions showing significant sex differential occupancy by cohesin and CTCF, two key 3D nuclear organizing factors. These sex-differential binding sites were primarily distal to sex-biased genes but rarely generated sex-differential TAD (topologically associating domain) or intra-TAD loop anchors, and were sometimes found in TADs without sex-biased genes. A substantial subset of sex-biased cohesin-non-CTCF binding sites, but not sex-biased cohesin-and-CTCF binding sites, overlapped sex-biased enhancers. Cohesin depletion reduced the expression of male-biased genes with distal, but not proximal, sex-biased enhancers by >10-fold, implicating cohesin in long-range enhancer interactions regulating sex-biased genes. Using circularized chromosome conformation capture-based sequencing (4C-seq), we showed that sex differences in distal sex-biased enhancer-promoter interactions are common. Intra-TAD loops with sex-independent cohesin-and-CTCF anchors conferred sex specificity to chromatin interactions indirectly, by insulating sex-biased enhancer-promoter contacts and by bringing sex-biased genes into closer proximity to sex-biased enhancers. Furthermore, sex-differential chromatin interactions involving sex-biased gene promoters, enhancers, and lncRNAs were associated with sex-biased binding of cohesin and/or CTCF. These studies elucidate how 3D genome organization impacts sex-biased gene expression in a non-reproductive tissue through both direct and indirect effects of cohesin and CTCF looping on distal enhancer interactions with sex-differentially expressed genes.
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Affiliation(s)
- Bryan J Matthews
- Department of Biology and Bioinformatics Program, Boston University, 5 Cummington Mall, Boston, MA, 02215, USA
| | - David J Waxman
- Department of Biology and Bioinformatics Program, Boston University, 5 Cummington Mall, Boston, MA, 02215, USA.
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78
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Mei W, Jiang Z, Chen Y, Chen L, Sancar A, Jiang Y. Genome-wide circadian rhythm detection methods: systematic evaluations and practical guidelines. Brief Bioinform 2020; 22:5872170. [PMID: 32672832 DOI: 10.1093/bib/bbaa135] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 05/18/2020] [Accepted: 06/04/2020] [Indexed: 12/31/2022] Open
Abstract
Circadian rhythms are oscillations of behavior, physiology and metabolism in many organisms. Recent advancements in omics technology make it possible for genome-wide profiling of circadian rhythms. Here, we conducted a comprehensive analysis of seven existing algorithms commonly used for circadian rhythm detection. Using gold-standard circadian and non-circadian genes, we systematically evaluated the accuracy and reproducibility of the algorithms on empirical datasets generated from various omics platforms under different experimental designs. We also carried out extensive simulation studies to test each algorithm's robustness to key variables, including sampling patterns, replicates, waveforms, signal-to-noise ratios, uneven samplings and missing values. Furthermore, we examined the distributions of the nominal $P$-values under the null and raised issues with multiple testing corrections using traditional approaches. With our assessment, we provide method selection guidelines for circadian rhythm detection, which are applicable to different types of high-throughput omics data.
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Affiliation(s)
- Wenwen Mei
- Department of Biostatistics, University of North Carolina at Chapel Hill
| | - Zhiwen Jiang
- Department of Biostatistics, University of North Carolina at Chapel Hill
| | - Yang Chen
- Department of Statistics and the Michigan Institute of Data Science, University of Michigan
| | - Li Chen
- Department of Medicine and a member of the Center for Computational Biology and Bioinformatics, Indiana University School of Medicine
| | - Aziz Sancar
- Biochemistry and Biophysics at the University of North Carolina School of Medicine
| | - Yuchao Jiang
- Department of Biostatistics and the Department of Genetics, University of North Carolina at Chapel Hill and a member of UNC Lineberger Comprehensive Cancer Center
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79
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Genome-wide circadian regulation: A unique system for computational biology. Comput Struct Biotechnol J 2020; 18:1914-1924. [PMID: 32774786 PMCID: PMC7385043 DOI: 10.1016/j.csbj.2020.07.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Revised: 06/30/2020] [Accepted: 07/02/2020] [Indexed: 01/20/2023] Open
Abstract
Circadian rhythms are 24-hour oscillations affecting an organism at multiple levels from gene expression all the way to tissues and organs. They have been observed in organisms across the kingdom of life, spanning from cyanobacteria to humans. In mammals, the master circadian pacemaker is located in the hypothalamic suprachiasmatic nuclei (SCN) in the brain where it synchronizes the peripheral oscillators that exist in other tissues. This system regulates the circadian activity of a large part of the transcriptome and recent findings indicate that almost every cell in the body has this clock at the molecular level. In this review, we briefly summarize the different factors that can influence the circadian transcriptome, including light, temperature, and food intake. We then summarize recently identified general principles governing genome-scale circadian regulation, as well as future lines of research. Genome-scale circadian activity represents a fascinating study model for computational biology. For this purpose, systems biology methods are promising exploratory tools to decode the global regulatory principles of circadian regulation.
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Key Words
- ABSR, Autoregressive Bayesian spectral regression
- AMPK, AMP-activated protein kinase
- AR, Arrhythmic feeding
- ARSER, Harmonic regression based on autoregressive spectral estimation
- BMAL1, The aryl hydrocarbon receptor nuclear translocator-like (ARNTL)
- CCD, Cortical collecting duct
- CR, Calorie-restricted diet
- CRY, Cryptochrome
- Circadian regulatory network
- Circadian rhythms
- Circadian transcriptome
- Cycling genes
- DCT/CNT, Distal convoluted tubule and connecting tubule
- DD, Dark: dark
- Energetic cost
- HF, High fat diet
- JTK_CYCLE, Jonckheere-Terpstra-Kendall (JTK) cycle
- KD, Ketogenic diet
- LB, Ad libitum
- LD, Light:dark
- LS, Lomb-Scargle
- Liver-RE, Liver clock reconstituted BMAL1-deficient mice
- NAD, Nicotinamide adenine dinucleotides
- ND, Normal diet
- NR, Night-restricted feeding
- PAS, PER-ARNT-SIM
- PER, Period
- RAIN, Rhythmicity Analysis Incorporating Nonparametric methods
- RF, Restricted feeding
- SCN, Suprachiasmatic nucleus
- SREBP, The sterol regulatory element binding protein
- TTFL, Transcriptional-translational feedback loop
- WT, Wild type
- eJTK_CYCLE, Empirical JTK_CYCLE
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80
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Abstract
Transcription in several organisms from certain bacteria to humans has been observed to be stochastic in nature: toggling between active and inactive states. Periods of active nascent RNA synthesis known as bursts represent individual gene activation events in which multiple polymerases are initiated. Therefore, bursting is the single locus illustration of both gene activation and repression. Although transcriptional bursting was originally observed decades ago, only recently have technological advances enabled the field to begin elucidating gene regulation at the single-locus level. In this review, we focus on how biochemical, genomic, and single-cell data describe the regulatory steps of transcriptional bursts.
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Affiliation(s)
- Joseph Rodriguez
- National Institute of Environmental Health Sciences, Durham, North Carolina 27709, USA
| | - Daniel R. Larson
- Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892, USA
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81
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Levine DC, Hong H, Weidemann BJ, Ramsey KM, Affinati AH, Schmidt MS, Cedernaes J, Omura C, Braun R, Lee C, Brenner C, Peek CB, Bass J. NAD + Controls Circadian Reprogramming through PER2 Nuclear Translocation to Counter Aging. Mol Cell 2020; 78:835-849.e7. [PMID: 32369735 PMCID: PMC7275919 DOI: 10.1016/j.molcel.2020.04.010] [Citation(s) in RCA: 94] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 02/12/2020] [Accepted: 04/07/2020] [Indexed: 12/18/2022]
Abstract
Disrupted sleep-wake and molecular circadian rhythms are a feature of aging associated with metabolic disease and reduced levels of NAD+, yet whether changes in nucleotide metabolism control circadian behavioral and genomic rhythms remains unknown. Here, we reveal that supplementation with the NAD+ precursor nicotinamide riboside (NR) markedly reprograms metabolic and stress-response pathways that decline with aging through inhibition of the clock repressor PER2. NR enhances BMAL1 chromatin binding genome-wide through PER2K680 deacetylation, which in turn primes PER2 phosphorylation within a domain that controls nuclear transport and stability and that is mutated in human advanced sleep phase syndrome. In old mice, dampened BMAL1 chromatin binding, transcriptional oscillations, mitochondrial respiration rhythms, and late evening activity are restored by NAD+ repletion to youthful levels with NR. These results reveal effects of NAD+ on metabolism and the circadian system with aging through the spatiotemporal control of the molecular clock.
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Affiliation(s)
- Daniel C Levine
- Department of Medicine, Division of Endocrinology, Metabolism, and Molecular Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Heekyung Hong
- Department of Medicine, Division of Endocrinology, Metabolism, and Molecular Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Benjamin J Weidemann
- Department of Medicine, Division of Endocrinology, Metabolism, and Molecular Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Kathryn M Ramsey
- Department of Medicine, Division of Endocrinology, Metabolism, and Molecular Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Alison H Affinati
- Department of Internal Medicine, Michigan Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Mark S Schmidt
- Department of Biochemistry, University of Iowa, Iowa City, IA 52242, USA
| | - Jonathan Cedernaes
- Department of Medicine, Division of Endocrinology, Metabolism, and Molecular Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Department of Medical Sciences, Uppsala University, Uppsala SE-75124, Sweden
| | - Chiaki Omura
- Department of Medicine, Division of Endocrinology, Metabolism, and Molecular Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Rosemary Braun
- Biostatistics Division, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Department of Engineering Sciences and Applied Mathematics, Northwestern University, Evanston, IL 60208, USA; NSF-Simons Center for Quantitative Biology at Northwestern University, Evanston, IL 60208, USA
| | - Choogon Lee
- Department of Biomedical Sciences, Florida State University, Tallahassee, FL 32306, USA
| | - Charles Brenner
- Department of Biochemistry, University of Iowa, Iowa City, IA 52242, USA
| | - Clara Bien Peek
- Department of Medicine, Division of Endocrinology, Metabolism, and Molecular Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Joseph Bass
- Department of Medicine, Division of Endocrinology, Metabolism, and Molecular Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA.
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82
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Molecular Regulation of Circadian Chromatin. J Mol Biol 2020; 432:3466-3482. [PMID: 31954735 DOI: 10.1016/j.jmb.2020.01.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 12/13/2019] [Accepted: 01/07/2020] [Indexed: 02/06/2023]
Abstract
Circadian rhythms are generated by transcriptional negative feedback loops and require histone modifications and chromatin remodeling to ensure appropriate timing and amplitude of clock gene expression. Circadian modifications to histones are important for transcriptional initiation and feedback inhibition serving as signaling platform for chromatin-remodeling enzymes. Current models indicate circadian-regulated facultative heterochromatin (CRFH) is a conserved mechanism at clock genes in Neurospora, Drosophila, and mice. CRFH consists of antiphasic rhythms in activating and repressive modifications generating chromatin states that cycle between transcriptionally permissive and nonpermissive. There are rhythms in histone H3 lysine 9 and 27 acetylation (H3K9ac and H3K27ac) and histone H3 lysine 4 methylation (H3K4me) during activation; while deacetylation, histone H3 lysine 9 methylation (H3K9me) and heterochromatin protein 1 (HP1) are hallmarks of repression. ATP-dependent chromatin-remodeling enzymes control accessibility, nucleosome positioning/occupancy, and nuclear organization. In Neurospora, the rhythm in facultative heterochromatin is mediated by the frequency (frq) natural antisense transcript (NAT) qrf. While in mammals, histone deacetylases (HDACs), histone H3 lysine 9 methyltransferase (KMT1/SUV39), and components of nucleosome remodeling and deacetylase (NuRD) are part of the nuclear PERIOD complex (PER complex). Genomics efforts have found relationships among rhythmic chromatin modifications at clock-controlled genes (ccg) revealing circadian control of genome-wide chromatin states. There are also circadian clock-regulated lncRNAs with an emerging function that includes assisting in chromatin dynamics. In this review, we explore the connections between circadian clock, chromatin remodeling, lncRNAs, and CRFH and how these impact rhythmicity, amplitude, period, and phase of circadian clock genes.
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83
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Mia S, Kane MS, Latimer MN, Reitz CJ, Sonkar R, Benavides GA, Smith SR, Frank SJ, Martino TA, Zhang J, Darley-Usmar VM, Young ME. Differential effects of REV-ERBα/β agonism on cardiac gene expression, metabolism, and contractile function in a mouse model of circadian disruption. Am J Physiol Heart Circ Physiol 2020; 318:H1487-H1508. [PMID: 32357113 PMCID: PMC7311693 DOI: 10.1152/ajpheart.00709.2019] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Cell-autonomous circadian clocks have emerged as temporal orchestrators of numerous biological processes. For example, the cardiomyocyte circadian clock modulates transcription, translation, posttranslational modifications, ion homeostasis, signaling cascades, metabolism, and contractility of the heart over the course of the day. Circadian clocks are composed of more than 10 interconnected transcriptional modulators, all of which have the potential to influence the cardiac transcriptome (and ultimately cardiac processes). These transcriptional modulators include BMAL1 and REV-ERBα/β; BMAL1 induces REV-ERBα/β, which in turn feeds back to inhibit BMAL1. Previous studies indicate that cardiomyocyte-specific BMAL1-knockout (CBK) mice exhibit a dysfunctional circadian clock (including decreased REV-ERBα/β expression) in the heart associated with abnormalities in cardiac mitochondrial function, metabolism, signaling, and contractile function. Here, we hypothesized that decreased REV-ERBα/β activity is responsible for distinct phenotypical alterations observed in CBK hearts. To test this hypothesis, CBK (and littermate control) mice were administered with the selective REV-ERBα/β agonist SR-9009 (100 mg·kg-1·day-1 for 8 days). SR-9009 administration was sufficient to normalize cardiac glycogen synthesis rates, cardiomyocyte size, interstitial fibrosis, and contractility in CBK hearts (without influencing mitochondrial complex activities, nor normalizing substrate oxidation and Akt/mTOR/GSK3β signaling). Collectively, these observations highlight a role for REV-ERBα/β as a mediator of a subset of circadian clock-controlled processes in the heart.
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Affiliation(s)
- Sobuj Mia
- Division of Cardiovascular Disease, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama
| | - Mariame S Kane
- Division of Cardiovascular Disease, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama.,Division of Molecular Cellular Pathology, Department of Pathology, University of Alabama at Birmingham, Birmingham, Alabama
| | - Mary N Latimer
- Division of Cardiovascular Disease, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama
| | - Cristine J Reitz
- Centre for Cardiovascular Investigations, Department of Biomedical Science, University of Guelph, Guelph, Ontario, Canada
| | - Ravi Sonkar
- Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama
| | - Gloria A Benavides
- Division of Molecular Cellular Pathology, Department of Pathology, University of Alabama at Birmingham, Birmingham, Alabama
| | - Samuel R Smith
- Division of Cardiovascular Disease, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama
| | - Stuart J Frank
- Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama.,Endocrinology Section, Birmingham Veterans Affairs Medical Center Medical Service, Birmingham, Alabama
| | - Tami A Martino
- Centre for Cardiovascular Investigations, Department of Biomedical Science, University of Guelph, Guelph, Ontario, Canada
| | - Jianhua Zhang
- Division of Molecular Cellular Pathology, Department of Pathology, University of Alabama at Birmingham, Birmingham, Alabama
| | - Victor M Darley-Usmar
- Division of Molecular Cellular Pathology, Department of Pathology, University of Alabama at Birmingham, Birmingham, Alabama
| | - Martin E Young
- Division of Cardiovascular Disease, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama
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84
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Doering JA, Beitel SC, Patterson S, Eisner BK, Giesy JP, Hecker M, Wiseman S. Aryl hydrocarbon receptor nuclear translocators (ARNT1, ARNT2, and ARNT3) of white sturgeon (Acipenser transmontanus): Sequences, tissue-specific expressions, and response to β-naphthoflavone. Comp Biochem Physiol C Toxicol Pharmacol 2020; 231:108726. [PMID: 32081761 DOI: 10.1016/j.cbpc.2020.108726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 02/11/2020] [Accepted: 02/15/2020] [Indexed: 12/01/2022]
Abstract
Sturgeons (Acipenseridae) are ancient fishes that have tissue-specific profiles of transcriptional responses to dioxin-like compounds (DLCs) that are unique from those generally measured in teleost fishes. Because DLCs exert their critical toxicities through activation of the aryl hydrocarbon receptor (AHR), this transcription factor has been the subject of intensive study. However, less attention has focused on the aryl hydrocarbon receptor nuclear translocator (ARNT), which is the dimerization partner of the AHR and required for AHR-mediated transcription. The present study sequenced ARNT1, ARNT2, and ARNT3 in a representative species of sturgeon, the white sturgeon (Acipenser transmontanus), and quantified tissue-specific basal transcript abundance for each ARNT and the response following exposure to the model agonist of the AHR, β-naphthoflavone. In common with other proteins in sturgeons, the amino acid sequences of ARNTs are more similar to those of tetrapods than are ARNTs of other fishes. Transcripts of ARNT1, ARNT2, and ARNT3 were detected in all tissues investigated. Expression of ARNTs are tightly regulated in vertebrates, but β-naphthoflavone caused down-regulation in liver and up-regulation in gill, while an upward trend was measured in intestine. ARNTs are dimeric partners for multiple proteins, including the hypoxia inducible factor 1α (HIF1α), which mediates response to hypoxia. A downward trend in abundance of HIF1α transcript was measured in liver of white sturgeon exposed to β-naphthoflavone. Altered expression of ARNTs and HIF1α caused by activation of the AHR might affect the ability of certain tissues in sturgeons to respond to hypoxia when co-exposed to DLCs or other agonists.
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Affiliation(s)
- Jon A Doering
- Department of Biological Sciences, University of Lethbridge, Lethbridge, Alberta T1K 3M4, Canada; Toxicology Centre, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5B3, Canada.
| | - Shawn C Beitel
- Toxicology Centre, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5B3, Canada
| | - Sarah Patterson
- Toxicology Centre, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5B3, Canada
| | - Bryanna K Eisner
- Toxicology Centre, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5B3, Canada
| | - John P Giesy
- Toxicology Centre, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5B3, Canada; Department of Veterinary Biomedical Sciences, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5B4, Canada; Department of Environmental Sciences, Baylor University, Waco, TX 76706, United States
| | - Markus Hecker
- Toxicology Centre, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5B3, Canada; School of the Environment and Sustainability, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5C8, Canada
| | - Steve Wiseman
- Department of Biological Sciences, University of Lethbridge, Lethbridge, Alberta T1K 3M4, Canada
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85
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Wang S, Li F, Lin Y, Wu B. Targeting REV-ERBα for therapeutic purposes: promises and challenges. Theranostics 2020; 10:4168-4182. [PMID: 32226546 PMCID: PMC7086371 DOI: 10.7150/thno.43834] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 02/08/2020] [Indexed: 12/12/2022] Open
Abstract
REV-ERBα (NR1D1) is a circadian clock component that functions as a transcriptional repressor. Due to its role in direct modulation of metabolic genes, REV-ERBα is regarded as an integrator of cell metabolism with circadian clock. Accordingly, REV-ERBα is first proposed as a drug target for treating sleep disorders and metabolic syndromes (e.g., dyslipidaemia, hyperglycaemia and obesity). Recent years of studies uncover a rather broad role of REV-ERBα in pathological conditions including local inflammatory diseases, heart failure and cancers. Moreover, REV-ERBα is involved in regulation of circadian drug metabolism that has implications in chronopharmacology. In the meantime, recent years have witnessed discovery of an array of new REV-ERBα ligands most of which have pharmacological activities in vivo. In this article, we review the regulatory role of REV-ERBα in various types of diseases and discuss the underlying mechanisms. We also describe the newly discovered ligands and the old ones together with their targeting potential. Despite well-established pharmacological effects of REV-ERBα ligands in animals (preclinical studies), no progress has been made regarding their translation to clinical trials. This implies certain challenges associated with drug development of REV-ERBα ligands. In particular, we discuss the potential challenges related to drug safety (or adverse effects) and bioavailability. For new drug development, it is advocated that REV-ERBα should be targeted to treat local diseases and a targeting drug should be locally distributed, avoiding the adverse effects on other tissues.
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Affiliation(s)
- Shuai Wang
- College of Pharmacy, Jinan University, Guangzhou, 510632, China
- Integrated Chinese and Western Medicine Postdoctoral research station, Jinan University, Guangzhou, 510632, China
| | - Feng Li
- Guangzhou Jinan Biomedicine Research and Development Center, Jinan University, Guangzhou, 510632, China
| | - Yanke Lin
- College of Pharmacy, Jinan University, Guangzhou, 510632, China
| | - Baojian Wu
- College of Pharmacy, Jinan University, Guangzhou, 510632, China
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Chinese Ministry of Education (MOE), College of Pharmacy, Jinan University, Guangzhou, 510632, China
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86
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Ray S, Valekunja UK, Stangherlin A, Howell SA, Snijders AP, Damodaran G, Reddy AB. Circadian rhythms in the absence of the clock gene Bmal1. Science 2020; 367:800-806. [PMID: 32054765 DOI: 10.1126/science.aaw7365] [Citation(s) in RCA: 120] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2019] [Revised: 07/18/2019] [Accepted: 01/14/2020] [Indexed: 12/14/2022]
Abstract
Circadian (~24 hour) clocks have a fundamental role in regulating daily physiology. The transcription factor BMAL1 is a principal driver of a molecular clock in mammals. Bmal1 deletion abolishes 24-hour activity patterning, one measure of clock output. We determined whether Bmal1 function is necessary for daily molecular oscillations in skin fibroblasts and liver slices. Unexpectedly, in Bmal1 knockout mice, both tissues exhibited 24-hour oscillations of the transcriptome, proteome, and phosphoproteome over 2 to 3 days in the absence of any exogenous drivers such as daily light or temperature cycles. This demonstrates a competent 24-hour molecular pacemaker in Bmal1 knockouts. We suggest that such oscillations might be underpinned by transcriptional regulation by the recruitment of ETS family transcription factors, and nontranscriptionally by co-opting redox oscillations.
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Affiliation(s)
- Sandipan Ray
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Utham K Valekunja
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Alessandra Stangherlin
- Institute of Metabolic Science, University of Cambridge, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK
| | | | | | | | - Akhilesh B Reddy
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
- Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
- Chronobiology and Sleep institute (CSI), Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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87
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Pan Y, Ballance H, Meng H, Gonzalez N, Kim SM, Abdurehman L, York B, Chen X, Schnytzer Y, Levy O, Dacso CC, McClung CA, O’Malley BW, Liu S, Zhu B. 12-h clock regulation of genetic information flow by XBP1s. PLoS Biol 2020; 18:e3000580. [PMID: 31935211 PMCID: PMC6959563 DOI: 10.1371/journal.pbio.3000580] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 12/11/2019] [Indexed: 12/15/2022] Open
Abstract
Our group recently characterized a cell-autonomous mammalian 12-h clock independent from the circadian clock, but its function and mechanism of regulation remain poorly understood. Here, we show that in mouse liver, transcriptional regulation significantly contributes to the establishment of 12-h rhythms of mRNA expression in a manner dependent on Spliced Form of X-box Binding Protein 1 (XBP1s). Mechanistically, the motif stringency of XBP1s promoter binding sites dictates XBP1s’s ability to drive 12-h rhythms of nascent mRNA transcription at dawn and dusk, which are enriched for basal transcription regulation, mRNA processing and export, ribosome biogenesis, translation initiation, and protein processing/sorting in the Endoplasmic Reticulum (ER)-Golgi in a temporal order consistent with the progressive molecular processing sequence described by the central dogma information flow (CEDIF). We further identified GA-binding proteins (GABPs) as putative novel transcriptional regulators driving 12-h rhythms of gene expression with more diverse phases. These 12-h rhythms of gene expression are cell autonomous and evolutionarily conserved in marine animals possessing a circatidal clock. Our results demonstrate an evolutionarily conserved, intricate network of transcriptional control of the mammalian 12-h clock that mediates diverse biological pathways. We speculate that the 12-h clock is coopted to accommodate elevated gene expression and processing in mammals at the two rush hours, with the particular genes processed at each rush hour regulated by the circadian and/or tissue-specific pathways. Distinct from the well-known 24-hour circadian clock, this study shows that the mammalian 12-hour clock upregulates genetic information flow capacity during the two "rush hours" (dawn and dusk) in a manner dependent on the transcription factor XBP1s.
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Affiliation(s)
- Yinghong Pan
- UPMC Genome Center, Pittsburgh, Pennsylvania, United States of America
| | - Heather Ballance
- Aging Institute of UPMC, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Huan Meng
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Naomi Gonzalez
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Sam-Moon Kim
- Translational Neuroscience Program, Department of Psychiatry, Center for Neuroscience, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Leymaan Abdurehman
- Aging Institute of UPMC, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Brian York
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Xi Chen
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Yisrael Schnytzer
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Oren Levy
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Clifford C. Dacso
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Colleen A. McClung
- Translational Neuroscience Program, Department of Psychiatry, Center for Neuroscience, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Bert W. O’Malley
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Silvia Liu
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
- Pittsburgh Liver Research Center, University of Pittsburgh, Pennsylvania, United States of America
- * E-mail: (SL); (BZ)
| | - Bokai Zhu
- Aging Institute of UPMC, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
- Pittsburgh Liver Research Center, University of Pittsburgh, Pennsylvania, United States of America
- Division of Endocrinology and Metabolism, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
- * E-mail: (SL); (BZ)
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88
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Abstract
Circadian clocks are endogenous oscillators that control 24-h physiological and behavioral processes. The central circadian clock exerts control over myriad aspects of mammalian physiology, including the regulation of sleep, metabolism, and the immune system. Here, we review advances in understanding the genetic regulation of sleep through the circadian system, as well as the impact of dysregulated gene expression on metabolic function. We also review recent studies that have begun to unravel the circadian clock’s role in controlling the cardiovascular and nervous systems, gut microbiota, cancer, and aging. Such circadian control of these systems relies, in part, on transcriptional regulation, with recent evidence for genome-wide regulation of the clock through circadian chromosome organization. These novel insights into the genomic regulation of human physiology provide opportunities for the discovery of improved treatment strategies and new understanding of the biological underpinnings of human disease.
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89
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Mauvoisin D, Gachon F. Proteomics in Circadian Biology. J Mol Biol 2019; 432:3565-3577. [PMID: 31843517 DOI: 10.1016/j.jmb.2019.12.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 12/09/2019] [Accepted: 12/09/2019] [Indexed: 02/06/2023]
Abstract
The circadian clock is an endogenous molecular timekeeping system that allows organisms to adjust their physiology and behavior to the time of day in an anticipatory fashion. In different organisms, the circadian clock coordinates physiology and metabolism through regulation of gene expression at the transcriptional and post-transcriptional levels. Until now, circadian gene expression studies have mostly focused primarily on transcriptomics approaches. This type of analyses revealed that many protein-encoding genes show circadian expression in a tissue-specific manner. During the last three decades, a long way has been traveled since the pioneering work on dinoflagellates, and new advances in mass spectrometry offered new perspectives in the characterization of the circadian dynamics of the proteome. Altogether, these efforts highlighted that rhythmic protein oscillation is driven equally by gene transcription, post-transcriptional and post-translational regulations. The determination of the role of the circadian clock in these three levels of regulation appears to be the next major challenge in the field.
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Affiliation(s)
- Daniel Mauvoisin
- L'institut Du Thorax, INSERM, CNRS, UNIV Nantes, Nantes, France.
| | - Frédéric Gachon
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD, 4072, Australia.
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90
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Kinouchi K, Magnan C, Ceglia N, Liu Y, Cervantes M, Pastore N, Huynh T, Ballabio A, Baldi P, Masri S, Sassone-Corsi P. Fasting Imparts a Switch to Alternative Daily Pathways in Liver and Muscle. Cell Rep 2019; 25:3299-3314.e6. [PMID: 30566858 DOI: 10.1016/j.celrep.2018.11.077] [Citation(s) in RCA: 86] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Revised: 09/08/2018] [Accepted: 11/19/2018] [Indexed: 01/09/2023] Open
Abstract
The circadian clock operates as intrinsic time-keeping machinery to preserve homeostasis in response to the changing environment. While food is a known zeitgeber for clocks in peripheral tissues, it remains unclear how lack of food influences clock function. We demonstrate that the transcriptional response to fasting operates through molecular mechanisms that are distinct from time-restricted feeding regimens. First, fasting affects core clock genes and proteins, resulting in blunted rhythmicity of BMAL1 and REV-ERBα both in liver and skeletal muscle. Second, fasting induces a switch in temporal gene expression through dedicated fasting-sensitive transcription factors such as GR, CREB, FOXO, TFEB, and PPARs. Third, the rhythmic genomic response to fasting is sustainable by prolonged fasting and reversible by refeeding. Thus, fasting imposes specialized dynamics of transcriptional coordination between the clock and nutrient-sensitive pathways, thereby achieving a switch to fasting-specific temporal gene regulation.
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Affiliation(s)
- Kenichiro Kinouchi
- Department of Biological Chemistry, Center for Epigenetics and Metabolism, U1233 INSERM, University of California, Irvine, Irvine, CA 92697, USA
| | - Christophe Magnan
- Department of Computer Science, Institute for Genomics and Bioinformatics, University of California, Irvine, Irvine, CA 92697, USA
| | - Nicholas Ceglia
- Department of Computer Science, Institute for Genomics and Bioinformatics, University of California, Irvine, Irvine, CA 92697, USA
| | - Yu Liu
- Department of Computer Science, Institute for Genomics and Bioinformatics, University of California, Irvine, Irvine, CA 92697, USA
| | - Marlene Cervantes
- Department of Biological Chemistry, Center for Epigenetics and Metabolism, U1233 INSERM, University of California, Irvine, Irvine, CA 92697, USA
| | - Nunzia Pastore
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Tuong Huynh
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Andrea Ballabio
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Telethon Institute of Genetics and Medicine, 80078 Pozzuoli, Naples, Italy
| | - Pierre Baldi
- Department of Computer Science, Institute for Genomics and Bioinformatics, University of California, Irvine, Irvine, CA 92697, USA
| | - Selma Masri
- Department of Biological Chemistry, Center for Epigenetics and Metabolism, U1233 INSERM, University of California, Irvine, Irvine, CA 92697, USA
| | - Paolo Sassone-Corsi
- Department of Biological Chemistry, Center for Epigenetics and Metabolism, U1233 INSERM, University of California, Irvine, Irvine, CA 92697, USA.
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91
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Molecular mechanisms and physiological importance of circadian rhythms. Nat Rev Mol Cell Biol 2019; 21:67-84. [PMID: 31768006 DOI: 10.1038/s41580-019-0179-2] [Citation(s) in RCA: 566] [Impact Index Per Article: 113.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/19/2019] [Indexed: 12/12/2022]
Abstract
To accommodate daily recurring environmental changes, animals show cyclic variations in behaviour and physiology, which include prominent behavioural states such as sleep-wake cycles but also a host of less conspicuous oscillations in neurological, metabolic, endocrine, cardiovascular and immune functions. Circadian rhythmicity is created endogenously by genetically encoded molecular clocks, whose components cooperate to generate cyclic changes in their own abundance and activity, with a periodicity of about a day. Throughout the body, such molecular clocks convey temporal control to the function of organs and tissues by regulating pertinent downstream programmes. Synchrony between the different circadian oscillators and resonance with the solar day is largely enabled by a neural pacemaker, which is directly responsive to certain environmental cues and able to transmit internal time-of-day representations to the entire body. In this Review, we discuss aspects of the circadian clock in Drosophila melanogaster and mammals, including the components of these molecular oscillators, the function and mechanisms of action of central and peripheral clocks, their synchronization and their relevance to human health.
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92
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Tong Z, Liu Y, Yu X, Martinez JD, Xu J. The transcriptional co-activator NCOA6 promotes estrogen-induced GREB1 transcription by recruiting ERα and enhancing enhancer-promoter interactions. J Biol Chem 2019; 294:19667-19682. [PMID: 31744881 DOI: 10.1074/jbc.ra119.010704] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 11/13/2019] [Indexed: 11/06/2022] Open
Abstract
Estrogen and its cognate receptor, ERα, regulate cell proliferation, differentiation, and carcinogenesis in the endometrium by controlling gene transcription. ERα requires co-activators to mediate transcription via mechanisms that are largely uncharacterized. Herein, using growth-regulating estrogen receptor binding 1 (GREB1) as an ERα target gene in Ishikawa cells, we demonstrate that nuclear receptor co-activator 6 (NCOA6) is essential for estradiol (E2)/ERα-activated GREB1 transcription. We found that NCOA6 associates with the GREB1 promoter and enhancer in an E2-independent manner and that NCOA6 knockout reduces chromatin looping, enhancer-promoter interactions, and basal GREB1 expression in the absence of E2. In the presence of E2, ERα bound the GREB1 enhancer and also associated with its promoter, and p300, myeloid/lymphoid or mixed-lineage leukemia protein 4 (MLL4), and RNA polymerase II were recruited to the GREB1 enhancer and promoter. Consequently, the levels of the histone modifications H3K4me1/3, H3K9ac, and H3K27ac were significantly increased; enhancer and promoter regions were transcribed; and GREB1 mRNA was robustly transcribed. NCOA6 knockout reduced ERα recruitment and abolished all of the aforementioned E2-induced events, making GREB1 completely insensitive to E2 induction. We also found that GREB1-deficient Ishikawa cells are much more resistant to chemotherapy and that human endometrial cancers with low GREB1 expression predict poor overall survival. These results indicate that NCOA6 has an essential role in ERα-mediated transcription by increasing enhancer-promoter interactions through chromatin looping and by recruiting RNA polymerase II and the histone-code modifiers p300 and MLL4. Moreover, GREB1 loss may predict chemoresistance of endometrial cancer.
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Affiliation(s)
- Zhangwei Tong
- Department of Molecular and Cellular Biology and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas 77030
| | - Yonghong Liu
- Department of Molecular and Cellular Biology and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas 77030
| | - Xiaobin Yu
- Department of Molecular and Cellular Biology and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas 77030
| | - Jarrod D Martinez
- Department of Molecular and Cellular Biology and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas 77030
| | - Jianming Xu
- Department of Molecular and Cellular Biology and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas 77030
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93
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Quagliarini F, Mir AA, Balazs K, Wierer M, Dyar KA, Jouffe C, Makris K, Hawe J, Heinig M, Filipp FV, Barish GD, Uhlenhaut NH. Cistromic Reprogramming of the Diurnal Glucocorticoid Hormone Response by High-Fat Diet. Mol Cell 2019; 76:531-545.e5. [PMID: 31706703 DOI: 10.1016/j.molcel.2019.10.007] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 08/02/2019] [Accepted: 10/07/2019] [Indexed: 12/21/2022]
Abstract
The glucocorticoid receptor (GR) is a potent metabolic regulator and a major drug target. While GR is known to play integral roles in circadian biology, its rhythmic genomic actions have never been characterized. Here we mapped GR's chromatin occupancy in mouse livers throughout the day and night cycle. We show how GR partitions metabolic processes by time-dependent target gene regulation and controls circulating glucose and triglycerides differentially during feeding and fasting. Highlighting the dominant role GR plays in synchronizing circadian amplitudes, we find that the majority of oscillating genes are bound by and depend on GR. This rhythmic pattern is altered by high-fat diet in a ligand-independent manner. We find that the remodeling of oscillatory gene expression and postprandial GR binding results from a concomitant increase of STAT5 co-occupancy in obese mice. Altogether, our findings highlight GR's fundamental role in the rhythmic orchestration of hepatic metabolism.
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Affiliation(s)
- Fabiana Quagliarini
- Institute for Diabetes and Obesity (IDO), Helmholtz Center Munich (HMGU) and German Center for Diabetes Research (DZD), Ingolstaedter Landstr. 1, 85764 Neuherberg (Munich), Germany; Institute for Diabetes and Cancer (IDC), Helmholtz Center Munich (HMGU) and German Center for Diabetes Research (DZD), Ingolstaedter Landstr. 1, 85764 Neuherberg (Munich), Germany
| | - Ashfaq Ali Mir
- Institute for Diabetes and Obesity (IDO), Helmholtz Center Munich (HMGU) and German Center for Diabetes Research (DZD), Ingolstaedter Landstr. 1, 85764 Neuherberg (Munich), Germany; Institute for Diabetes and Cancer (IDC), Helmholtz Center Munich (HMGU) and German Center for Diabetes Research (DZD), Ingolstaedter Landstr. 1, 85764 Neuherberg (Munich), Germany
| | - Kinga Balazs
- Institute for Diabetes and Obesity (IDO), Helmholtz Center Munich (HMGU) and German Center for Diabetes Research (DZD), Ingolstaedter Landstr. 1, 85764 Neuherberg (Munich), Germany; Institute for Diabetes and Cancer (IDC), Helmholtz Center Munich (HMGU) and German Center for Diabetes Research (DZD), Ingolstaedter Landstr. 1, 85764 Neuherberg (Munich), Germany
| | - Michael Wierer
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried (Munich), Germany
| | - Kenneth Allen Dyar
- Institute for Diabetes and Obesity (IDO), Helmholtz Center Munich (HMGU) and German Center for Diabetes Research (DZD), Ingolstaedter Landstr. 1, 85764 Neuherberg (Munich), Germany; Institute for Diabetes and Cancer (IDC), Helmholtz Center Munich (HMGU) and German Center for Diabetes Research (DZD), Ingolstaedter Landstr. 1, 85764 Neuherberg (Munich), Germany
| | - Celine Jouffe
- Institute for Diabetes and Obesity (IDO), Helmholtz Center Munich (HMGU) and German Center for Diabetes Research (DZD), Ingolstaedter Landstr. 1, 85764 Neuherberg (Munich), Germany; Institute for Diabetes and Cancer (IDC), Helmholtz Center Munich (HMGU) and German Center for Diabetes Research (DZD), Ingolstaedter Landstr. 1, 85764 Neuherberg (Munich), Germany
| | - Konstantinos Makris
- Institute for Diabetes and Obesity (IDO), Helmholtz Center Munich (HMGU) and German Center for Diabetes Research (DZD), Ingolstaedter Landstr. 1, 85764 Neuherberg (Munich), Germany; Institute for Diabetes and Cancer (IDC), Helmholtz Center Munich (HMGU) and German Center for Diabetes Research (DZD), Ingolstaedter Landstr. 1, 85764 Neuherberg (Munich), Germany
| | - Johann Hawe
- Institute of Computational Biology (ICB), HMGU, Ingolstaedter Landstr. 1, 85764 Neuherberg (Munich), Germany
| | - Matthias Heinig
- Institute of Computational Biology (ICB), HMGU, Ingolstaedter Landstr. 1, 85764 Neuherberg (Munich), Germany; Department of Informatics, Boltzmannstr. 3, 85748 Garching, Technische Universitaet Muenchen (TUM), Munich, Germany
| | - Fabian Volker Filipp
- Institute of Computational Biology (ICB), HMGU, Ingolstaedter Landstr. 1, 85764 Neuherberg (Munich), Germany; School of Life Sciences Weihenstephan, Maximus-von-Imhof-Forum 3, 85354 Freising, Technische Universitaet Muenchen (TUM), Munich, Germany
| | - Grant Daniel Barish
- Department of Medicine, Division of Endocrinology, Metabolism and Molecular Medicine, Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Jesse Brown VA Medical Center, Chicago, IL 60612, USA
| | - Nina Henriette Uhlenhaut
- Institute for Diabetes and Obesity (IDO), Helmholtz Center Munich (HMGU) and German Center for Diabetes Research (DZD), Ingolstaedter Landstr. 1, 85764 Neuherberg (Munich), Germany; Institute for Diabetes and Cancer (IDC), Helmholtz Center Munich (HMGU) and German Center for Diabetes Research (DZD), Ingolstaedter Landstr. 1, 85764 Neuherberg (Munich), Germany; Metabolic Programming, School of Life Sciences Weihenstephan, Gregor Mendel Str. 2, 85354 Freising, Technische Universitaet Muenchen (TUM), Munich, Germany.
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94
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Zhou C, Yu F, Zeng P, Zhang T, Huang H, Chen W, Wu B. Circadian sensitivity to the cardiac glycoside oleandrin is associated with diurnal intestinal P-glycoprotein expression. Biochem Pharmacol 2019; 169:113622. [PMID: 31472126 DOI: 10.1016/j.bcp.2019.08.024] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2019] [Accepted: 08/26/2019] [Indexed: 12/21/2022]
Abstract
The cardiac glycoside oleandrin is a main active constituent of the botanical anti-cancer drug candidate PBI-05204, an extract of Nerium oleander. Here, we aimed to determine the circadian sensitivity of mice to oleandrin, and to investigate the role of intestinal P-gp in generating rhythmic drug toxicity. Toxicity and pharmacokinetic experiments were performed with wild-type, Bmal1iKO (intestine-specific Bmal1 knockout) and Bmal1fl/fl (control littermates of Bmal1iKO) mice. The cardiac toxicity (reflected by plasma CK-MB, LDH and cTn-I levels) varied significantly with the times of drug dosing in wild-type mice (a lower toxicity at ZT10 and more severe at ZT2/22). Dosing at ZT2 generated a higher drug exposure than ZT10, supporting a lower toxicity at ZT10. Intracellular accumulation of oleandrin (2.5-10 μM) was reduced in MDCKⅡ-MDR1 than in parental cells. MDR1 overexpression decreased the cell sensitivity to oleandrin toxicity. The net flux ratio (MDCKⅡ-MDR1 versus parental cells) was 2.9 for oleandrin. These data indicated oleandrin as a P-gp substrate. Both mdr1a mRNA and P-gp protein oscillated with the times of the day in small intestine of Bmal1fl/fl mice. Intestinal ablation of Bmal1 down-regulated mdr1a mRNA and P-gp protein, and abrogated their rhythms. Likewise, Bmal1 silencing led to down-regulated mdr1a mRNA and to a loss of its rhythmicity in serum-shocked CT26 cells. Based on luciferase reporter assays, Bmal1 regulated rhythmic mdr1a transcription through the clock output genes Hlf and E4bp4. Intestinal ablation of Bmal1 exacerbated oleandrin toxicity and enhanced drug exposure. Moreover, time dependency of toxicity and drug exposure were lost in Bmal1iKO mice. In conclusion, diurnal intestinal P-gp is a critical factor influencing daily oleandrin exposure and toxicity. Our findings have implications in minimizing oleandrin (and possibly Nerium oleander) toxicity and improving drug efficacy via dosing time optimization.
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Affiliation(s)
- Cui Zhou
- Research Center for Biopharmaceutics and Pharmacokinetics, College of Pharmacy, Jinan University, Guangzhou, China; College of Chemistry and Biology Engineering, Yichun University, Jiangxi, China
| | - Fangjun Yu
- Research Center for Biopharmaceutics and Pharmacokinetics, College of Pharmacy, Jinan University, Guangzhou, China; International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Chinese Ministry of Education (MOE), College of Pharmacy, Jinan University, Guangzhou 510632, China
| | - Peng Zeng
- School of Food and Pharmaceutical Engineering, Zhaoqing University, Zhaoqing, Guangdong, China
| | - Tianpeng Zhang
- Research Center for Biopharmaceutics and Pharmacokinetics, College of Pharmacy, Jinan University, Guangzhou, China
| | - Hao Huang
- College of Chemistry and Biology Engineering, Yichun University, Jiangxi, China
| | - Wenying Chen
- The Third Affiliated Hospital of Southern Medical University, Guangzhou, China
| | - Baojian Wu
- Research Center for Biopharmaceutics and Pharmacokinetics, College of Pharmacy, Jinan University, Guangzhou, China; International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Chinese Ministry of Education (MOE), College of Pharmacy, Jinan University, Guangzhou 510632, China.
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95
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Cedernaes J, Waldeck N, Bass J. Neurogenetic basis for circadian regulation of metabolism by the hypothalamus. Genes Dev 2019; 33:1136-1158. [PMID: 31481537 PMCID: PMC6719618 DOI: 10.1101/gad.328633.119] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Circadian rhythms are driven by a transcription-translation feedback loop that separates anabolic and catabolic processes across the Earth's 24-h light-dark cycle. Central pacemaker neurons that perceive light entrain a distributed clock network and are closely juxtaposed with hypothalamic neurons involved in regulation of sleep/wake and fast/feeding states. Gaps remain in identifying how pacemaker and extrapacemaker neurons communicate with energy-sensing neurons and the distinct role of circuit interactions versus transcriptionally driven cell-autonomous clocks in the timing of organismal bioenergetics. In this review, we discuss the reciprocal relationship through which the central clock drives appetitive behavior and metabolic homeostasis and the pathways through which nutrient state and sleep/wake behavior affect central clock function.
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Affiliation(s)
- Jonathan Cedernaes
- Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
| | - Nathan Waldeck
- Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
| | - Joseph Bass
- Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
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96
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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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97
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RORα suppresses interleukin-6-mediated hepatic acute phase response. Sci Rep 2019; 9:11798. [PMID: 31409825 PMCID: PMC6692401 DOI: 10.1038/s41598-019-48171-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 07/29/2019] [Indexed: 12/31/2022] Open
Abstract
Acute liver failure (ALF) is characterized by loss of liver function in response to sustained augmentation of the acute-phase response (APR) in the liver, which can progress even to death. Although the inflammatory interleukin-6 (IL-6)–axis is a crucial factor that drives the hepatic APR by releasing diverse acute-phase proteins (APPs), therapeutic strategies to block the IL-6–STAT3-mediated APR are not well developed. Here, we show that the nuclear receptor retinoic acid-related orphan receptor α (RORα) limits APR-mediated liver injury by inhibiting the hepatic IL-6–STAT3 signaling pathway. Administration of JC1-40, an RORα activator, diminished diethylnitrosamine-induced acute liver injury and repressed transcriptional expression of APPs such as CXCL1 and LCN2 in mice. IL-6-mediated activation of STAT3 was repressed after RORα activation by either adenoviral infusion of RORα or JC1-40 treatment in primary hepatocytes. Activation of RORα decreased transcriptional expression of IL-6 receptor α, an upstream activator of STAT3, both in vitro and in vivo. This may be one mechanism underlying the RORα-mediated inhibition of STAT3. Taken together, our results suggest that RORα is a regulator of the hepatic IL-6–STAT3 signaling pathway and may be a new therapeutic target for treating APR-associated inflammatory ALF.
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Yoshitane H, Asano Y, Sagami A, Sakai S, Suzuki Y, Okamura H, Iwasaki W, Ozaki H, Fukada Y. Functional D-box sequences reset the circadian clock and drive mRNA rhythms. Commun Biol 2019; 2:300. [PMID: 31428688 PMCID: PMC6687812 DOI: 10.1038/s42003-019-0522-3] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 06/28/2019] [Indexed: 01/12/2023] Open
Abstract
The circadian clock drives gene expression rhythms, leading to daily changes in physiology and behavior. In mammals, Albumin D-site-Binding Protein (DBP) rhythmically activates transcription of various genes through a DNA cis-element, D-box. The DBP-dependent transactivation is repressed by competitive binding of E4BP4 to the D-box. Despite the elaborate regulation, physiological roles of the D-box in the circadian clockwork are still elusive. Here we identified 1490 genomic regions recognized commonly by DBP and E4BP4 in the mouse liver. We comprehensively defined functional D-box sequences using an improved bioinformatics method, MOCCS2. In RNA-Seq analysis of E4bp4-knockout and wild type liver, we showed the importance of E4BP4-mediated circadian repression in gene expression rhythms. In addition to the circadian control, we found that environmental stimuli caused acute induction of E4BP4 protein, evoking phase-dependent phase shifts of cellular circadian rhythms and resetting the clock. Collectively, D-box-mediated transcriptional regulation plays pivotal roles in input and output in the circadian clock system.
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Affiliation(s)
- Hikari Yoshitane
- Department of Biological Sciences, School of Science, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku Tokyo, 113-0033 Japan
| | - Yoshimasa Asano
- Department of Biological Sciences, School of Science, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku Tokyo, 113-0033 Japan
| | - Aya Sagami
- Department of Biological Sciences, School of Science, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku Tokyo, 113-0033 Japan
| | - Seinosuke Sakai
- Department of Biological Sciences, School of Science, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku Tokyo, 113-0033 Japan
| | - Yutaka Suzuki
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwanoha 5-1-5,, Kashiwa Chiba, 277-8568 Japan
| | - Hitoshi Okamura
- Department of Systems Biology, Graduate School of Pharmaceutical Sciences, Kyoto University, Yoshida-Shimo-Adachi-cho 46-29, Kyoto, 606-8501 Japan
| | - Wataru Iwasaki
- Department of Biological Sciences, School of Science, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku Tokyo, 113-0033 Japan
| | - Haruka Ozaki
- Bioinformatics Laboratory, Faculty of Medicine, University of Tsukuba, Tennodai 1-1-1, Tsukuba, Ibaraki, 305-8575 Japan
- Center for Artificial Intelligence Research, University of Tsukuba, Tennodai 1-1-1, Tsukuba, Ibaraki, 305-8577 Japan
| | - Yoshitaka Fukada
- Department of Biological Sciences, School of Science, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku Tokyo, 113-0033 Japan
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99
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Li X, Shi L, Zhang K, Wei W, Liu Q, Mao F, Li J, Cai W, Chen H, Teng H, Li J, Sun Z. CirGRDB: a database for the genome-wide deciphering circadian genes and regulators. Nucleic Acids Res 2019; 46:D64-D70. [PMID: 29059379 PMCID: PMC5753205 DOI: 10.1093/nar/gkx944] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 10/03/2017] [Indexed: 01/16/2023] Open
Abstract
Circadian rhythms govern various kinds of physiological and behavioral functions of the living organisms, and disruptions of the rhythms are highly detrimental to health. Although several databases have been built for circadian genes, a resource for comprehensive post-transcriptional regulatory information of circadian RNAs and expression patterns of disease-related circadian RNAs is still lacking. Here, we developed CirGRDB (http://cirgrdb.biols.ac.cn) by integrating more than 4936 genome-wide assays, with the aim of fulfilling the growing need to understand the rhythms of life. CirGRDB presents a friendly web interface that allows users to search and browse temporal expression patterns of interested genes in 37 human/mouse tissues or cell lines, and three clinical disorders including sleep disorder, aging and tumor. More importantly, eight kinds of potential transcriptional and post-transcriptional regulators involved in the rhythmic expression of the specific genes, including transcription factors, histone modifications, chromatin accessibility, enhancer RNAs, miRNAs, RNA-binding proteins, RNA editing and RNA methylation, can also be retrieved. Furthermore, a regulatory network could be generated based on the regulatory information. In summary, CirGRDB offers a useful repository for exploring disease-related circadian RNAs, and deciphering the transcriptional and post-transcriptional regulation of circadian rhythms.
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Affiliation(s)
- Xianfeng Li
- State Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan 410078, China
| | - Leisheng Shi
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China.,Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Kun Zhang
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China.,Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Wenqing Wei
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
| | - Qi Liu
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Fengbiao Mao
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jinchen Li
- State Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan 410078, China
| | - Wanshi Cai
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
| | - Huiqian Chen
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Huajing Teng
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
| | - Jiada Li
- State Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan 410078, China
| | - Zhongsheng Sun
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
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100
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Lugena AB, Zhang Y, Menet JS, Merlin C. Genome-wide discovery of the daily transcriptome, DNA regulatory elements and transcription factor occupancy in the monarch butterfly brain. PLoS Genet 2019; 15:e1008265. [PMID: 31335862 PMCID: PMC6677324 DOI: 10.1371/journal.pgen.1008265] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 08/02/2019] [Accepted: 06/21/2019] [Indexed: 12/20/2022] Open
Abstract
The Eastern North American monarch butterfly, Danaus plexippus, is famous for its spectacular seasonal long-distance migration. In recent years, it has also emerged as a novel system to study how animal circadian clocks keep track of time and regulate ecologically relevant daily rhythmic activities and seasonal behavioral outputs. However, unlike in Drosophila and the mouse, little work has been undertaken in the monarch to identify rhythmic genes at the genome-wide level and elucidate the regulation of their diurnal expression. Here, we used RNA-sequencing and Assay for Transposase-Accessible Chromatin (ATAC)-sequencing to profile the diurnal transcriptome, open chromatin regions, and transcription factor (TF) footprints in the brain of wild-type monarchs and of monarchs with impaired clock function, including Cryptochrome 2 (Cry2), Clock (Clk), and Cycle-like loss-of-function mutants. We identified 217 rhythmically expressed genes in the monarch brain; many of them were involved in the regulation of biological processes key to brain function, such as glucose metabolism and neurotransmission. Surprisingly, we found no significant time-of-day and genotype-dependent changes in chromatin accessibility in the brain. Instead, we found the existence of a temporal regulation of TF occupancy within open chromatin regions in the vicinity of rhythmic genes in the brains of wild-type monarchs, which is disrupted in clock deficient mutants. Together, this work identifies for the first time the rhythmic genes and modes of regulation by which diurnal transcription rhythms are regulated in the monarch brain. It also illustrates the power of ATAC-sequencing to profile genome-wide regulatory elements and TF binding in a non-model organism for which TF-specific antibodies are not yet available. With a rich biology that includes a clock-regulated migratory behavior and a circadian clock possessing mammalian clock orthologues, the monarch butterfly is an unconventional system with broad appeal to study circadian and seasonal rhythms. While clockwork mechanisms and rhythmic behavioral outputs have been studied in this species, the rhythmic genes that regulate rhythmic daily and seasonal activities remain largely unknown. Likewise, the mechanisms regulating rhythmic gene expression have not been explored in the monarch. Here, we applied genome-wide sequencing approaches to identify genes with rhythmic diurnal expression in the monarch brain, revealing the coordination of key pathways for brain function. We also identified the monarch brain open chromatin regions and provide evidence that regulation of rhythmic gene expression does not occur through temporal regulation of chromatin opening but rather by the time-of-day dependent binding of transcription factors in cis-regulatory elements. Together, our data extend our knowledge of the molecular rhythmic pathways, which may prove important in understanding the mechanisms underlying the daily and seasonal biology of the migratory monarch butterflies.
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Affiliation(s)
- Aldrin B. Lugena
- Department of Biology and Center for Biological Clocks Research, Texas A&M University, College Station, Texas, United States of America
| | - Ying Zhang
- Department of Biology and Center for Biological Clocks Research, Texas A&M University, College Station, Texas, United States of America
| | - Jerome S. Menet
- Department of Biology and Center for Biological Clocks Research, Texas A&M University, College Station, Texas, United States of America
| | - Christine Merlin
- Department of Biology and Center for Biological Clocks Research, Texas A&M University, College Station, Texas, United States of America
- * E-mail:
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