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Dufor T, Grehl S, Tang AD, Doulazmi M, Traoré M, Debray N, Dubacq C, Deng ZD, Mariani J, Lohof AM, Sherrard RM. Neural circuit repair by low-intensity magnetic stimulation requires cellular magnetoreceptors and specific stimulation patterns. SCIENCE ADVANCES 2019; 5:eaav9847. [PMID: 31692960 PMCID: PMC6821463 DOI: 10.1126/sciadv.aav9847] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 09/16/2019] [Indexed: 05/10/2023]
Abstract
Although electromagnetic brain stimulation is a promising treatment in neurology and psychiatry, clinical outcomes are variable, and underlying mechanisms are ill-defined, which impedes the development of new effective stimulation protocols. Here, we show, in vivo and ex vivo, that repetitive transcranial magnetic stimulation at low-intensity (LI-rTMS) induces axon outgrowth and synaptogenesis to repair a neural circuit. This repair depends on stimulation pattern, with complex biomimetic patterns being particularly effective, and the presence of cryptochrome, a putative magnetoreceptor. Only repair-promoting LI-rTMS patterns up-regulated genes involved in neuronal repair; almost 40% of were cryptochrome targets. Our data open a new framework to understand the mechanisms underlying structural neuroplasticity induced by electromagnetic stimulation. Rather than neuronal activation by induced electric currents, we propose that weak magnetic fields act through cryptochrome to activate cellular signaling cascades. This information opens new routes to optimize electromagnetic stimulation and develop effective treatments for different neurological diseases.
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Affiliation(s)
- T. Dufor
- Sorbonne Université and CNRS, IBPS, UMR 8256 Biological Adaptation and Ageing, Paris, France
| | - S. Grehl
- Sorbonne Université and CNRS, IBPS, UMR 8256 Biological Adaptation and Ageing, Paris, France
- Experimental and Regenerative Neuroscience, School of Animal Biology, University of Western Australia, Perth, Australia
| | - A. D. Tang
- Experimental and Regenerative Neuroscience, School of Animal Biology, University of Western Australia, Perth, Australia
| | - M. Doulazmi
- Sorbonne Université and CNRS, IBPS, UMR 8256 Biological Adaptation and Ageing, Paris, France
| | | | - N. Debray
- Sorbonne Université and CNRS, IBPS, UMR 8256 Biological Adaptation and Ageing, Paris, France
| | - C. Dubacq
- Sorbonne Université, IBPS, CNRS UMR 8246 and INSERM U1130 Neuroscience Paris Seine, Paris, France
| | - Z.-D. Deng
- Noninvasive Neuromodulation Unit, Experimental Therapeutics and Pathophysiology Branch, Intramural Research Program, National Institute of Mental Health, National Institutes of Health, Bethesda, MD, USA
| | - J. Mariani
- Sorbonne Université and CNRS, IBPS, UMR 8256 Biological Adaptation and Ageing, Paris, France
- Sorbonne Université and Assistance Publique Hôpitaux de Paris, Institut de la Longévité, Charles Foix Hospital, Ivry-sur-Seine, France
| | - A. M. Lohof
- Sorbonne Université and CNRS, IBPS, UMR 8256 Biological Adaptation and Ageing, Paris, France
| | - R. M. Sherrard
- Sorbonne Université and CNRS, IBPS, UMR 8256 Biological Adaptation and Ageing, Paris, France
- Sorbonne Université and Assistance Publique Hôpitaux de Paris, Institut de la Longévité, Charles Foix Hospital, Ivry-sur-Seine, France
- Corresponding author.
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Huang H, Zou X, Zhong L, Hou Y, Zhou J, Zhang Z, Xing X, Sun J. CRISPR/dCas9-mediated activation of multiple endogenous target genes directly converts human foreskin fibroblasts into Leydig-like cells. J Cell Mol Med 2019; 23:6072-6084. [PMID: 31264792 PMCID: PMC6714237 DOI: 10.1111/jcmm.14470] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 04/29/2019] [Accepted: 05/21/2019] [Indexed: 01/21/2023] Open
Abstract
Recently, Leydig cell (LC) transplantation has been revealed as a promising strategy for treating male hypogonadism; however, the key problem restricting the application of LC transplantation is a severe lack of seed cells. It seems that targeted activation of endogenous genes may provide a potential alternative. Therefore, the aim of this study was to determine whether targeted activation of Nr5a1, Gata4 and Dmrt1 (NGD) via the CRISPR/dCas9 synergistic activation mediator system could convert human foreskin fibroblasts (HFFs) into functional Leydig-like cells. We first constructed the stable Hsd3b-dCas9-MPH-HFF cell line using the Hsd3b-EGFP, dCas9-VP64 and MS2-P65-HSF1 lentiviral vectors and then infected it with single guide RNAs. Next, we evaluated the reprogrammed cells for their reprogramming efficiency, testosterone production characteristics and expression levels of Leydig steroidogenic markers by quantitative real-time polymerase chain reaction or Western blotting. Our results showed that the reprogramming efficiency was close to 10% and that the reprogrammed Leydig-like cells secreted testosterone rapidly and, more importantly, responded effectively to stimulation with human chorionic gonadotropin and expressed Leydig steroidogenic markers. Our findings demonstrate that simultaneous targeted activation of the endogenous NGD genes directly reprograms HFFs into functional Leydig-like cells, providing an innovative technology that may have promising potential for the treatment of male androgen deficiency diseases.
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Affiliation(s)
- Hua Huang
- Department of Urology, Shanghai Children's Medical CenterShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Xiangyu Zou
- Department of Urology, Shanghai Children's Medical CenterShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Liang Zhong
- Department of Urology, Shanghai Children's Medical CenterShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Yanping Hou
- Department of Urology, Shanghai Children's Medical CenterShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Jin Zhou
- Department of Urology, Shanghai Children's Medical CenterShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Zhiyuan Zhang
- Department of Urology, Shanghai Children's Medical CenterShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Xiaoyu Xing
- Department of Urology, Shanghai Children's Medical CenterShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Jie Sun
- Department of Urology, Shanghai Children's Medical CenterShanghai Jiao Tong University School of MedicineShanghaiChina
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BRCA1 and BRCA2 Gene Expression: Diurnal Variability and Influence of Shift Work. Cancers (Basel) 2019; 11:cancers11081146. [PMID: 31405066 PMCID: PMC6721503 DOI: 10.3390/cancers11081146] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 08/05/2019] [Accepted: 08/07/2019] [Indexed: 12/12/2022] Open
Abstract
BRCA1 and BRCA2 genes are involved in DNA double-strand break repair and related to breast cancer. Shift work is associated with biological clock alterations and with a higher risk of breast cancer. The aim of this study was to investigate the variability of expression of BRCA genes through the day in healthy subjects and to measure BRCA expression levels in shift workers. The study was approached in two ways. First, we examined diurnal variation of BRCA1 and BRCA2 genes in lymphocytes of 15 volunteers over a 24-hour period. Second, we measured the expression of these genes in lymphocytes from a group of shift and daytime workers. The change in 24-hour expression levels of BRCA1 and BRCA2 genes was statistically significant, decreasing from the peak at midday to the lowest level at midnight. Lower levels for both genes were found in shift workers compared to daytime workers. Diurnal variability of BRCA1 and BRCA2 expression suggests a relation of DNA double-strand break repair system with biological clock. Lower levels of BRCA1 and BRCA2 found in shift workers may be one of the potential factors related to the higher risk of breast cancer.
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Wu E, Zhang T, Tan C, Peng C, Chisti Y, Wang Q, Gong J. Theabrownin from Pu-erh tea together with swinging exercise synergistically ameliorates obesity and insulin resistance in rats. Eur J Nutr 2019; 59:1937-1950. [PMID: 31273522 DOI: 10.1007/s00394-019-02044-y] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 06/30/2019] [Indexed: 01/03/2023]
Abstract
PURPOSE Theabrownin (TB)-containing Pu-erh tea has been shown to be hypolipidemic in rats fed a high-fat diet. Physical exercise such as swinging is also known to reduce obesity. We hypothesized that TB in combination with swinging can synergistically ameliorate obesity and insulin resistance in rats with metabolic syndrome. METHODS TB, rosiglitazone, or lovastatin (controls) was administered by gavage to rats fed a diet high in fat, sugar, and salt. A subgroup of the rats was subjected to a 30-min daily swinging exercise regimen, whereas the other rats did not exercise. RESULTS Theabrownin in combination with swinging was found to significantly improve serum lipid status and prevent development of obesity and insulin resistance in rats. Liver transcriptomics data suggested that theabrownin activated circadian rhythm, protein kinase A, the adenosine monophosphate-activated protein kinase, and insulin signaling pathways by enhancing cyclic adenosine monophosphate levels and, hence, accelerating nutrient metabolism and the consumption of sugar and fat. The serum dopamine levels in rats increased significantly after exercise. In parallel work, intraperitoneal dopamine injections were shown to significantly reduce weight gain and prevent the elevation in triglyceride levels that would otherwise be induced by the high fat-sugar-salt diet. Theabrownin prevented obesity and insulin resistance mainly by affecting the circadian rhythm, while swinging exercise stimulated the overproduction of dopamine to accelerate metabolism of glucose and lipid. CONCLUSIONS Theabrownin and exercise synergistically ameliorated metabolic syndrome in rats and effectively prevented obesity.
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Affiliation(s)
- Enkai Wu
- College of Food Science and Technology, Yunnan Agricultural University, Heilong Tan, Kunming, 650201, Yunnan, China
| | - Tingting Zhang
- College of Food Science and Technology, Yunnan Agricultural University, Heilong Tan, Kunming, 650201, Yunnan, China
| | - Chao Tan
- College of Food Science and Technology, Yunnan Agricultural University, Heilong Tan, Kunming, 650201, Yunnan, China
| | - Chunxiu Peng
- College of Horticulture and Landscape, Yunnan Agricultural University, Heilong Tan, Kunming, 650201, Yunnan, China
| | - Yusuf Chisti
- School of Engineering, Massey University, Private Bag 11 222, Palmerston North, New Zealand
| | - Qiuping Wang
- College of Food Science and Technology, Yunnan Agricultural University, Heilong Tan, Kunming, 650201, Yunnan, China.
| | - Jiashun Gong
- College of Food Science and Technology, Yunnan Agricultural University, Heilong Tan, Kunming, 650201, Yunnan, China.
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Marbach-Breitrück E, Matz-Soja M, Abraham U, Schmidt-Heck W, Sales S, Rennert C, Kern M, Aleithe S, Spormann L, Thiel C, Gerlini R, Arnold K, Klöting N, Guthke R, Rozman D, Teperino R, Shevchenko A, Kramer A, Gebhardt R. Tick-tock hedgehog-mutual crosstalk with liver circadian clock promotes liver steatosis. J Hepatol 2019; 70:1192-1202. [PMID: 30711403 DOI: 10.1016/j.jhep.2019.01.022] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 12/20/2018] [Accepted: 01/16/2019] [Indexed: 12/29/2022]
Abstract
BACKGROUND & AIMS The mammalian circadian clock controls various aspects of liver metabolism and integrates nutritional signals. Recently, we described Hedgehog (Hh) signaling as a novel regulator of liver lipid metabolism. Herein, we investigated crosstalk between hepatic Hh signaling and circadian rhythm. METHODS Diurnal rhythms of Hh signaling were investigated in liver and hepatocytes from mice with ablation of Smoothened (SAC-KO) and crossbreeds with PER2::LUC reporter mice. By using genome-wide screening, qPCR, immunostaining, ELISA and RNAi experiments in vitro we identified relevant transcriptional regulatory steps. Shotgun lipidomics and metabolic cages were used for analysis of metabolic alterations and behavior. RESULTS Hh signaling showed diurnal oscillations in liver and hepatocytes in vitro. Correspondingly, the level of Indian Hh, oscillated in serum. Depletion of the clock gene Bmal1 in hepatocytes resulted in significant alterations in the expression of Hh genes. Conversely, SAC-KO mice showed altered expression of clock genes, confirmed by RNAi against Gli1 and Gli3. Genome-wide screening revealed that SAC-KO hepatocytes showed time-dependent alterations in various genes, particularly those associated with lipid metabolism. The clock/hedgehog module further plays a role in rhythmicity of steatosis, and in the response of the liver to a high-fat diet or to differently timed starvation. CONCLUSIONS For the first time, Hh signaling in hepatocytes was found to be time-of-day dependent and to feed back on the circadian clock. Our findings suggest an integrative role of Hh signaling, mediated mainly by GLI factors, in maintaining homeostasis of hepatic lipid metabolism by balancing the circadian clock. LAY SUMMARY The results of our investigation show for the first time that the Hh signaling in hepatocytes is time-of-day dependent, leading to differences not only in transcript levels but also in the amount of Hh ligands in peripheral blood. Conversely, Hh signaling is able to feed back to the circadian clock.
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Affiliation(s)
- Eugenia Marbach-Breitrück
- Rudolf-Schönheimer-Institute of Biochemistry, Faculty of Medicine, Leipzig University, Leipzig, Germany; Institute of Biochemistry, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Germany
| | - Madlen Matz-Soja
- Rudolf-Schönheimer-Institute of Biochemistry, Faculty of Medicine, Leipzig University, Leipzig, Germany.
| | - Ute Abraham
- Laboratory of Chronobiology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Germany
| | - Wolfgang Schmidt-Heck
- Leibniz Institute for Natural Product Research and Infection Biology - Hans Knoell Institute, Jena, Germany
| | - Susanne Sales
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Christiane Rennert
- Rudolf-Schönheimer-Institute of Biochemistry, Faculty of Medicine, Leipzig University, Leipzig, Germany; Department of Hepatobiliary Surgery and Visceral Transplantation, University Hospital, Leipzig University, Leipzig, Germany
| | - Matthias Kern
- IFB Adiposity Diseases, University of Leipzig, Leipzig, Germany
| | - Susanne Aleithe
- Rudolf-Schönheimer-Institute of Biochemistry, Faculty of Medicine, Leipzig University, Leipzig, Germany; Clinic and Polyclinic of Neurology, Faculty of Medicine, Leipzig University, Germany
| | - Luise Spormann
- Rudolf-Schönheimer-Institute of Biochemistry, Faculty of Medicine, Leipzig University, Leipzig, Germany
| | - Carlo Thiel
- Rudolf-Schönheimer-Institute of Biochemistry, Faculty of Medicine, Leipzig University, Leipzig, Germany
| | - Raffaele Gerlini
- Institute of Experimental Genetics (IEG), HDC, Neuherberg, Germany
| | - Katrin Arnold
- Rudolf-Schönheimer-Institute of Biochemistry, Faculty of Medicine, Leipzig University, Leipzig, Germany
| | - Nora Klöting
- IFB Adiposity Diseases, University of Leipzig, Leipzig, Germany
| | - Reinhard Guthke
- Leibniz Institute for Natural Product Research and Infection Biology - Hans Knoell Institute, Jena, Germany
| | - Damjana Rozman
- Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, Slovenia
| | - Raffaele Teperino
- Institute of Experimental Genetics (IEG), HDC, Neuherberg, Germany; DZD, German Center for Diabetes Research, Neuherberg, Germany
| | - Andrej Shevchenko
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Achim Kramer
- Laboratory of Chronobiology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Germany
| | - Rolf Gebhardt
- Rudolf-Schönheimer-Institute of Biochemistry, Faculty of Medicine, Leipzig University, Leipzig, Germany.
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Greenwell BJ, Trott AJ, Beytebiere JR, Pao S, Bosley A, Beach E, Finegan P, Hernandez C, Menet JS. Rhythmic Food Intake Drives Rhythmic Gene Expression More Potently than the Hepatic Circadian Clock in Mice. Cell Rep 2019; 27:649-657.e5. [PMID: 30995463 DOI: 10.1016/j.celrep.2019.03.064] [Citation(s) in RCA: 87] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 01/03/2019] [Accepted: 03/15/2019] [Indexed: 02/02/2023] Open
Abstract
Every mammalian tissue exhibits daily rhythms in gene expression to control the activation of tissue-specific processes at the most appropriate time of the day. Much of this rhythmic expression is thought to be driven cell autonomously by molecular circadian clocks present throughout the body. By manipulating the daily rhythm of food intake in the mouse, we here show that more than 70% of the cycling mouse liver transcriptome loses rhythmicity under arrhythmic feeding. Remarkably, core clock genes are not among the 70% of genes losing rhythmic expression, and their expression continues to exhibit normal oscillations in arrhythmically fed mice. Manipulation of rhythmic food intake also alters the timing of key signaling and metabolic pathways without altering the hepatic clock oscillations. Our findings thus demonstrate that systemic signals driven by rhythmic food intake significantly contribute to driving rhythms in liver gene expression and metabolic functions independently of the cell-autonomous hepatic clock.
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Affiliation(s)
- Ben J Greenwell
- Program of Genetics, Texas A&M University, College Station, TX 77843, USA; Department of Biology, Texas A&M University, College Station, TX 77843, USA
| | - Alexandra J Trott
- Program of Genetics, Texas A&M University, College Station, TX 77843, USA; Department of Biology, Texas A&M University, College Station, TX 77843, USA
| | | | - Shanny Pao
- Department of Biology, Texas A&M University, College Station, TX 77843, USA
| | - Alexander Bosley
- Department of Biology, Texas A&M University, College Station, TX 77843, USA
| | - Erin Beach
- Department of Biology, Texas A&M University, College Station, TX 77843, USA
| | - Patrick Finegan
- Department of Biology, Texas A&M University, College Station, TX 77843, USA
| | | | - Jerome S Menet
- Program of Genetics, Texas A&M University, College Station, TX 77843, USA; Department of Biology, Texas A&M University, College Station, TX 77843, USA.
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Circatidal gene expression in the mangrove cricket Apteronemobius asahinai. Sci Rep 2019; 9:3719. [PMID: 30842498 PMCID: PMC6403293 DOI: 10.1038/s41598-019-40197-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 02/08/2019] [Indexed: 11/11/2022] Open
Abstract
The mangrove cricket Apteronemobius asahinai is endemic to mangrove forest floors. It shows circatidal rhythmicity, with a 12.6-h period of locomotor activity under constant conditions. Its free-running activity also has a circadian component; i.e. it is more active during the subjective night than during the day. In this study, we investigated rhythmic gene expression under constant darkness by RNA sequencing to identify genes controlled by the biological clock. Samples collected every 3 h for 48 h were analysed (one cricket per time-point). We identified 284 significant circatidal cycling transcripts (period length 12–15 h). Almost half of them were annotated with known genes in the NCBI nr database, including enzymes related to metabolic processes and molecular chaperones. There were less transcripts with circadian rhythmicity than with circatidal rhythmicity, and the expression of core circadian clock genes did not show significant rhythmicity. This may reflect the nature of the mangrove cricket or may be due to the paucity of the sampling repeats: only two periods for circadian cycle with no replications. We evaluated for the first time the rhythmic transcriptome of an insect that shows circatidal rhythmic activity; our findings will contribute to future studies of circatidal clock genes.
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Qu M, Duffy T, Hirota T, Kay SA. Nuclear receptor HNF4A transrepresses CLOCK:BMAL1 and modulates tissue-specific circadian networks. Proc Natl Acad Sci U S A 2018; 115:E12305-E12312. [PMID: 30530698 PMCID: PMC6310821 DOI: 10.1073/pnas.1816411115] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Either expression level or transcriptional activity of various nuclear receptors (NRs) have been demonstrated to be under circadian control. With a few exceptions, little is known about the roles of NRs as direct regulators of the circadian circuitry. Here we show that the nuclear receptor HNF4A strongly transrepresses the transcriptional activity of the CLOCK:BMAL1 heterodimer. We define a central role for HNF4A in maintaining cell-autonomous circadian oscillations in a tissue-specific manner in liver and colon cells. Not only transcript level but also genome-wide chromosome binding of HNF4A is rhythmically regulated in the mouse liver. ChIP-seq analyses revealed cooccupancy of HNF4A and CLOCK:BMAL1 at a wide array of metabolic genes involved in lipid, glucose, and amino acid homeostasis. Taken together, we establish that HNF4A defines a feedback loop in tissue-specific mammalian oscillators and demonstrate its recruitment in the circadian regulation of metabolic pathways.
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Affiliation(s)
- Meng Qu
- Keck School of Medicine, University of Southern California, Los Angeles, CA 90089
| | - Tomas Duffy
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037
| | - Tsuyoshi Hirota
- Institute of Transformative Bio-Molecules, Nagoya University, 464-8602 Nagoya, Japan
| | - Steve A Kay
- Keck School of Medicine, University of Southern California, Los Angeles, CA 90089;
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Ella K, Mócsai A, Káldi K. Circadian regulation of neutrophils: Control by a cell-autonomous clock or systemic factors? Eur J Clin Invest 2018; 48 Suppl 2:e12965. [PMID: 29877596 DOI: 10.1111/eci.12965] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Accepted: 06/05/2018] [Indexed: 12/28/2022]
Abstract
BACKGROUND The circadian time-measuring system enables the organism to anticipate and effectively respond to regular daily changes in the environment and is therefore a crucial factor of adaptation. A large body of epidemiological data underlines the circadian characteristics of human immune functions. Circadian control of neutrophil responsiveness contributes to daily changes in the pathology of both acute and chronic inflammation and may therefore time-dependently influence the outcome of therapeutic approaches. AIM This review summarizes recent data on the role of the circadian clock in the control of immune responses, particularly of those linked to neutrophil activity, and possible mechanisms of the regulation. DISCUSSION In the first section of this review we present the recent model of the mammalian molecular clock by introducing the main transcription-translation feedback loops and discussing the pace-setting role of post-translational modifications. The next sections summarize clinical, epidemiological and experimental data regarding the daily control of immune responses and studies analysing expression of clock components in various leukocytes and particularly, in human peripheral neutrophils. As the latter data indicate that expression of components of the cell-autonomous clock is relatively low in neutrophils, in the last section we review recent findings suggesting a role for systemic and local factors in the regulation of rhythmic neutrophil responses.
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Affiliation(s)
- Krisztina Ella
- Department of Physiology, Semmelweis University, Budapest, Hungary
| | - Attila Mócsai
- Department of Physiology, Semmelweis University, Budapest, Hungary
| | - Krisztina Káldi
- Department of Physiology, Semmelweis University, Budapest, Hungary.,Department of Laboratory Medicine, Semmelweis University, Budapest, Hungary
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Wada T, Ichihashi Y, Suzuki E, Kosuge Y, Ishige K, Uchiyama T, Makishima M, Nakao R, Oishi K, Shimba S. Deletion of Bmal1 Prevents Diet-Induced Ectopic Fat Accumulation by Controlling Oxidative Capacity in the Skeletal Muscle. Int J Mol Sci 2018; 19:E2813. [PMID: 30231537 PMCID: PMC6164026 DOI: 10.3390/ijms19092813] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2018] [Revised: 09/12/2018] [Accepted: 09/15/2018] [Indexed: 01/05/2023] Open
Abstract
Brain and muscle arnt-like protein 1 (BMAL1), is a transcription factor known to regulate circadian rhythm. BMAL1 was originally characterized by its high expression in the skeletal muscle. Since the skeletal muscle is the dominant organ system in energy metabolism, the possible functions of BMAL1 in the skeletal muscle include the control of metabolism. Here, we established that its involvement in the regulation of oxidative capacity in the skeletal muscle. Muscle-specific Bmal1 KO mice (MKO mice) displayed several physiological hallmarks for the increase of oxidative capacity. This included increased energy expenditure and oxygen consumption, high running endurance and resistance to obesity with improved metabolic profiles. Also, the phosphorylation status of AMP-activated protein kinase and its downstream signaling substrate acetyl-CoA carboxylase in the MKO mice were substantially higher than those in the Bmal1flox/flox mice. In addition, biochemical and histological studies confirmed the substantial activation of oxidative fibers in the skeletal muscle of the MKO mice. The mechanism includes the regulation of Cacna1s expression, followed by the activation of calcium-nuclear factor of activated T cells (NFAT) axis. We thus conclude that BMAL1 is a critical regulator of the muscular fatty acid level under nutrition overloading and that the mechanism involves the control of oxidative capacity.
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Affiliation(s)
- Taira Wada
- Laboratory of Health Science, School of Pharmacy, Nihon University, 7-7-1 Narashinodai, Chiba, Funabshi 274-8555, Japan.
| | - Yuya Ichihashi
- Laboratory of Health Science, School of Pharmacy, Nihon University, 7-7-1 Narashinodai, Chiba, Funabshi 274-8555, Japan.
| | - Emi Suzuki
- Laboratory of Health Science, School of Pharmacy, Nihon University, 7-7-1 Narashinodai, Chiba, Funabshi 274-8555, Japan.
| | - Yasuhiro Kosuge
- Laboratory of Pharmacology, School of Pharmacy, Nihon University, 7-7-1 Narashinodai, Chiba, Funabshi 274-8555, Japan.
| | - Kumiko Ishige
- Laboratory of Pharmacology, School of Pharmacy, Nihon University, 7-7-1 Narashinodai, Chiba, Funabshi 274-8555, Japan.
| | - Taketo Uchiyama
- Laboratory of Organic Chemistry, School of Pharmacy, Nihon University, 7-7-1 Narashinodai, Chiba, Funabshi 274-8555, Japan.
| | - Makoto Makishima
- Division of Biochemistry, Department of Biomedical Sciences, School of Medicine, Nihon University, 30-1 Oyaguchi-Kamicho, Itabashi-ku, Tokyo 173-8610, Japan.
| | - Reiko Nakao
- Biological Clock Research Group, Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8566, Japan.
| | - Katsutaka Oishi
- Biological Clock Research Group, Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8566, Japan.
| | - Shigeki Shimba
- Laboratory of Health Science, School of Pharmacy, Nihon University, 7-7-1 Narashinodai, Chiba, Funabshi 274-8555, Japan.
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de Assis LVM, Kinker GS, Moraes MN, Markus RP, Fernandes PA, Castrucci AMDL. Expression of the Circadian Clock Gene BMAL1 Positively Correlates With Antitumor Immunity and Patient Survival in Metastatic Melanoma. Front Oncol 2018; 8:185. [PMID: 29946530 PMCID: PMC6005821 DOI: 10.3389/fonc.2018.00185] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2018] [Accepted: 05/10/2018] [Indexed: 12/11/2022] Open
Abstract
Introduction Melanoma is the most lethal type of skin cancer, with increasing incidence and mortality rates worldwide. Multiple studies have demonstrated a link between cancer development/progression and circadian disruption; however, the complex role of tumor-autonomous molecular clocks remains poorly understood. With that in mind, we investigated the pathophysiological relevance of clock genes expression in metastatic melanoma. Methods We analyzed gene expression, somatic mutation, and clinical data from 340 metastatic melanomas from The Cancer Genome Atlas, as well as gene expression data from 234 normal skin samples from genotype-tissue expression. Findings were confirmed in independent datasets. Results In melanomas, the expression of most clock genes was remarkably reduced and displayed a disrupted pattern of co-expression compared to the normal skins, indicating a dysfunctional circadian clock. Importantly, we demonstrate that the expression of the clock gene aryl hydrocarbon receptor nuclear translocator-like protein 1 (BMAL1) positively correlates with patient overall survival and with the expression of T-cell activity and exhaustion markers in the tumor bulk. Accordingly, high BMAL1 expression in pretreatment samples was significantly associated with clinical benefit from immune checkpoint inhibitors. The robust intratumoral T-cell infiltration/activation observed in patients with high BMAL1 expression was associated with a decreased expression of key DNA-repair enzymes, and with an increased mutational/neoantigen load. Conclusion Overall, our data corroborate previous reports regarding the impact of BMAL1 expression on the cellular DNA-repair capacity and indicate that alterations in the tumor-autonomous molecular clock could influence the cellular composition of the surrounding microenvironment. Moreover, we revealed the potential of BMAL1 as a clinically relevant prognostic factor and biomarker for T-cell-based immunotherapies.
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Affiliation(s)
- Leonardo Vinícius Monteiro de Assis
- Laboratory of Comparative Physiology of Pigmentation, Department of Physiology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Gabriela Sarti Kinker
- Laboratory of Neuroimmunemodulation, Department of Physiology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Maria Nathália Moraes
- Laboratory of Comparative Physiology of Pigmentation, Department of Physiology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Regina P Markus
- Laboratory of Neuroimmunemodulation, Department of Physiology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Pedro Augusto Fernandes
- Laboratory of Neuroimmunemodulation, Department of Physiology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Ana Maria de Lauro Castrucci
- Laboratory of Comparative Physiology of Pigmentation, Department of Physiology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil.,Department of Biology, University of Virginia, Charlottesville, VA, United States
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62
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Wong JCY, Smyllie NJ, Banks GT, Pothecary CA, Barnard AR, Maywood ES, Jagannath A, Hughes S, van der Horst GTJ, MacLaren RE, Hankins MW, Hastings MH, Nolan PM, Foster RG, Peirson SN. Differential roles for cryptochromes in the mammalian retinal clock. FASEB J 2018; 32:4302-4314. [PMID: 29561690 PMCID: PMC6071063 DOI: 10.1096/fj.201701165rr] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Cryptochromes 1 and 2 (CRY1/2) are key components of the negative limb of the mammalian circadian clock. Like many peripheral tissues, Cry1 and -2 are expressed in the retina, where they are thought to play a role in regulating rhythmic physiology. However, studies differ in consensus as to their localization and function, and CRY1 immunostaining has not been convincingly demonstrated in the retina. Here we describe the expression and function of CRY1 and -2 in the mouse retina in both sexes. Unexpectedly, we show that CRY1 is expressed throughout all retinal layers, whereas CRY2 is restricted to the photoreceptor layer. Retinal period 2::luciferase recordings from CRY1-deficient mice show reduced clock robustness and stability, while those from CRY2-deficient mice show normal, albeit long-period, rhythms. In functional studies, we then investigated well-defined rhythms in retinal physiology. Rhythms in the photopic electroretinogram, contrast sensitivity, and pupillary light response were all severely attenuated or abolished in CRY1-deficient mice. In contrast, these physiological rhythms are largely unaffected in mice lacking CRY2, and only photopic electroretinogram rhythms are affected. Together, our data suggest that CRY1 is an essential component of the mammalian retinal clock, whereas CRY2 has a more limited role.—Wong, J. C. Y., Smyllie, N. J., Banks, G. T., Pothecary, C. A., Barnard, A. R., Maywood, E. S., Jagannath, A., Hughes, S., van der Horst, G. T. J., MacLaren, R. E., Hankins, M. W., Hastings, M. H., Nolan, P. M., Foster, R. G., Peirson, S. N. Differential roles for cryptochromes in the mammalian retinal clock.
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Affiliation(s)
- Jovi C Y Wong
- Sleep and Circadian Neuroscience Institute, University of Oxford, Oxford, United Kingdom
| | - Nicola J Smyllie
- Medical Research Council (MRC) Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Gareth T Banks
- Medical Research Council (MRC) Harwell, Harwell Science and Innovation Campus, Harwell, United Kingdom
| | - Carina A Pothecary
- Sleep and Circadian Neuroscience Institute, University of Oxford, Oxford, United Kingdom
| | - Alun R Barnard
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom
| | - Elizabeth S Maywood
- Medical Research Council (MRC) Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Aarti Jagannath
- Sleep and Circadian Neuroscience Institute, University of Oxford, Oxford, United Kingdom
| | - Steven Hughes
- Sleep and Circadian Neuroscience Institute, University of Oxford, Oxford, United Kingdom
| | | | - Robert E MacLaren
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom
| | - Mark W Hankins
- Sleep and Circadian Neuroscience Institute, University of Oxford, Oxford, United Kingdom
| | - Michael H Hastings
- Medical Research Council (MRC) Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Patrick M Nolan
- Medical Research Council (MRC) Harwell, Harwell Science and Innovation Campus, Harwell, United Kingdom
| | - Russell G Foster
- Sleep and Circadian Neuroscience Institute, University of Oxford, Oxford, United Kingdom
| | - Stuart N Peirson
- Sleep and Circadian Neuroscience Institute, University of Oxford, Oxford, United Kingdom
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63
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Abstract
The daily rhythm of mammalian energy metabolism is subject to the circadian clock system, which is made up of the molecular clock machinery residing in nearly all cells throughout the body. The clock genes have been revealed not only to form the molecular clock but also to function as a mediator that regulates both circadian and metabolic functions. While the circadian signals generated by clock genes produce metabolic rhythms, clock gene function is tightly coupled to fundamental metabolic processes such as glucose and lipid metabolism. Therefore, defects in the clock genes not only result in the dysregulation of physiological rhythms but also induce metabolic disorders including diabetes and obesity. Among the clock genes, Dec1 (Bhlhe40/Stra13/Sharp2), Dec2 (Bhlhe41/Sharp1), and Bmal1 (Mop3/Arntl) have been shown to be particularly relevant to the regulation of energy metabolism at the cellular, tissue, and organismal levels. This paper reviews our current knowledge of the roles of Dec1, Dec2, and Bmal1 in coordinating the circadian and metabolic pathways.
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64
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Abstract
Self-sustained and synchronized to environmental stimuli, circadian clocks are under genetic and epigenetic regulation. Recent findings have greatly increased our understanding of epigenetic plasticity governed by circadian clock. Thus, the link between circadian clock and epigenetic machinery is reciprocal. Circadian clock can affect epigenetic features including genomic DNA methylation, noncoding RNA, mainly miRNA expression, and histone modifications resulted in their 24-h rhythms. Concomitantly, these epigenetic events can directly modulate cyclic system of transcription and translation of core circadian genes and indirectly clock output genes. Significant findings interlocking circadian clock, epigenetics, and cancer have been revealed, particularly in breast, colorectal, and blood cancers. Aberrant methylation of circadian gene promoter regions and miRNA expression affected circadian gene expression, together with 24-h expression oscillation pace have been frequently observed.
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65
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Liao HK, Hatanaka F, Araoka T, Reddy P, Wu MZ, Sui Y, Yamauchi T, Sakurai M, O'Keefe DD, Núñez-Delicado E, Guillen P, Campistol JM, Wu CJ, Lu LF, Esteban CR, Izpisua Belmonte JC. In Vivo Target Gene Activation via CRISPR/Cas9-Mediated Trans-epigenetic Modulation. Cell 2017; 171:1495-1507.e15. [PMID: 29224783 DOI: 10.1016/j.cell.2017.10.025] [Citation(s) in RCA: 296] [Impact Index Per Article: 42.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Revised: 10/02/2017] [Accepted: 10/16/2017] [Indexed: 12/11/2022]
Abstract
Current genome-editing systems generally rely on inducing DNA double-strand breaks (DSBs). This may limit their utility in clinical therapies, as unwanted mutations caused by DSBs can have deleterious effects. CRISPR/Cas9 system has recently been repurposed to enable target gene activation, allowing regulation of endogenous gene expression without creating DSBs. However, in vivo implementation of this gain-of-function system has proven difficult. Here, we report a robust system for in vivo activation of endogenous target genes through trans-epigenetic remodeling. The system relies on recruitment of Cas9 and transcriptional activation complexes to target loci by modified single guide RNAs. As proof-of-concept, we used this technology to treat mouse models of diabetes, muscular dystrophy, and acute kidney disease. Results demonstrate that CRISPR/Cas9-mediated target gene activation can be achieved in vivo, leading to measurable phenotypes and amelioration of disease symptoms. This establishes new avenues for developing targeted epigenetic therapies against human diseases. VIDEO ABSTRACT.
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Affiliation(s)
- Hsin-Kai Liao
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Fumiyuki Hatanaka
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Toshikazu Araoka
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA; Universidad Catolica, San Antonio de Murcia, Campus de los Jeronimos, 135, 30107 Guadalupe, Spain
| | - Pradeep Reddy
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Min-Zu Wu
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA; Universidad Catolica, San Antonio de Murcia, Campus de los Jeronimos, 135, 30107 Guadalupe, Spain
| | - Yinghui Sui
- Department of Pediatrics and Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Takayoshi Yamauchi
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA; Universidad Catolica, San Antonio de Murcia, Campus de los Jeronimos, 135, 30107 Guadalupe, Spain
| | - Masahiro Sakurai
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - David D O'Keefe
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Estrella Núñez-Delicado
- Universidad Catolica, San Antonio de Murcia, Campus de los Jeronimos, 135, 30107 Guadalupe, Spain
| | - Pedro Guillen
- Fundacion Pedro Guillen, Clinica CEMTRO, Avenida Ventisquero de la Condesa, 42, 28035 Madrid, Spain
| | - Josep M Campistol
- Hospital Clinic of Barcelona, Carrer Villarroel, 170, 08036 Barcelona, Spain
| | - Cheng-Jang Wu
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92037, USA
| | - Li-Fan Lu
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92037, USA
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66
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Zampieri M, Sauer U. Metabolomics-driven understanding of genotype-phenotype relations in model organisms. ACTA ACUST UNITED AC 2017. [DOI: 10.1016/j.coisb.2017.08.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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67
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Abstract
The physiological identity of every cell is maintained by highly specific transcriptional networks that establish a coherent molecular program that is in tune with nutritional conditions. The regulation of cell-specific transcriptional networks is accomplished by an epigenetic program via chromatin-modifying enzymes, whose activity is directly dependent on metabolites such as acetyl-coenzyme A, S-adenosylmethionine, and NAD+, among others. Therefore, these nuclear activities are directly influenced by the nutritional status of the cell. In addition to nutritional availability, this highly collaborative program between epigenetic dynamics and metabolism is further interconnected with other environmental cues provided by the day-night cycles imposed by circadian rhythms. Herein, we review molecular pathways and their metabolites associated with epigenetic adaptations modulated by histone- and DNA-modifying enzymes and their responsiveness to the environment in the context of health and disease.
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68
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Abstract
Circadian rhythms are a critical part of the body's homeostatic mechanisms. These rhythms repeat with a cycle-length of approximately 24 h and are generated by a transcriptional-translational feedback loop. These rhythms are critical for proper behavioral, physiological, and molecular functions. CHRONO, a novel circadian clock gene, forms a complex with other clock proteins and modulates the circadian machinery. CHRONO also interacts with histone deacetylase (HDAC) to modulate the epigenetic status of the transcriptional regulation. Chrono knockout mice display a longer period of circadian behavior and an elevated stress response. This paper reviews the molecular function of CHRONO with a focus on epigenetic regulation and speculates on the possible function of CHRONO in physiological processes. Key messages Chrono is a circadian clock gene whose transcription exhibits a robust circadian oscillation. CHRONO is a repressor of circadian transcriptional/translational feedback loops. CHRONO may function to link epigenetic control mechanisms to stress responses.
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Affiliation(s)
| | - Toru Takumi
- a RIKEN Brain Science Institute , Wako , Saitama , Japan
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69
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Cardinal Epigenetic Role of non-coding Regulatory RNAs in Circadian Rhythm. Mol Neurobiol 2017; 55:3564-3576. [PMID: 28516429 DOI: 10.1007/s12035-017-0573-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Accepted: 04/25/2017] [Indexed: 10/19/2022]
Abstract
Circadian rhythm which governs basic physiological activities like sleeping, feeding and energy consumption is regulated by light-controlled central clock genes in the pacemaker neuron. The timekeeping machinery with unique transcriptional and post-transcriptional feedback loops is controlled by different small regulatory RNAs in the brain. Roles of the multiple neuronal genes, especially post-transcriptional regulation, splicing, polyadenylation, mature mRNA editing, and stability of translation products, are controlled by epigenetic activities orchestrated via small RNAs. Collectively, these mechanisms regulate clock and light-controlled genes for effecting pacemaker activity and entrainment. Regulatory small RNAs of the circadian circuit, timekeeping mechanism, synchronization of regular entrainment, oscillation, and rhythmicity are regulated by diversified RNA molecules. Regulatory small RNAs operate critical roles in brain activities including the neuronal clock activity. In this report, we propose the emergence of the earlier unexpected small RNAs for a historic perspective of epigenetic regulation of the brain clock system.
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70
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Selfridge JM, Gotoh T, Schiffhauer S, Liu J, Stauffer PE, Li A, Capelluto DGS, Finkielstein CV. Chronotherapy: Intuitive, Sound, Founded…But Not Broadly Applied. Drugs 2017; 76:1507-1521. [PMID: 27699644 PMCID: PMC5082589 DOI: 10.1007/s40265-016-0646-4] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Circadian rhythms are a collection of endogenously driven biochemical, physiological, and behavioral processes that oscillate in a 24-h cycle and can be entrained by external cues. Circadian clock molecules are responsible for the expression of regulatory components that modulate, among others, the cell’s metabolism and energy consumption. In clinical practice, the regulation of clock mechanisms is relevant to biotransformation of therapeutics. Accordingly, xenobiotic metabolism and detoxification, the two processes that directly influence drug effectiveness and toxicity, are direct manifestations of the daily oscillations of the cellular and biochemical processes taking place within the gastrointestinal, hepatic/biliary, and renal/urologic systems. Consequently, the impact of circadian timing should be factored in when developing therapeutic regimens aimed at achieving maximum efficacy, minimum toxicity, and decreased adverse effects in a patient. However, and despite a strong mechanistic foundation, only 0.16 % of ongoing clinical trials worldwide exploit the concept of ‘time-of-day’ administration to develop safer and more effective therapies. In this article, we (1) emphasize points of control at which circadian biology intersects critical processes governing treatment interventions; (2) explore the extent to which chronotherapeutics are incorporated into clinical trials; (3) recognize roadblocks; and (4) recommend approaches to precipitate the integration of chronobiological concepts into clinical practice.
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Affiliation(s)
- Julia M Selfridge
- Virginia Tech Carilion School of Medicine and Research Institute, 2 Riverside Circle, Roanoke, VA, 24016, USA.,Integrated Cellular Responses Laboratory, Department of Biological Sciences, Biocomplexity Institute, 1015 Life Science Circle, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Tetsuya Gotoh
- Integrated Cellular Responses Laboratory, Department of Biological Sciences, Biocomplexity Institute, 1015 Life Science Circle, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Samuel Schiffhauer
- Integrated Cellular Responses Laboratory, Department of Biological Sciences, Biocomplexity Institute, 1015 Life Science Circle, Virginia Tech, Blacksburg, VA, 24061, USA
| | - JingJing Liu
- Integrated Cellular Responses Laboratory, Department of Biological Sciences, Biocomplexity Institute, 1015 Life Science Circle, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Philip E Stauffer
- Integrated Cellular Responses Laboratory, Department of Biological Sciences, Biocomplexity Institute, 1015 Life Science Circle, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Andrew Li
- Virginia Tech Carilion School of Medicine and Research Institute, 2 Riverside Circle, Roanoke, VA, 24016, USA.,Integrated Cellular Responses Laboratory, Department of Biological Sciences, Biocomplexity Institute, 1015 Life Science Circle, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Daniel G S Capelluto
- Protein Signaling Domains Laboratory, Department of Biological Sciences, Biocomplexity Institute, 1015 Life Science Circle, Virginia Tech, Blacksburg, VA, 24061, USA.,Center for Soft Matter and Biological Physics, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Carla V Finkielstein
- Virginia Tech Carilion School of Medicine and Research Institute, 2 Riverside Circle, Roanoke, VA, 24016, USA. .,Integrated Cellular Responses Laboratory, Department of Biological Sciences, Biocomplexity Institute, 1015 Life Science Circle, Virginia Tech, Blacksburg, VA, 24061, USA.
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71
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Millius A, Ueda HR. Systems Biology-Derived Discoveries of Intrinsic Clocks. Front Neurol 2017; 8:25. [PMID: 28220104 PMCID: PMC5292584 DOI: 10.3389/fneur.2017.00025] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Accepted: 01/17/2017] [Indexed: 12/19/2022] Open
Abstract
A systems approach to studying biology uses a variety of mathematical, computational, and engineering tools to holistically understand and model properties of cells, tissues, and organisms. Building from early biochemical, genetic, and physiological studies, systems biology became established through the development of genome-wide methods, high-throughput procedures, modern computational processing power, and bioinformatics. Here, we highlight a variety of systems approaches to the study of biological rhythms that occur with a 24-h period-circadian rhythms. We review how systems methods have helped to elucidate complex behaviors of the circadian clock including temperature compensation, rhythmicity, and robustness. Finally, we explain the contribution of systems biology to the transcription-translation feedback loop and posttranslational oscillator models of circadian rhythms and describe new technologies and "-omics" approaches to understand circadian timekeeping and neurophysiology.
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Affiliation(s)
- Arthur Millius
- Laboratory for Synthetic Biology, RIKEN Quantitative Biology Center, Suita, Osaka, Japan
| | - Hiroki R. Ueda
- Laboratory for Synthetic Biology, RIKEN Quantitative Biology Center, Suita, Osaka, Japan
- Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
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72
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Zhou J, Yu W, Hardin PE. CLOCKWORK ORANGE Enhances PERIOD Mediated Rhythms in Transcriptional Repression by Antagonizing E-box Binding by CLOCK-CYCLE. PLoS Genet 2016; 12:e1006430. [PMID: 27814361 PMCID: PMC5096704 DOI: 10.1371/journal.pgen.1006430] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Accepted: 10/17/2016] [Indexed: 01/13/2023] Open
Abstract
The Drosophila circadian oscillator controls daily rhythms in physiology, metabolism and behavior via transcriptional feedback loops. CLOCK-CYCLE (CLK-CYC) heterodimers initiate feedback loop function by binding E-box elements to activate per and tim transcription. PER-TIM heterodimers then accumulate, bind CLK-CYC to inhibit transcription, and are ultimately degraded to enable the next round of transcription. The timing of transcriptional events in this feedback loop coincide with, and are controlled by, rhythms in CLK-CYC binding to E-boxes. PER rhythmically binds CLK-CYC to initiate transcriptional repression, and subsequently promotes the removal of CLK-CYC from E-boxes. However, little is known about the mechanism by which CLK-CYC is removed from DNA. Previous studies demonstrated that the transcription repressor CLOCKWORK ORANGE (CWO) contributes to core feedback loop function by repressing per and tim transcription in cultured S2 cells and in flies. Here we show that CWO rhythmically binds E-boxes upstream of core clock genes in a reciprocal manner to CLK, thereby promoting PER-dependent removal of CLK-CYC from E-boxes, and maintaining repression until PER is degraded and CLK-CYC displaces CWO from E-boxes to initiate transcription. These results suggest a model in which CWO co-represses CLK-CYC transcriptional activity in conjunction with PER by competing for E-box binding once CLK-CYC-PER complexes have formed. Given that CWO orthologs DEC1 and DEC2 also target E-boxes bound by CLOCK-BMAL1, a similar mechanism may operate in the mammalian clock.
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Affiliation(s)
- Jian Zhou
- Department of Biology, Texas A&M University, College Station, Texas, United States of America
- Center for Biological Clocks Research, Texas A&M University, College Station, Texas, United States of America
| | - Wangjie Yu
- Department of Biology, Texas A&M University, College Station, Texas, United States of America
- Center for Biological Clocks Research, Texas A&M University, College Station, Texas, United States of America
| | - Paul E. Hardin
- Department of Biology, Texas A&M University, College Station, Texas, United States of America
- Center for Biological Clocks Research, Texas A&M University, College Station, Texas, United States of America
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73
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Ella K, Csépányi-Kömi R, Káldi K. Circadian regulation of human peripheral neutrophils. Brain Behav Immun 2016; 57:209-221. [PMID: 27132055 DOI: 10.1016/j.bbi.2016.04.016] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Revised: 04/13/2016] [Accepted: 04/26/2016] [Indexed: 01/12/2023] Open
Abstract
Neutrophils are the most abundant leukocytes in human blood. Beside being essential responders in bacterial and fungal infections, they also contribute to tissue reactions in many autoimmune and inflammatory diseases. Although several immune responses linked to neutrophil functions have been described to be rhythmic, the mechanism of the circadian regulation of these cells is still not understood. Characterization of the time-of-day-specific control of neutrophil responsiveness could help to better understand the pathomechanism of these inflammatory responses and design effective chronotherapy. Here we report that the time-dependent expression of core clock components in human neutrophils characteristically differs from that in mononuclear cells. Both the low expression and the reduced nuclear accumulation of the essential clock protein BMAL1 suggest that the molecular oscillator is down-regulated in neutrophils. By following the expression of the maturation marker Cxcr4 and morphological attributes (side-scattering properties and nuclear segmentation), we found that the distribution of young and aged cells within the peripheral neutrophil pool displays a daily rhythm. In addition, we detected synchronous fluctuations in the plasma level of the CXCR4 ligand CXCL12, an important regulator of cell trafficking within the bone marrow. We found that expression of another maturation marker, the core component of the superoxide generating NADPH oxidase, and parallelly, the superoxide producing capacity of neutrophils were also dependent on the time of the day. In line with this, number of opsonized bacteria engulfed by neutrophils also showed time-dependent differences, supporting that clearance of pathogens shows a daily rhythm. We suggest that maturation-dependent changes in neutrophil responsiveness rather than the cellular autonomous clock are involved in the daily regulation of human neutrophil functions.
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Affiliation(s)
- Krisztina Ella
- Department of Physiology, Semmelweis University, Tűzoltó u. 37-47, Budapest H-1094, Hungary
| | - Roland Csépányi-Kömi
- Department of Physiology, Semmelweis University, Tűzoltó u. 37-47, Budapest H-1094, Hungary
| | - Krisztina Káldi
- Department of Physiology, Semmelweis University, Tűzoltó u. 37-47, Budapest H-1094, Hungary.
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74
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Košir R, Prosenc Zmrzljak U, Korenčič A, Juvan P, Ačimovič J, Rozman D. Mouse genotypes drive the liver and adrenal gland clocks. Sci Rep 2016; 6:31955. [PMID: 27535584 PMCID: PMC4989183 DOI: 10.1038/srep31955] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2015] [Accepted: 07/25/2016] [Indexed: 12/18/2022] Open
Abstract
Circadian rhythms regulate a plethora of physiological processes. Perturbations of the rhythm can result in pathologies which are frequently studied in inbred mouse strains. We show that the genotype of mouse lines defines the circadian gene expression patterns. Expression of majority of core clock and output metabolic genes are phase delayed in the C56BL/6J line compared to 129S2 in the adrenal glands and the liver. Circadian amplitudes are generally higher in the 129S2 line. Experiments in dark - dark (DD) and light - dark conditions (LD), exome sequencing and data mining proposed that mouse lines differ in single nucleotide variants in the binding regions of clock related transcription factors in open chromatin regions. A possible mechanisms of differential circadian expression could be the entrainment and transmission of the light signal to peripheral organs. This is supported by the genotype effect in adrenal glands that is largest under LD, and by the high number of single nucleotide variants in the Receptor, Kinase and G-protein coupled receptor Panther molecular function categories. Different phenotypes of the two mouse lines and changed amino acid sequence of the Period 2 protein possibly contribute further to the observed differences in circadian gene expression.
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Affiliation(s)
- Rok Košir
- Center for Functional Genomics and Bio-Chips, Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, Zaloska cesta 4, Ljubljana, Slovenia
| | - Uršula Prosenc Zmrzljak
- Center for Functional Genomics and Bio-Chips, Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, Zaloska cesta 4, Ljubljana, Slovenia
| | - Anja Korenčič
- Center for Functional Genomics and Bio-Chips, Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, Zaloska cesta 4, Ljubljana, Slovenia
| | - Peter Juvan
- Center for Functional Genomics and Bio-Chips, Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, Zaloska cesta 4, Ljubljana, Slovenia
| | - Jure Ačimovič
- Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, Zaloska cesta 4, Ljubljana, Slovenia
| | - Damjana Rozman
- Center for Functional Genomics and Bio-Chips, Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, Zaloska cesta 4, Ljubljana, Slovenia.,Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, Zaloska cesta 4, Ljubljana, Slovenia
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75
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Jaeger C, Tischkau SA. Role of Aryl Hydrocarbon Receptor in Circadian Clock Disruption and Metabolic Dysfunction. ENVIRONMENTAL HEALTH INSIGHTS 2016; 10:133-141. [PMID: 27559298 PMCID: PMC4990151 DOI: 10.4137/ehi.s38343] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Revised: 07/12/2016] [Accepted: 07/14/2016] [Indexed: 06/01/2023]
Abstract
The prevalence of metabolic syndrome, a clustering of three or more risk factors that include abdominal obesity, increased blood pressure, and high levels of glucose, triglycerides, and high-density lipoproteins, has reached dangerous and costly levels worldwide. Increases in morbidity and mortality result from a combination of factors that promote altered glucose metabolism, insulin resistance, and metabolic dysfunction. Although diet and exercise are commonly touted as important determinants in the development of metabolic dysfunction, other environmental factors, including circadian clock disruption and activation of the aryl hydrocarbon receptor (AhR) by dietary or other environmental sources, must also be considered. AhR binds a range of ligands, which prompts protein-protein interactions with other Per-Arnt-Sim (PAS)-domain-containing proteins and subsequent transcriptional activity. This review focuses on the reciprocal crosstalk between the activated AhR and the molecular circadian clock. AhR exhibits a rhythmic expression and time-dependent sensitivity to activation by AhR agonists. Conversely, AhR activation influences the amplitude and phase of expression of circadian clock genes, hormones, and the behavioral responses of the clock system to changes in environmental illumination. Both the clock and AhR status and activation play significant and underappreciated roles in metabolic homeostasis. This review highlights the state of knowledge regarding how AhR may act together with the circadian clock to influence energy metabolism. Understanding the variety of AhR-dependent mechanisms, including its interactions with the circadian timing system that promote metabolic dysfunction, reveals new targets of interest for maintenance of healthy metabolism.
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Fleet T, Stashi E, Zhu B, Rajapakshe K, Marcelo KL, Kettner NM, Gorman BK, Coarfa C, Fu L, O'Malley BW, York B. Genetic and Environmental Models of Circadian Disruption Link SRC-2 Function to Hepatic Pathology. J Biol Rhythms 2016; 31:443-60. [PMID: 27432117 DOI: 10.1177/0748730416657921] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Circadian rhythmicity is a fundamental process that synchronizes behavioral cues with metabolic homeostasis. Disruption of daily cycles due to jet lag or shift work results in severe physiological consequences including advanced aging, metabolic syndrome, and even cancer. Our understanding of the molecular clock, which is regulated by intricate positive feedforward and negative feedback loops, has expanded to include an important metabolic transcriptional coregulator, Steroid Receptor Coactivator-2 (SRC-2), that regulates both the central clock of the suprachiasmatic nucleus (SCN) and peripheral clocks including the liver. We hypothesized that an environmental uncoupling of the light-dark phases, termed chronic circadian disruption (CCD), would lead to pathology similar to the genetic circadian disruption observed with loss of SRC-2 We found that CCD and ablation of SRC-2 in mice led to a common comorbidity of metabolic syndrome also found in humans with circadian disruption, non-alcoholic fatty liver disease (NAFLD). The combination of SRC-2(-/-) and CCD results in a more robust phenotype that correlates with human non-alcoholic steatohepatitis (NASH) and hepatocellular carcinoma (HCC) gene signatures. Either CCD or SRC-2 ablation produces an advanced aging phenotype leading to increased mortality consistent with other circadian mutant mouse models. Collectively, our studies demonstrate that SRC-2 provides an essential link between the behavioral activities influenced by light cues and the metabolic homeostasis maintained by the liver.
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Affiliation(s)
- Tiffany Fleet
- Interdepartmental Department in Translational Biology and Molecular Medicine, Baylor College of Medicine, Houston, Texas
| | - Erin Stashi
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas
| | - Bokai Zhu
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas
| | - Kimal Rajapakshe
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas
| | - Kathrina L Marcelo
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas
| | - Nicole M Kettner
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas
| | - Blythe K Gorman
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas Weill Medical College, Cornell University, New York, New York
| | - Cristian Coarfa
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas
| | - Loning Fu
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas
| | - Bert W O'Malley
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Brian York
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas
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Abstract
The circadian system temporally coordinates daily rhythms in feeding behaviour and energy metabolism. The objective of the present paper is to review the mechanisms that underlie circadian regulation of lipid metabolic pathways. Circadian rhythms in behaviour and physiology are generated by master clock neurons in the suprachiasmatic nucleus (SCN). The SCN and its efferent targets in the hypothalamus integrate light and feeding signals to entrain behavioural rhythms as well as clock cells located in peripheral tissues, including the liver, adipose tissue and muscle. Circadian rhythms in gene expression are regulated at the cellular level by a molecular clock comprising a core set of clock genes/proteins. In peripheral tissues, hundreds of genes involved in lipid biosynthesis and fatty acid oxidation are rhythmically activated and repressed by clock proteins, hence providing a direct mechanism for circadian regulation of lipids. Disruption of clock gene function results in abnormal metabolic phenotypes and impaired lipid absorption, demonstrating that the circadian system is essential for normal energy metabolism. The composition and timing of meals influence diurnal regulation of metabolic pathways, with food intake during the usual rest phase associated with dysregulation of lipid metabolism. Recent studies using metabolomics and lipidomics platforms have shown that hundreds of lipid species are circadian-regulated in human plasma, including but not limited to fatty acids, TAG, glycerophospholipids, sterol lipids and sphingolipids. In future work, these lipid profiling approaches can be used to understand better the interaction between diet, mealtimes and circadian rhythms on lipid metabolism and risk for obesity and metabolic diseases.
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Xue T, Song C, Wang Q, Wang Y, Chen G. Investigations of the CLOCK and BMAL1 Proteins Binding to DNA: A Molecular Dynamics Simulation Study. PLoS One 2016; 11:e0155105. [PMID: 27153104 PMCID: PMC4859532 DOI: 10.1371/journal.pone.0155105] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2015] [Accepted: 04/25/2016] [Indexed: 11/18/2022] Open
Abstract
The circadian locomotor output cycles kaput (CLOCK), and brain and muscle ARNT-like 1 (BMAL1) proteins are important transcriptional factors of the endogenous circadian clock. The CLOCK and BMAL1 proteins can regulate the transcription-translation activities of the clock-related genes through the DNA binding. The hetero-/homo-dimerization and DNA combination of the CLOCK and BMAL1 proteins play a key role in the positive and negative transcriptional feedback processes. In the present work, we constructed a series of binary and ternary models for the bHLH/bHLH-PAS domains of the CLOCK and BMAL1 proteins, and the DNA molecule, and carried out molecular dynamics simulations, free energy calculations and conformational analysis to explore the interaction properties of the CLOCK and BMAL1 proteins with DNA. The results show that the bHLH domains of CLOCK and BMAL1 can favorably form the heterodimer of the bHLH domains of CLOCK and BMAL1 and the homodimer of the bHLH domains of BMAL1. And both dimers could respectively bind to DNA at its H1-H1 interface. The DNA bindings of the H1 helices in the hetero- and homo-bHLH dimers present the rectangular and diagonal binding modes, respectively. Due to the function of the α-helical forceps in these dimers, the tight gripping of the H1 helices to the major groove of DNA would cause the decrease of interactions at the H1-H2 interfaces in the CLOCK and BMAL1 proteins. The additional PAS domains in the CLOCK and BMAL1 proteins affect insignificantly the interactions of the CLOCK and BMAL1 proteins with the DNA molecule due to the flexible and long loop linkers located at the middle of the PAS and bHLH domains. The present work theoretically explains the interaction mechanisms of the bHLH domains of the CLOCK and BMAL1 proteins with DNA.
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Affiliation(s)
- Tuo Xue
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, China
| | - Chunnian Song
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, China
| | - Qing Wang
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, China
| | - Yan Wang
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, China
| | - Guangju Chen
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, China
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Jiang W, Zhao S, Jiang X, Zhang E, Hu G, Hu B, Zheng P, Xiao J, Lu Z, Lu Y, Ni J, Chen C, Wang X, Yang L, Wan R. The circadian clock gene Bmal1 acts as a potential anti-oncogene in pancreatic cancer by activating the p53 tumor suppressor pathway. Cancer Lett 2016; 371:314-25. [PMID: 26683776 DOI: 10.1016/j.canlet.2015.12.002] [Citation(s) in RCA: 104] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Revised: 12/02/2015] [Accepted: 12/02/2015] [Indexed: 12/29/2022]
Abstract
Disruption of the circadian clock has been shown to be associated with tumor development. This study aimed to investigate the role of the core circadian gene Bmal1 in pancreatic cancer (PC). We first found that the levels of Bmal1 were downregulated in PC samples and were closely correlated with the clinicopathological features of patients. To dissect the underlying mechanism, we performed a RNA-seq assay followed by systematic gene function and pathway enrichment analyses. We detected an anti-apoptotic and pro-proliferative transcriptome profile after Bmal1 knockdown in PC cells. Further in vitro and in vivo studies confirmed that Bmal1 overexpression significantly inhibited cell proliferation and invasion and induced G2/M cell cycle arrest, whereas Bmal1 knockdown promoted PC growth, as demonstrated in Bmal1-manipulated AsPC-1 and BxPC-3 cell lines. Our mechanistic studies indicated that Bmal1 could directly bind to the p53 gene promoter and thereby transcriptionally activate the downstream tumor suppressor pathway in a p53-dependent manner. In sum, our findings suggest that Bmal1 acts as an anti-oncogene in PC and represents a potential biomarker for its diagnosis.
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Affiliation(s)
- Weiliang Jiang
- Department of Gastroenterology, Shanghai First People's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Senlin Zhao
- Department of General Surgery, Shanghai First People's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaohua Jiang
- Department of Gastrointestinal Surgery, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Erquan Zhang
- National Institute of Biological Sciences, Beijing, China
| | - Guoyong Hu
- Department of Gastroenterology, Shanghai First People's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Bin Hu
- Department of Gastroenterology, Shanghai First People's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Ping Zheng
- Department of Gastroenterology, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Junhua Xiao
- Department of Gastroenterology, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Zhanjun Lu
- Department of Gastroenterology, Shanghai First People's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yingying Lu
- Department of Gastroenterology, Shanghai First People's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jianbo Ni
- Department of Gastroenterology, Shanghai First People's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Congying Chen
- Department of Gastroenterology, Shanghai First People's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xingpeng Wang
- Department of Gastroenterology, Shanghai First People's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Lijuan Yang
- Department of Gastroenterology, Shanghai First People's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
| | - Rong Wan
- Department of Gastroenterology, Shanghai First People's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
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Boucsein A, Benzler J, Hempp C, Stöhr S, Helfer G, Tups A. Photoperiodic and Diurnal Regulation of WNT Signaling in the Arcuate Nucleus of the Female Djungarian Hamster, Phodopus sungorus. Endocrinology 2016; 157:799-809. [PMID: 26646203 DOI: 10.1210/en.2015-1708] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The WNT pathway was shown to play an important role in the adult central nervous system. We previously identified the WNT pathway as a novel integration site of the adipokine leptin in mediating its neuroendocrine control of metabolism in obese mice. Here we investigated the implication of WNT signaling in seasonal body weight regulation exhibited by the Djungarian hamster (Phodopus sungorus), a seasonal mammal that exhibits profound annual changes in leptin sensitivity. We furthermore investigated whether crucial components of the WNT pathway are regulated in a diurnal manner. Gene expression of key components of the WNT pathway in the hypothalamus of hamsters acclimated to either long day (LD) or short day (SD) photoperiod was analyzed by in situ hybridization. We detected elevated expression of the genes WNT-4, Axin-2, Cyclin-D1, and SFRP-2, in the hypothalamic arcuate nucleus, a key energy balance integration site, during LD compared with SD as well as a diurnal regulation of Axin-2, Cyclin-D1, and DKK-3. Investigating the effect of photoperiod as well as leptin on the activation (phosphorylation) of the WNT coreceptor LRP-6-(Ser1490) by immunohistochemistry, we found elevated activity in the arcuate nucleus during LD relative to SD as well as after leptin treatment (2 mg/kg body weight). These findings indicate that differential WNT signaling may be associated with seasonal body weight regulation and is partially regulated in a diurnal manner in the adult brain. Furthermore, they suggest that this pathway plays a key role in the neuroendocrine regulation of body weight and integration of the leptin signal.
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Affiliation(s)
- Alisa Boucsein
- Department of Physiology (A.B., A.T.), Centre for Neuroendocrinology and Brain Health Research Centre, University of Otago, Dunedin 9054, New Zealand; Department of Animal Physiology (A.B., J.B., C.H., S.S., A.T.), Faculty of Biology, Philipps University of Marburg, D-35032 Marburg, Germany; and Rowett Institute of Nutrition and Health (G.H.), University of Aberdeen, Aberdeen AB21 9SB, Scotland, United Kingdom
| | - Jonas Benzler
- Department of Physiology (A.B., A.T.), Centre for Neuroendocrinology and Brain Health Research Centre, University of Otago, Dunedin 9054, New Zealand; Department of Animal Physiology (A.B., J.B., C.H., S.S., A.T.), Faculty of Biology, Philipps University of Marburg, D-35032 Marburg, Germany; and Rowett Institute of Nutrition and Health (G.H.), University of Aberdeen, Aberdeen AB21 9SB, Scotland, United Kingdom
| | - Cindy Hempp
- Department of Physiology (A.B., A.T.), Centre for Neuroendocrinology and Brain Health Research Centre, University of Otago, Dunedin 9054, New Zealand; Department of Animal Physiology (A.B., J.B., C.H., S.S., A.T.), Faculty of Biology, Philipps University of Marburg, D-35032 Marburg, Germany; and Rowett Institute of Nutrition and Health (G.H.), University of Aberdeen, Aberdeen AB21 9SB, Scotland, United Kingdom
| | - Sigrid Stöhr
- Department of Physiology (A.B., A.T.), Centre for Neuroendocrinology and Brain Health Research Centre, University of Otago, Dunedin 9054, New Zealand; Department of Animal Physiology (A.B., J.B., C.H., S.S., A.T.), Faculty of Biology, Philipps University of Marburg, D-35032 Marburg, Germany; and Rowett Institute of Nutrition and Health (G.H.), University of Aberdeen, Aberdeen AB21 9SB, Scotland, United Kingdom
| | - Gisela Helfer
- Department of Physiology (A.B., A.T.), Centre for Neuroendocrinology and Brain Health Research Centre, University of Otago, Dunedin 9054, New Zealand; Department of Animal Physiology (A.B., J.B., C.H., S.S., A.T.), Faculty of Biology, Philipps University of Marburg, D-35032 Marburg, Germany; and Rowett Institute of Nutrition and Health (G.H.), University of Aberdeen, Aberdeen AB21 9SB, Scotland, United Kingdom
| | - Alexander Tups
- Department of Physiology (A.B., A.T.), Centre for Neuroendocrinology and Brain Health Research Centre, University of Otago, Dunedin 9054, New Zealand; Department of Animal Physiology (A.B., J.B., C.H., S.S., A.T.), Faculty of Biology, Philipps University of Marburg, D-35032 Marburg, Germany; and Rowett Institute of Nutrition and Health (G.H.), University of Aberdeen, Aberdeen AB21 9SB, Scotland, United Kingdom
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81
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Dong C, Gongora R, Sosulski ML, Luo F, Sanchez CG. Regulation of transforming growth factor-beta1 (TGF-β1)-induced pro-fibrotic activities by circadian clock gene BMAL1. Respir Res 2016; 17:4. [PMID: 26753996 PMCID: PMC5477854 DOI: 10.1186/s12931-016-0320-0] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Accepted: 12/27/2015] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND BMAL1 is a transcriptional activator of the molecular clock feedback network. Besides its role in generating circadian rhythms, it has also been shown to be involved in the modulation of cell proliferation, autophagy and cancer cell invasion. However, the role of BMAL1 in pulmonary fibrogenesis is still largely unknown. In this study, we investigated the crosstalk between BMAL1 and the signaling transduction and cellular activities of TGF-β1, a key player in lung fibrogenesis. METHODS Lungs from wild type and TGF-β1-adenovirus-infected mice were harvested and homogenized for isolation of RNA and protein. RT-PCR and Western Blotting were employed to measure the expression level of clock genes and TGF-β1-induced downstream target genes. siRNA against human BMAL1 gene was transfected by using lipofectamine RNAiMAX to knockdown the endogenous BMAL1 in both lung epithelial cells and fibroblasts. RESULTS Our results showed that TGF-β1 is able to up-regulate BMAL1 expression in both lung epithelial cells and normal lung fibroblasts. In animal models of pulmonary fibrosis, BMAL1 expression was also significantly higher in adenovirus-TGF-β1-infected mice than in the control group. Interestingly, BMAL1 was mostly found in a deacetylated form in the presence of TGF-β1. Importantly, siRNA-mediated knockdown of BMAL1 significantly attenuated the canonical TGF-β1 signaling pathway and altered TGF-β1-induced epithelial-mesenchymal transition and MMP9 production in lung epithelial cells. In addition, BMAL1 knockdown inhibited the fibroblast to myofibroblast differentiation of normal human lung fibroblasts. CONCLUSIONS Our results indicate that activation of TGF-β1 promotes the transcriptional induction of BMAL1. Furthermore, BMAL1 is required for the TGF-β1-induced signaling transduction and pro-fibrotic activities in the lung.
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Affiliation(s)
- Chunmin Dong
- Department of Medicine, Section of Pulmonary Disease and Critical Care, Tulane University School of Medicine, New Orleans, LA USA
| | - Rafael Gongora
- Department of Medicine, Section of Pulmonary Disease and Critical Care, Tulane University School of Medicine, New Orleans, LA USA
| | - Meredith L. Sosulski
- Department of Medicine, Section of Pulmonary Disease and Critical Care, Tulane University School of Medicine, New Orleans, LA USA
| | - Fayong Luo
- Department of Medicine, Section of Pulmonary Disease and Critical Care, Tulane University School of Medicine, New Orleans, LA USA
| | - Cecilia G. Sanchez
- Department of Medicine, Section of Pulmonary Disease and Critical Care, Tulane University School of Medicine, New Orleans, LA USA
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82
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Abstract
Exploring the putative impact of circadian rhythms is a relatively novel approach to illuminating hormone-related female breast cancer etiology and prognosis. One of several proposed mechanisms underlying breast cancer risk among individuals exposed to light at night involves circadian gene alterations. Although in vitro and animal studies indicate a key role of circadian genes in breast tumor suppression, there is a paucity of data on the role of circadian genes in human breast cancer. This review summarizes recent findings of circadian gene expression and DNA methylation profile from human breast cancer studies in relation to hormonal status, clinicopathological features of tumors, and exposure to night shift work. The major findings from human studies indicate that expression of circadian genes is deregulated in breast cancer. Breast cancer etiology and prognosis-associated PERs, CRYs, CLOCK downregulation, and TIMELESS upregulation may be related to relevant gene methylation in tumor tissue. Alterations and desynchronization of molecular clock machinery found on genetic and epigenetic level were observed in more aggressive breast cancer tumors and those lacking estrogen receptors.
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Affiliation(s)
- E Reszka
- Nofer Institute of Occupational Medicine, Lodz, Poland.
| | - M Przybek
- Nofer Institute of Occupational Medicine, Lodz, Poland
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83
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Valenzuela FJ, Vera J, Venegas C, Muñoz S, Oyarce S, Muñoz K, Lagunas C. Evidences of Polymorphism Associated with Circadian System and Risk of Pathologies: A Review of the Literature. Int J Endocrinol 2016; 2016:2746909. [PMID: 27313610 PMCID: PMC4893437 DOI: 10.1155/2016/2746909] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Revised: 04/14/2016] [Accepted: 04/19/2016] [Indexed: 12/15/2022] Open
Abstract
The circadian system is a supraphysiological system that modulates different biological functions such as metabolism, sleep-wake, cellular proliferation, and body temperature. Different chronodisruptors have been identified, such as shift work, feeding time, long days, and stress. The environmental changes and our modern lifestyle can alter the circadian system and increase the risk of developing pathologies such as cancer, preeclampsia, diabetes, and mood disorder. This system is organized by transcriptional/tranductional feedback loops of clock genes Clock, Bmal1, Per1-3, and Cry1-2. How molecular components of the clock are able to influence the development of diseases and their risk relation with genetic components of polymorphism of clock genes is unknown. This research describes different genetic variations in the population and how these are associated with risk of cancer, metabolic diseases such as diabetes, obesity, and dyslipidemias, and also mood disorders such as depression, bipolar disease, excessive alcohol intake, and infertility. Finally, these findings will need to be implemented and evaluated at the level of genetic interaction and how the environment factors trigger the expression of these pathologies will be examined.
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Affiliation(s)
- F. J. Valenzuela
- Department of Basic Sciences, Universidad del Bío-Bío, Campus Fernando May, 378000 Chillán, Chile
- Group of Biotechnological Sciences, Department of Basic Sciences, Universidad del Bío-Bío, Campus Fernando May, 378000 Chillán, Chile
- *F. J. Valenzuela:
| | - J. Vera
- Department of Basic Sciences, Universidad del Bío-Bío, Campus Fernando May, 378000 Chillán, Chile
- Group of Biotechnological Sciences, Department of Basic Sciences, Universidad del Bío-Bío, Campus Fernando May, 378000 Chillán, Chile
| | - C. Venegas
- Department of Basic Sciences, Universidad del Bío-Bío, Campus Fernando May, 378000 Chillán, Chile
| | - S. Muñoz
- Department of Basic Sciences, Universidad del Bío-Bío, Campus Fernando May, 378000 Chillán, Chile
| | - S. Oyarce
- Department of Basic Sciences, Universidad del Bío-Bío, Campus Fernando May, 378000 Chillán, Chile
| | - K. Muñoz
- Department of Basic Sciences, Universidad del Bío-Bío, Campus Fernando May, 378000 Chillán, Chile
| | - C. Lagunas
- Department of Basic Sciences, Universidad del Bío-Bío, Campus Fernando May, 378000 Chillán, Chile
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84
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Liu TL, Newton L, Liu MJ, Shiu SH, Farré EM. A G-Box-Like Motif Is Necessary for Transcriptional Regulation by Circadian Pseudo-Response Regulators in Arabidopsis. PLANT PHYSIOLOGY 2016; 170:528-39. [PMID: 26586835 PMCID: PMC4704597 DOI: 10.1104/pp.15.01562] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Accepted: 11/17/2015] [Indexed: 05/18/2023]
Abstract
PSEUDO-RESPONSE REGULATORs (PRRs) play overlapping and distinct roles in maintaining circadian rhythms and regulating diverse biological processes, including the photoperiodic control of flowering, growth, and abiotic stress responses. PRRs act as transcriptional repressors and associate with chromatin via their conserved C-terminal CCT (CONSTANS, CONSTANS-like, and TIMING OF CAB EXPRESSION 1 [TOC1/PRR1]) domains by a still-poorly understood mechanism. Here, we identified genome-wide targets of PRR9 using chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) and compared them with PRR7, PRR5, and TOC1/PRR1 ChIP-seq data. We found that PRR binding sites are located within genomic regions of low nucleosome occupancy and high DNase I hypersensitivity. Moreover, conserved noncoding regions among Brassicaceae species are enriched around PRR binding sites, indicating that PRRs associate with functionally relevant cis-regulatory regions. The PRRs shared a significant number of binding regions, and our results indicate that they coordinately restrict the expression of target genes to around dawn. A G-box-like motif was overrepresented at PRR binding regions, and we showed that this motif is necessary for mediating transcriptional regulation of CIRCADIAN CLOCK ASSOCIATED 1 and PRR9 by the PRRs. Our results further our understanding of how PRRs target specific promoters and provide an extensive resource for studying circadian regulatory networks in plants.
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Affiliation(s)
- Tiffany L Liu
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
| | - Linsey Newton
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
| | - Ming-Jung Liu
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
| | - Shin-Han Shiu
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
| | - Eva M Farré
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
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Forni D, Pozzoli U, Cagliani R, Tresoldi C, Menozzi G, Riva S, Guerini FR, Comi GP, Bolognesi E, Bresolin N, Clerici M, Sironi M. Genetic adaptation of the human circadian clock to day-length latitudinal variations and relevance for affective disorders. Genome Biol 2015; 15:499. [PMID: 25358694 PMCID: PMC4237747 DOI: 10.1186/s13059-014-0499-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Indexed: 01/18/2023] Open
Abstract
Background The temporal coordination of biological processes into daily cycles is a common feature of most living organisms. In humans, disruption of circadian rhythms is commonly observed in psychiatric diseases, including schizophrenia, bipolar disorder, depression and autism. Light therapy is the most effective treatment for seasonal affective disorder and circadian-related treatments sustain antidepressant response in bipolar disorder patients. Day/night cycles represent a major circadian synchronizing signal and vary widely with latitude. Results We apply a geographically explicit model to show that out-of-Africa migration, which led humans to occupy a wide latitudinal area, affected the evolutionary history of circadian regulatory genes. The SNPs we identify using this model display consistent signals of natural selection using tests based on population genetic differentiation and haplotype homozygosity. Signals of natural selection driven by annual photoperiod variation are detected for schizophrenia, bipolar disorder, and restless leg syndrome risk variants, in line with the circadian component of these conditions. Conclusions Our results suggest that human populations adapted to life at different latitudes by tuning their circadian clock systems. This process also involves risk variants for neuropsychiatric conditions, suggesting possible genetic modulators for chronotherapies and candidates for interaction analysis with photoperiod-related environmental variables, such as season of birth, country of residence, shift-work or lifestyle habits. Electronic supplementary material The online version of this article (doi:10.1186/s13059-014-0499-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Diego Forni
- Scientific Institute IRCCS E. Medea, 23842 Bosisio Parini, LC, Italy
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Tanoue S, Fujimoto K, Myung J, Hatanaka F, Kato Y, Takumi T. DEC2-E4BP4 Heterodimer Represses the Transcriptional Enhancer Activity of the EE Element in the Per2 Promoter. Front Neurol 2015; 6:166. [PMID: 26257703 PMCID: PMC4512152 DOI: 10.3389/fneur.2015.00166] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Accepted: 07/09/2015] [Indexed: 01/12/2023] Open
Abstract
The circadian oscillation of clock gene expression in mammals is based on the interconnected transcriptional/translational feedback loops of Period (Per) and Bmal1. The Per feedback loop initiates transcription through direct binding of the BMAL1–CLOCK (NPAS2) heterodimer to the E-box of the Per2 promoter region. Negative feedback of PER protein on this promoter subsequently represses transcription. Other circadian transcription regulators, particularly E4BP4 and DEC2, regulate the amplitude and phase of Per2 expression rhythms. Moreover, a direct repeat of E-box-like (EE) elements in the Per2 promoter is required for its cell-autonomous circadian rhythm. However, the detailed mechanism for repression of the two core sequences of the EE element in the Per2 promoter region is unknown. Here, we show that E4BP4 binds to the Per2 EE element with DEC2 to repress transcription and identify the DEC2–E4BP4 heterodimer as a key repressor of the tightly interlocked Per2 feedback loop in the mammalian circadian oscillator. Our results suggest an additional modulatory mechanism for tuning of the phase of cell-autonomous Per2 gene expression cycling.
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Affiliation(s)
- Shintaro Tanoue
- Graduate School of Biomedical Sciences, Hiroshima University , Hiroshima , Japan
| | - Katsumi Fujimoto
- Graduate School of Biomedical Sciences, Hiroshima University , Hiroshima , Japan
| | - Jihwan Myung
- Graduate School of Biomedical Sciences, Hiroshima University , Hiroshima , Japan ; RIKEN Brain Science Institute , Wako, Saitama , Japan
| | - Fumiyuki Hatanaka
- Graduate School of Biomedical Sciences, Hiroshima University , Hiroshima , Japan ; RIKEN Brain Science Institute , Wako, Saitama , Japan
| | - Yukio Kato
- Graduate School of Biomedical Sciences, Hiroshima University , Hiroshima , Japan
| | - Toru Takumi
- Graduate School of Biomedical Sciences, Hiroshima University , Hiroshima , Japan ; RIKEN Brain Science Institute , Wako, Saitama , Japan ; CREST, Japan Science and Technology Agency , Tokyo , Japan
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87
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Circadian enhancers coordinate multiple phases of rhythmic gene transcription in vivo. Cell 2015; 159:1140-1152. [PMID: 25416951 DOI: 10.1016/j.cell.2014.10.022] [Citation(s) in RCA: 174] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2014] [Revised: 08/28/2014] [Accepted: 09/24/2014] [Indexed: 12/12/2022]
Abstract
Mammalian transcriptomes display complex circadian rhythms with multiple phases of gene expression that cannot be accounted for by current models of the molecular clock. We have determined the underlying mechanisms by measuring nascent RNA transcription around the clock in mouse liver. Unbiased examination of enhancer RNAs (eRNAs) that cluster in specific circadian phases identified functional enhancers driven by distinct transcription factors (TFs). We further identify on a global scale the components of the TF cistromes that function to orchestrate circadian gene expression. Integrated genomic analyses also revealed mechanisms by which a single circadian factor controls opposing transcriptional phases. These findings shed light on the diversity and specificity of TF function in the generation of multiple phases of circadian gene transcription in a mammalian organ.
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88
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Vanderlinden LA, Saba LM, Bennett B, Hoffman PL, Tabakoff B. Influence of sex on genetic regulation of "drinking in the dark" alcohol consumption. Mamm Genome 2015; 26:43-56. [PMID: 25559016 DOI: 10.1007/s00335-014-9553-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Accepted: 12/17/2014] [Indexed: 10/24/2022]
Abstract
The ILSXISS (LXS) recombinant inbred (RI) panel of mice is a valuable resource for genetic mapping studies of complex traits, due to its genetic diversity and large number of strains. Male and female mice from this panel were used to investigate genetic influences on alcohol consumption in the "drinking in the dark" (DID) model. Male mice (38 strains) and female mice (36 strains) were given access to 20% ethanol during the early phase of their circadian dark cycle for four consecutive days. The first principal component of alcohol consumption measures on days 2, 3, and 4 was used as a phenotype (DID phenotype) to calculate QTLs, using a SNP marker set for the LXS RI panel. Five QTLs were identified, three of which included a significant genotype by sex interaction, i.e., a significant genotype effect in males and not females. To investigate candidate genes associated with the DID phenotype, data from brain microarray analysis (Affymetrix Mouse Exon 1.0 ST Arrays) of male LXS RI strains were combined with RNA-Seq data (mouse brain transcriptome reconstruction) from the parental ILS and ISS strains in order to identify expressed mouse brain transcripts. Candidate genes were determined based on common eQTL and DID phenotype QTL regions and correlation of transcript expression levels with the DID phenotype. The resulting candidate genes (in particular, Arntl/Bmal1) focused attention on the influence of circadian regulation on the variation in the DID phenotype in this population of mice.
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Affiliation(s)
- Lauren A Vanderlinden
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy & Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, 12850 E. Montview Blvd., Campus Box: C238, Aurora, CO, 80045, USA,
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89
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Takahashi JS, Kumar V, Nakashe P, Koike N, Huang HC, Green CB, Kim TK. ChIP-seq and RNA-seq methods to study circadian control of transcription in mammals. Methods Enzymol 2014; 551:285-321. [PMID: 25662462 DOI: 10.1016/bs.mie.2014.10.059] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Genome-wide analyses have revolutionized our ability to study the transcriptional regulation of circadian rhythms. The advent of next-generation sequencing methods has facilitated the use of two such technologies, ChIP-seq and RNA-seq. In this chapter, we describe detailed methods and protocols for these two techniques, with emphasis on their usage in circadian rhythm experiments in the mouse liver, a major target organ of the circadian clock system. Critical factors for these methods are highlighted and issues arising with time series samples for ChIP-seq and RNA-seq are discussed. Finally, detailed protocols for library preparation suitable for Illumina sequencing platforms are presented.
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Affiliation(s)
- Joseph S Takahashi
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, Texas, USA; Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas, USA.
| | - Vivek Kumar
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, Texas, USA; Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Prachi Nakashe
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Nobuya Koike
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Hung-Chung Huang
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Carla B Green
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Tae-Kyung Kim
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, Texas, USA
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90
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Chromatin landscape and circadian dynamics: Spatial and temporal organization of clock transcription. Proc Natl Acad Sci U S A 2014; 112:6863-70. [PMID: 25378702 DOI: 10.1073/pnas.1411264111] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Circadian rhythms drive the temporal organization of a wide variety of physiological and behavioral functions in ∼24-h cycles. This control is achieved through a complex program of gene expression. In mammals, the molecular clock machinery consists of interconnected transcriptional-translational feedback loops that ultimately ensure the proper oscillation of thousands of genes in a tissue-specific manner. To achieve circadian transcriptional control, chromatin remodelers serve the clock machinery by providing appropriate oscillations to the epigenome. Recent findings have revealed the presence of circadian interactomes, nuclear "hubs" of genome topology where coordinately expressed circadian genes physically interact in a spatial and temporal-specific manner. Thus, a circadian nuclear landscape seems to exist, whose interplay with metabolic pathways and clock regulators translates into specific transcriptional programs. Deciphering the molecular mechanisms that connect the circadian clock machinery with the nuclear landscape will reveal yet unexplored pathways that link cellular metabolism to epigenetic control.
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91
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Gooley JJ, Chua ECP. Diurnal regulation of lipid metabolism and applications of circadian lipidomics. J Genet Genomics 2014; 41:231-50. [PMID: 24894351 DOI: 10.1016/j.jgg.2014.04.001] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2014] [Revised: 04/10/2014] [Accepted: 04/10/2014] [Indexed: 02/04/2023]
Abstract
The circadian timing system plays a key role in orchestrating lipid metabolism. In concert with the solar cycle, the circadian system ensures that daily rhythms in lipid absorption, storage, and transport are temporally coordinated with rest-activity and feeding cycles. At the cellular level, genes involved in lipid synthesis and fatty acid oxidation are rhythmically activated and repressed by core clock proteins in a tissue-specific manner. Consequently, loss of clock gene function or misalignment of circadian rhythms with feeding cycles (e.g., in shift work) results in impaired lipid homeostasis. Herein, we review recent progress in circadian rhythms research using lipidomics, i.e., large-scale profiling of lipid metabolites, to characterize circadian-regulated lipid pathways in mammals. In mice, novel regulatory circuits involved in fatty acid metabolism have been identified in adipose tissue, liver, and muscle. Extensive diversity in circadian regulation of plasma lipids has also been revealed in humans using lipidomics and other metabolomics approaches. In future studies, lipidomics platforms will be increasingly used to better understand the effects of genetic variation, shift work, food intake, and drugs on circadian-regulated lipid pathways and metabolic health.
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Affiliation(s)
- Joshua J Gooley
- Program in Neuroscience and Behavioral Disorders, Duke-NUS Graduate Medical School, Singapore 169857, Singapore; Division of Sleep and Circadian Disorders, Departments of Medicine and Neurology, Brigham and Women's Hospital, Boston 02115, USA; Division of Sleep Medicine, Harvard Medical School, Boston 02115, USA.
| | - Eric Chern-Pin Chua
- Program in Neuroscience and Behavioral Disorders, Duke-NUS Graduate Medical School, Singapore 169857, Singapore
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92
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Anafi RC, Lee Y, Sato TK, Venkataraman A, Ramanathan C, Kavakli IH, Hughes ME, Baggs JE, Growe J, Liu AC, Kim J, Hogenesch JB. Machine learning helps identify CHRONO as a circadian clock component. PLoS Biol 2014; 12:e1001840. [PMID: 24737000 PMCID: PMC3988006 DOI: 10.1371/journal.pbio.1001840] [Citation(s) in RCA: 95] [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: 08/27/2013] [Accepted: 03/07/2014] [Indexed: 12/03/2022] Open
Abstract
Over the last decades, researchers have characterized a set of "clock genes" that drive daily rhythms in physiology and behavior. This arduous work has yielded results with far-reaching consequences in metabolic, psychiatric, and neoplastic disorders. Recent attempts to expand our understanding of circadian regulation have moved beyond the mutagenesis screens that identified the first clock components, employing higher throughput genomic and proteomic techniques. In order to further accelerate clock gene discovery, we utilized a computer-assisted approach to identify and prioritize candidate clock components. We used a simple form of probabilistic machine learning to integrate biologically relevant, genome-scale data and ranked genes on their similarity to known clock components. We then used a secondary experimental screen to characterize the top candidates. We found that several physically interact with known clock components in a mammalian two-hybrid screen and modulate in vitro cellular rhythms in an immortalized mouse fibroblast line (NIH 3T3). One candidate, Gene Model 129, interacts with BMAL1 and functionally represses the key driver of molecular rhythms, the BMAL1/CLOCK transcriptional complex. Given these results, we have renamed the gene CHRONO (computationally highlighted repressor of the network oscillator). Bi-molecular fluorescence complementation and co-immunoprecipitation demonstrate that CHRONO represses by abrogating the binding of BMAL1 to its transcriptional co-activator CBP. Most importantly, CHRONO knockout mice display a prolonged free-running circadian period similar to, or more drastic than, six other clock components. We conclude that CHRONO is a functional clock component providing a new layer of control on circadian molecular dynamics.
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Affiliation(s)
- Ron C. Anafi
- Division of Sleep Medicine, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
- Center for Sleep and Circadian Neurobiology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Yool Lee
- Department of Pharmacology and the Institute for Translational Medicine and Therapeutics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Trey K. Sato
- Department of Pharmacology and the Institute for Translational Medicine and Therapeutics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Anand Venkataraman
- Department of Pharmacology and the Institute for Translational Medicine and Therapeutics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Chidambaram Ramanathan
- Department of Biological Sciences, University of Memphis, Memphis, Tennessee, United States of America
| | - Ibrahim H. Kavakli
- Department of Chemical and Biological Engineering, Koc University, Istanbul, Turkey
| | - Michael E. Hughes
- Department of Biology, University of Missouri–St. Louis, St. Louis, Missouri, United States of America
| | - Julie E. Baggs
- Department of Pharmacology, Morehouse School of Medicine, Atlanta, Georgia, United States of America
| | - Jacqueline Growe
- Division of Sleep Medicine, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
- Center for Sleep and Circadian Neurobiology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Andrew C. Liu
- Department of Biological Sciences, University of Memphis, Memphis, Tennessee, United States of America
| | - Junhyong Kim
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - John B. Hogenesch
- Center for Sleep and Circadian Neurobiology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
- Department of Pharmacology and the Institute for Translational Medicine and Therapeutics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
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93
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Goriki A, Hatanaka F, Myung J, Kim JK, Yoritaka T, Tanoue S, Abe T, Kiyonari H, Fujimoto K, Kato Y, Todo T, Matsubara A, Forger D, Takumi T. A novel protein, CHRONO, functions as a core component of the mammalian circadian clock. PLoS Biol 2014; 12:e1001839. [PMID: 24736997 PMCID: PMC3988004 DOI: 10.1371/journal.pbio.1001839] [Citation(s) in RCA: 102] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Accepted: 03/07/2014] [Indexed: 02/06/2023] Open
Abstract
Circadian rhythms are controlled by a system of negative and positive genetic feedback loops composed of clock genes. Although many genes have been implicated in these feedback loops, it is unclear whether our current list of clock genes is exhaustive. We have recently identified Chrono as a robustly cycling transcript through genome-wide profiling of BMAL1 binding on the E-box. Here, we explore the role of Chrono in cellular timekeeping. Remarkably, endogenous CHRONO occupancy around E-boxes shows a circadian oscillation antiphasic to BMAL1. Overexpression of Chrono leads to suppression of BMAL1-CLOCK activity in a histone deacetylase (HDAC) -dependent manner. In vivo loss-of-function studies of Chrono including Avp neuron-specific knockout (KO) mice display a longer circadian period of locomotor activity. Chrono KO also alters the expression of core clock genes and impairs the response of the circadian clock to stress. CHRONO forms a complex with the glucocorticoid receptor and mediates glucocorticoid response. Our comprehensive study spotlights a previously unrecognized clock component of an unsuspected negative circadian feedback loop that is independent of another negative regulator, Cry2, and that integrates behavioral stress and epigenetic control for efficient metabolic integration of the clock.
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Affiliation(s)
- Akihiro Goriki
- RIKEN Brain Science Institute, Wako, Saitama, Japan
- Graduate School of Biomedical Sciences, Hiroshima University, Minami, Hiroshima, Japan
| | - Fumiyuki Hatanaka
- RIKEN Brain Science Institute, Wako, Saitama, Japan
- Graduate School of Biomedical Sciences, Hiroshima University, Minami, Hiroshima, Japan
| | - Jihwan Myung
- RIKEN Brain Science Institute, Wako, Saitama, Japan
- Graduate School of Biomedical Sciences, Hiroshima University, Minami, Hiroshima, Japan
| | - Jae Kyoung Kim
- Department of Mathematics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Takashi Yoritaka
- Graduate School of Biomedical Sciences, Hiroshima University, Minami, Hiroshima, Japan
| | - Shintaro Tanoue
- Graduate School of Biomedical Sciences, Hiroshima University, Minami, Hiroshima, Japan
| | - Takaya Abe
- Laboratory for Animal Resources and Genetic Engineering, RIKEN Center for Developmental Biology, Chuo, Kobe, Japan
| | - Hiroshi Kiyonari
- Laboratory for Animal Resources and Genetic Engineering, RIKEN Center for Developmental Biology, Chuo, Kobe, Japan
| | - Katsumi Fujimoto
- Graduate School of Biomedical Sciences, Hiroshima University, Minami, Hiroshima, Japan
| | - Yukio Kato
- Graduate School of Biomedical Sciences, Hiroshima University, Minami, Hiroshima, Japan
| | - Takashi Todo
- Department of Radiation Biology and Medical Genetics, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Akio Matsubara
- Graduate School of Biomedical Sciences, Hiroshima University, Minami, Hiroshima, Japan
| | - Daniel Forger
- Department of Mathematics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Toru Takumi
- RIKEN Brain Science Institute, Wako, Saitama, Japan
- Graduate School of Biomedical Sciences, Hiroshima University, Minami, Hiroshima, Japan
- Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, Chiyoda, Tokyo, Japan
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94
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CLOCK-controlled polyphonic regulation of circadian rhythms through canonical and noncanonical E-boxes. Mol Cell Biol 2014; 34:1776-87. [PMID: 24591654 DOI: 10.1128/mcb.01465-13] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
In mammalian circadian clockwork, the CLOCK-BMAL1 complex binds to DNA enhancers of target genes and drives circadian oscillation of transcription. Here we identified 7,978 CLOCK-binding sites in mouse liver by chromatin immunoprecipitation-sequencing (ChIP-Seq), and a newly developed bioinformatics method, motif centrality analysis of ChIP-Seq (MOCCS), revealed a genome-wide distribution of previously unappreciated noncanonical E-boxes targeted by CLOCK. In vitro promoter assays showed that CACGNG, CACGTT, and CATG(T/C)G are functional CLOCK-binding motifs. Furthermore, we extensively revealed rhythmically expressed genes by poly(A)-tailed RNA-Seq and identified 1,629 CLOCK target genes within 11,926 genes expressed in the liver. Our analysis also revealed rhythmically expressed genes that have no apparent CLOCK-binding site, indicating the importance of indirect transcriptional and posttranscriptional regulations. Indirect transcriptional regulation is represented by rhythmic expression of CLOCK-regulated transcription factors, such as Krüppel-like factors (KLFs). Indirect posttranscriptional regulation involves rhythmic microRNAs that were identified by small-RNA-Seq. Collectively, CLOCK-dependent direct transactivation through multiple E-boxes and indirect regulations polyphonically orchestrate dynamic circadian outputs.
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95
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Stashi E, Lanz RB, Mao J, Michailidis G, Zhu B, Kettner NM, Putluri N, Reineke EL, Reineke LC, Dasgupta S, Dean A, Stevenson CR, Sivasubramanian N, Sreekumar A, Demayo F, York B, Fu L, O'Malley BW. SRC-2 is an essential coactivator for orchestrating metabolism and circadian rhythm. Cell Rep 2014; 6:633-45. [PMID: 24529706 PMCID: PMC4096300 DOI: 10.1016/j.celrep.2014.01.027] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2013] [Revised: 12/05/2013] [Accepted: 01/22/2014] [Indexed: 01/31/2023] Open
Abstract
Synchrony of the mammalian circadian clock is achieved by complex transcriptional and translational feedback loops centered on the BMAL1:CLOCK heterodimer. Modulation of circadian feedback loops is essential for maintaining rhythmicity, yet the role of transcriptional coactivators in driving BMAL1:CLOCK transcriptional networks is largely unexplored. Here, we show diurnal hepatic steroid receptor coactivator 2 (SRC-2) recruitment to the genome that extensively overlaps with the BMAL1 cistrome during the light phase, targeting genes that enrich for circadian and metabolic processes. Notably, SRC-2 ablation impairs wheel-running behavior, alters circadian gene expression in several peripheral tissues, alters the rhythmicity of the hepatic metabolome, and deregulates the synchronization of cell-autonomous metabolites. We identify SRC-2 as a potent coregulator of BMAL1:CLOCK and find that SRC-2 targets itself with BMAL1:CLOCK in a feedforward loop. Collectively, our data suggest that SRC-2 is a transcriptional coactivator of the BMAL1:CLOCK oscillators and establish SRC-2 as a critical positive regulator of the mammalian circadian clock.
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Affiliation(s)
- Erin Stashi
- Department of Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Rainer B Lanz
- Department of Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Jianqiang Mao
- Department of Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - George Michailidis
- Department of Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA; Department of Statistics, University of Michigan, 500 South State Street, Ann Arbor, MI 48109, USA
| | - Bokai Zhu
- Department of Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Nicole M Kettner
- Department of Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Nagireddy Putluri
- Department of Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Erin L Reineke
- Department of Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Lucas C Reineke
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, One Baylor Plaza Houston, TX 77030, USA
| | - Subhamoy Dasgupta
- Department of Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Adam Dean
- Department of Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Connor R Stevenson
- Department of Biochemistry and Molecular Biology, Trinity University, One Trinity Place, San Antonio, TX 78212-7200, USA
| | - Natarajan Sivasubramanian
- Department of Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Arun Sreekumar
- Department of Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Francesco Demayo
- Department of Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Brian York
- Department of Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Loning Fu
- Department of Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Bert W O'Malley
- Department of Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA.
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96
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Annayev Y, Adar S, Chiou YY, Lieb JD, Sancar A, Ye R. Gene model 129 (Gm129) encodes a novel transcriptional repressor that modulates circadian gene expression. J Biol Chem 2014; 289:5013-24. [PMID: 24385426 DOI: 10.1074/jbc.m113.534651] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The mammalian circadian clock is a molecular oscillator composed of a feedback loop that involves transcriptional activators CLOCK and BMAL1, and repressors Cryptochrome (CRY) and Period (PER). Here we show that a direct CLOCK·BMAL1 target gene, Gm129, is a novel regulator of the feedback loop. ChIP analysis revealed that the CLOCK·BMAL1·CRY1 complex strongly occupies the promoter region of Gm129. Both mRNA and protein levels of GM129 exhibit high amplitude circadian oscillations in mouse liver, and Gm129 gene encodes a nuclear-localized protein that directly interacts with BMAL1 and represses CLOCK·BMAL1 activity. In vitro and in vivo protein-DNA interaction results demonstrate that, like CRY1, GM129 functions as a repressor by binding to the CLOCK·BMAL1 complex on DNA. Although Gm129(-/-) or Cry1(-/-) Gm129(-/-) mice retain a robust circadian rhythm, the peaks of Nr1d1 and Dbp mRNAs in liver exhibit a significant phase delay compared with control. Our results suggest that, in addition to CRYs and PERs, the GM129 protein contributes to the transcriptional feedback loop by modulating CLOCK·BMAL1 activity as a transcriptional repressor.
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Affiliation(s)
- Yunus Annayev
- From the Departments of Biochemistry and Biophysics and
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97
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Eckel-Mahan KL, Patel VR, de Mateo S, Orozco-Solis R, Ceglia NJ, Sahar S, Dilag-Penilla SA, Dyar KA, Baldi P, Sassone-Corsi P. Reprogramming of the circadian clock by nutritional challenge. Cell 2013; 155:1464-78. [PMID: 24360271 PMCID: PMC4573395 DOI: 10.1016/j.cell.2013.11.034] [Citation(s) in RCA: 482] [Impact Index Per Article: 43.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2013] [Revised: 10/16/2013] [Accepted: 11/21/2013] [Indexed: 12/29/2022]
Abstract
Circadian rhythms and cellular metabolism are intimately linked. Here, we reveal that a high-fat diet (HFD) generates a profound reorganization of specific metabolic pathways, leading to widespread remodeling of the liver clock. Strikingly, in addition to disrupting the normal circadian cycle, HFD causes an unexpectedly large-scale genesis of de novo oscillating transcripts, resulting in reorganization of the coordinated oscillations between coherent transcripts and metabolites. The mechanisms underlying this reprogramming involve both the impairment of CLOCK:BMAL1 chromatin recruitment and a pronounced cyclic activation of surrogate pathways through the transcriptional regulator PPARγ. Finally, we demonstrate that it is specifically the nutritional challenge, and not the development of obesity, that causes the reprogramming of the clock and that the effects of the diet on the clock are reversible.
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Affiliation(s)
- Kristin L Eckel-Mahan
- Center for Epigenetics and Metabolism, Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, USA
| | - Vishal R Patel
- Institute for Genomics and Bioinformatics, School of Information and Computer Sciences, University of California, Irvine, Irvine, CA 92697, USA
| | - Sara de Mateo
- Center for Epigenetics and Metabolism, Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, USA
| | - Ricardo Orozco-Solis
- Center for Epigenetics and Metabolism, Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, USA
| | - Nicholas J Ceglia
- Institute for Genomics and Bioinformatics, School of Information and Computer Sciences, University of California, Irvine, Irvine, CA 92697, USA
| | - Saurabh Sahar
- Center for Epigenetics and Metabolism, Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, USA
| | - Sherry A Dilag-Penilla
- Center for Epigenetics and Metabolism, Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, USA
| | - Kenneth A Dyar
- Venetian Institute of Molecular Medicine, Padova 35129, Italy
| | - Pierre Baldi
- Institute for Genomics and Bioinformatics, School of Information and Computer Sciences, University of California, Irvine, Irvine, CA 92697, USA
| | - Paolo Sassone-Corsi
- Center for Epigenetics and Metabolism, Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, USA.
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98
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Štorcelová M, Vicián M, Reis R, Zeman M, Herichová I. Expression of cell cycle regulatory factors hus1, gadd45a, rb1, cdkn2a and mre11a correlates with expression of clock gene per2 in human colorectal carcinoma tissue. Mol Biol Rep 2013; 40:6351-61. [PMID: 24062075 DOI: 10.1007/s11033-013-2749-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2012] [Accepted: 09/14/2013] [Indexed: 01/20/2023]
Abstract
Deregulated expression of clock gene per2 has previously been associated with progression of cancer. The aim of the present study was to identify genes related to per2 expression and involved in cell cycle control. Patients surgically treated for colorectal carcinoma with up-regulated and down-regulated per2 expression in cancer versus adjacent tissue were studied. Total RNA from cancer tissue of these patients was used to specify genes associated with altered per2 expression using the Human Cell Cycle RT(2) profiler PCR array system. We identified seven genes positively correlated (hus1, gadd45α, rb1, cdkn2a, cdk5rp1, mre11a, sumo1) and two genes negatively correlated (cdc20, birc5) with per2 expression. Expression of these seven genes was subsequently measured by real time PCR in all patients of the cohort. Patients were divided into three groups according to TNM classification. We observed an increase in gene expression in cancer tissue compared to adjacent tissue in the first group of patients in all genes measured. Expression of genes positively associated with per2 gene expression was dependent on tumor staging and changes were observed preferentially in cancer tissue. For genes negatively associated with per2 expression we also detected changes in expression dependent on tumor staging. Expression of cdc20 and birc5 was increasing in the proximal tissue and decreasing in the cancer tissue. These results implicate functional involvement of per2 in the process of carcinogenesis via newly uncovered genes. The relevancy of gene expression for determination of diagnosis and prognosis should be considered in relation to tumor staging.
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Affiliation(s)
- Mária Štorcelová
- Department of Animal Physiology and Ethology, Faculty of Natural Sciences, Comenius University Bratislava, Mlynska dolina B-2, 842 15, Bratislava, Slovak Republic
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99
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Molecular architecture of the mammalian circadian clock. Trends Cell Biol 2013; 24:90-9. [PMID: 23916625 DOI: 10.1016/j.tcb.2013.07.002] [Citation(s) in RCA: 937] [Impact Index Per Article: 85.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Revised: 07/01/2013] [Accepted: 07/02/2013] [Indexed: 12/31/2022]
Abstract
Circadian clocks coordinate physiology and behavior with the 24h solar day to provide temporal homeostasis with the external environment. The molecular clocks that drive these intrinsic rhythmic changes are based on interlocked transcription/translation feedback loops that integrate with diverse environmental and metabolic stimuli to generate internal 24h timing. In this review we highlight recent advances in our understanding of the core molecular clock and how it utilizes diverse transcriptional and post-transcriptional mechanisms to impart temporal control onto mammalian physiology. Understanding the way in which biological rhythms are generated throughout the body may provide avenues for temporally directed therapeutics to improve health and prevent disease.
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100
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Košir R, Španinger K, Rozman D. Circadian events in human diseases and in cytochrome P450-related drug metabolism and therapy. IUBMB Life 2013; 65:487-96. [PMID: 23554069 DOI: 10.1002/iub.1160] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2012] [Accepted: 02/06/2013] [Indexed: 01/24/2023]
Abstract
The biochemical basis of the mammalian circadian clock can be described by transcriptional-translational feedback loops with a period of about 24 h. Crucial endogenous factors are under circadian control (i.e., body temperature, blood pressure, hormone secretion and metabolite levels). Also, drug metabolism, including phases I-III and the drug-responsive nuclear receptors, is controlled by the clock. Disturbances in circadian rhythm in humans can lead to pathologies, which is exemplified by increased cancer risk in long-term shift workers. On the other hand, best tolerability of drugs with minimum side effects can be achieved if the timing of drug treatment is synchronized with the patients' individual clock. The aim of this review is to underline the importance of accepting the individuals' endogenous clock which can contribute to personalized, patient-friendly optimization of drug therapies.
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Affiliation(s)
- Rok Košir
- Center for Functional Genomics and Bio-chips, Institute of Biochemistry, Faculty of Medicine, University of Ljubljana Ljubljana, Slovenia
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