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Abstract
The blood-brain barrier (BBB) is a critical interface separating the central nervous system from the peripheral circulation, ensuring brain homeostasis and function. Recent research has unveiled a profound connection between the BBB and circadian rhythms, the endogenous oscillations synchronizing biological processes with the 24-hour light-dark cycle. This review explores the significance of circadian rhythms in the context of BBB functions, with an emphasis on substrate passage through the BBB. Our discussion includes efflux transporters and the molecular timing mechanisms that regulate their activities. A significant focus of this review is the potential implications of chronotherapy, leveraging our knowledge of circadian rhythms for improving drug delivery to the brain. Understanding the temporal changes in BBB can lead to optimized timing of drug administration, to enhance therapeutic efficacy for neurological disorders while reducing side effects. By elucidating the interplay between circadian rhythms and drug transport across the BBB, this review offers insights into innovative therapeutic interventions.
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Affiliation(s)
- Mari Kim
- Cell Biology Department, Emory University, Atlanta, GA, USA (M.K., S.L.Z.)
| | - Richard F Keep
- Neurosurgery, University of Michigan, Ann Arbor, MI, USA (R.F.K.)
| | - Shirley L Zhang
- Cell Biology Department, Emory University, Atlanta, GA, USA (M.K., S.L.Z.)
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2
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Kembro JM, Flesia AG, Acosta-Rodríguez VA, Takahashi JS, Nieto PS. Dietary restriction modulates ultradian rhythms and autocorrelation properties in mice behavior. Commun Biol 2024; 7:303. [PMID: 38461321 PMCID: PMC10925031 DOI: 10.1038/s42003-024-05991-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 02/28/2024] [Indexed: 03/11/2024] Open
Abstract
Animal behavior emerges from integration of many processes with different spatial and temporal scales. Dynamical behavioral patterns, including daily and ultradian rhythms and the dynamical microstructure of behavior (i.e., autocorrelations properties), can be differentially affected by external cues. Identifying these patterns is important for understanding how organisms adapt to their environment, yet unbiased methods to quantify dynamical changes over multiple temporal scales are lacking. Herein, we combine a wavelet approach with Detrended Fluctuation Analysis to identify behavioral patterns and evaluate changes over 42-days in mice subjected to different dietary restriction paradigms. We show that feeding restriction alters dynamical patterns: not only are daily rhythms modulated but also the presence, phase and/or strength of ~12h-rhythms, as well as the nature of autocorrelation properties of feed-intake and wheel running behaviors. These results highlight the underlying complexity of behavioral architecture and offer insights into the multi-scale impact of feeding habits on physiology.
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Affiliation(s)
- Jackelyn Melissa Kembro
- Universidad Nacional de Córdoba (UNC), Facultad de Ciencias Exactas, Físicas y Naturales, Instituto de Ciencia y Tecnología de los Alimentos (ICTA) and Departamento de Química, Cátedra de Química Biológica, Córdoba, Córdoba, X5000HUA, Argentina
- Instituto de Investigaciones Biológicas y Tecnológicas, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)- UNC, Córdoba, Córdoba, X5000HUA, Argentina
| | - Ana Georgina Flesia
- Universidad Nacional de Córdoba, Facultad de Matemática, Astronomía, Física y Computación, Córdoba, Córdoba, X5000HUA, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Centro de Investigaciones y Estudios de Matemática (CIEM, CONICET-UNC), Córdoba, Córdoba, X5000HUA, Argentina
| | - Victoria América Acosta-Rodríguez
- Department of Neuroscience, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX, 75390-9111, USA
| | - Joseph S Takahashi
- Department of Neuroscience, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX, 75390-9111, USA
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, 75390-9111, USA
| | - Paula Sofía Nieto
- Universidad Nacional de Córdoba, Facultad de Matemática, Astronomía, Física y Computación, Córdoba, Córdoba, X5000HUA, Argentina.
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto de Física Enrique Gaviola (IFEG, CONICET-UNC), Universidad Nacional de Córdoba, Córdoba, Córdoba, X5000HUA, Argentina.
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3
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Liu X, Cai YD, Chiu JC. Regulation of protein O-GlcNAcylation by circadian, metabolic, and cellular signals. J Biol Chem 2024; 300:105616. [PMID: 38159854 PMCID: PMC10810748 DOI: 10.1016/j.jbc.2023.105616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 12/12/2023] [Accepted: 12/13/2023] [Indexed: 01/03/2024] Open
Abstract
O-linked β-N-acetylglucosamine (O-GlcNAcylation) is a dynamic post-translational modification that regulates thousands of proteins and almost all cellular processes. Aberrant O-GlcNAcylation has been associated with numerous diseases, including cancer, neurodegenerative diseases, cardiovascular diseases, and type 2 diabetes. O-GlcNAcylation is highly nutrient-sensitive since it is dependent on UDP-GlcNAc, the end product of the hexosamine biosynthetic pathway (HBP). We previously observed daily rhythmicity of protein O-GlcNAcylation in a Drosophila model that is sensitive to the timing of food consumption. We showed that the circadian clock is pivotal in regulating daily O-GlcNAcylation rhythms given its control of the feeding-fasting cycle and hence nutrient availability. Interestingly, we reported that the circadian clock also modulates daily O-GlcNAcylation rhythm by regulating molecular mechanisms beyond the regulation of food consumption time. A large body of work now indicates that O-GlcNAcylation is likely a generalized cellular status effector as it responds to various cellular signals and conditions, such as ER stress, apoptosis, and infection. In this review, we summarize the metabolic regulation of protein O-GlcNAcylation through nutrient availability, HBP enzymes, and O-GlcNAc processing enzymes. We discuss the emerging roles of circadian clocks in regulating daily O-GlcNAcylation rhythm. Finally, we provide an overview of other cellular signals or conditions that impact O-GlcNAcylation. Many of these cellular pathways are themselves regulated by the clock and/or metabolism. Our review highlights the importance of maintaining optimal O-GlcNAc rhythm by restricting eating activity to the active period under physiological conditions and provides insights into potential therapeutic targets of O-GlcNAc homeostasis under pathological conditions.
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Affiliation(s)
- Xianhui Liu
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California, Davis, California, USA
| | - Yao D Cai
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California, Davis, California, USA
| | - Joanna C Chiu
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California, Davis, California, USA.
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4
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Barone I, Gilette NM, Hawks-Mayer H, Handy J, Zhang KJ, Chifamba FF, Mostafa E, Johnson-Venkatesh EM, Sun Y, Gibson JM, Rotenberg A, Umemori H, Tsai PT, Lipton JO. Synaptic BMAL1 phosphorylation controls circadian hippocampal plasticity. SCIENCE ADVANCES 2023; 9:eadj1010. [PMID: 37878694 PMCID: PMC10599629 DOI: 10.1126/sciadv.adj1010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 09/25/2023] [Indexed: 10/27/2023]
Abstract
The time of day strongly influences adaptive behaviors like long-term memory, but the correlating synaptic and molecular mechanisms remain unclear. The circadian clock comprises a canonical transcription-translation feedback loop (TTFL) strictly dependent on the BMAL1 transcription factor. We report that BMAL1 rhythmically localizes to hippocampal synapses in a manner dependent on its phosphorylation at Ser42 [pBMAL1(S42)]. pBMAL1(S42) regulates the autophosphorylation of synaptic CaMKIIα and circadian rhythms of CaMKIIα-dependent molecular interactions and LTP but not global rest/activity behavior. Therefore, our results suggest a model in which repurposing of the clock protein BMAL1 to synapses locally gates the circadian timing of plasticity.
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Affiliation(s)
- Ilaria Barone
- Department of Neurology and F.M. Kirby Center for Neurobiology, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Nicole M. Gilette
- Department of Neurology and F.M. Kirby Center for Neurobiology, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Hannah Hawks-Mayer
- Department of Neurology and F.M. Kirby Center for Neurobiology, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Jonathan Handy
- Department of Neurology and F.M. Kirby Center for Neurobiology, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Kevin J. Zhang
- Department of Neurology and F.M. Kirby Center for Neurobiology, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Fortunate F. Chifamba
- Department of Neurology and F.M. Kirby Center for Neurobiology, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Engie Mostafa
- Department of Neurology and F.M. Kirby Center for Neurobiology, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Erin M. Johnson-Venkatesh
- Department of Neurology and F.M. Kirby Center for Neurobiology, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Yan Sun
- Department of Neurology and F.M. Kirby Center for Neurobiology, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Jennifer M. Gibson
- Departments of Neurology, Neuroscience, Pediatrics, and Psychiatry, University of Texas at Southwestern, Dallas, TX 75390, USA
| | - Alexander Rotenberg
- Department of Neurology and F.M. Kirby Center for Neurobiology, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Hisashi Umemori
- Department of Neurology and F.M. Kirby Center for Neurobiology, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Peter T. Tsai
- Departments of Neurology, Neuroscience, Pediatrics, and Psychiatry, University of Texas at Southwestern, Dallas, TX 75390, USA
| | - Jonathan O. Lipton
- Department of Neurology and F.M. Kirby Center for Neurobiology, Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Neurology and Division of Sleep Medicine, Harvard Medical School, Boston, MA 02115, USA
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Chin CF, Galam DL, Gao L, Tan BC, Wong BH, Chua GL, Loke RY, Lim YC, Wenk MR, Lim MS, Leow WQ, Goh GB, Torta F, Silver DL. Blood-derived lysophospholipid sustains hepatic phospholipids and fat storage necessary for hepatoprotection in overnutrition. J Clin Invest 2023; 133:e171267. [PMID: 37463052 PMCID: PMC10471173 DOI: 10.1172/jci171267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 07/12/2023] [Indexed: 09/02/2023] Open
Abstract
The liver has a high demand for phosphatidylcholine (PC), particularly in overnutrition, where reduced phospholipid levels have been implicated in the development of nonalcoholic fatty liver disease (NAFLD). Whether other pathways exist in addition to de novo PC synthesis that contribute to hepatic PC pools remains unknown. Here, we identified the lysophosphatidylcholine (LPC) transporter major facilitator superfamily domain containing 2A (Mfsd2a) as critical for maintaining hepatic phospholipid pools. Hepatic Mfsd2a expression was induced in patients having NAFLD and in mice in response to dietary fat via glucocorticoid receptor action. Mfsd2a liver-specific deficiency in mice (L2aKO) led to a robust nonalcoholic steatohepatitis-like (NASH-like) phenotype within just 2 weeks of dietary fat challenge associated with reduced hepatic phospholipids containing linoleic acid. Reducing dietary choline intake in L2aKO mice exacerbated liver pathology and deficiency of liver phospholipids containing polyunsaturated fatty acids (PUFAs). Treating hepatocytes with LPCs containing oleate and linoleate, two abundant blood-derived LPCs, specifically induced lipid droplet biogenesis and contributed to phospholipid pools, while LPC containing the omega-3 fatty acid docosahexaenoic acid (DHA) promoted lipid droplet formation and suppressed lipogenesis. This study revealed that PUFA-containing LPCs drive hepatic lipid droplet formation, suppress lipogenesis, and sustain hepatic phospholipid pools - processes that are critical for protecting the liver from excess dietary fat.
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Affiliation(s)
- Cheen Fei Chin
- Signature Research Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore
| | - Dwight L.A. Galam
- Signature Research Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore
| | - Liang Gao
- Singapore Lipidomics Incubator, Life Sciences Institute and
- Precision Medicine Translational Research Programme and Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Bryan C. Tan
- Signature Research Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore
| | - Bernice H. Wong
- Signature Research Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore
| | - Geok-Lin Chua
- Signature Research Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore
| | - Randy Y.J. Loke
- Signature Research Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore
| | - Yen Ching Lim
- Signature Research Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore
| | - Markus R. Wenk
- Singapore Lipidomics Incubator, Life Sciences Institute and
- Precision Medicine Translational Research Programme and Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Miao-Shan Lim
- Department of Gastroenterology and Hepatology, Singapore General Hospital, Singapore
| | - Wei-Qiang Leow
- Department of Anatomical Pathology, Singapore General Hospital, and
| | - George B.B. Goh
- Department of Gastroenterology and Hepatology, Singapore General Hospital, Singapore
- Medicine Academic Clinical Program, Duke-NUS Medical School, Singapore
| | - Federico Torta
- Singapore Lipidomics Incubator, Life Sciences Institute and
- Precision Medicine Translational Research Programme and Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - David L. Silver
- Signature Research Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore
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Otsuka K, Cornelissen G, Kubo Y, Shibata K, Mizuno K, Aiba T, Furukawa S, Ohshima H, Mukai C. Methods for assessing change in brain plasticity at night and psychological resilience during daytime between repeated long-duration space missions. Sci Rep 2023; 13:10909. [PMID: 37407662 DOI: 10.1038/s41598-023-36389-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 06/02/2023] [Indexed: 07/07/2023] Open
Abstract
This study was designed to examine the feasibility of analyzing heart rate variability (HRV) data from repeat-flier astronauts at matching days on two separate missions to assess any effect of repeated missions on brain plasticity and psychological resilience, as conjectured by Demertzi. As an example, on the second mission of a healthy astronaut studied about 20 days after launch, sleep duration lengthened, sleep quality improved, and spectral power (ms2) co-varying with activity of the salience network (SN) increased at night. HF-component (0.15-0.50 Hz) increased by 61.55%, and HF-band (0.30-0.40 Hz) by 92.60%. Spectral power of HRV indices during daytime, which correlate negatively with psychological resilience, decreased, HF-component by 22.18% and HF-band by 37.26%. LF-component and LF-band, reflecting activity of the default mode network, did not change significantly. During the second mission, 24-h acrophases of HRV endpoints did not change but the 12-h acrophase of TF-HRV did (P < 0.0001), perhaps consolidating the circadian system to help adapt to space by taking advantage of brain plasticity at night and psychological resilience during daytime. While this N-of-1 study prevents drawing definitive conclusions, the methodology used herein to monitor markers of brain plasticity could pave the way for further studies that could add to the present results.
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Affiliation(s)
- Kuniaki Otsuka
- Space Biomedical Research Group, Japan Aerospace Exploration Agency, Ibaraki, Japan.
- Halberg Chronobiology Center, University of Minnesota, Minneapolis, MN, USA.
- Tokyo Women's Medical University, Tokyo, Japan.
| | | | - Yutaka Kubo
- Tokyo Women's Medical University, Tokyo, Japan
| | | | - Koh Mizuno
- Space Biomedical Research Group, Japan Aerospace Exploration Agency, Ibaraki, Japan
- Faculty of Education, Tohoku Fukushi University, Miyagi, Japan
| | - Tatsuya Aiba
- Space Biomedical Research Group, Japan Aerospace Exploration Agency, Ibaraki, Japan
| | - Satoshi Furukawa
- Space Biomedical Research Group, Japan Aerospace Exploration Agency, Ibaraki, Japan
| | - Hiroshi Ohshima
- Space Biomedical Research Group, Japan Aerospace Exploration Agency, Ibaraki, Japan
| | - Chiaki Mukai
- Space Biomedical Research Group, Japan Aerospace Exploration Agency, Ibaraki, Japan
- Tokyo University of Science, Tokyo, Japan
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7
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Otsuka K, Murakami S, Okajima K, Shibata K, Kubo Y, Gubin DG, Beaty LA, Cornelissen G. Appropriate Circadian-Circasemidian Coupling Protects Blood Pressure from Morning Surge and Promotes Human Resilience and Wellbeing. Clin Interv Aging 2023; 18:755-769. [PMID: 37193339 PMCID: PMC10183193 DOI: 10.2147/cia.s398957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 05/02/2023] [Indexed: 05/18/2023] Open
Abstract
Background Blood pressure (BP) variability is involved in the appraisal of threat and safety, and can serve as a potential marker of psychological resilience against stress. The relationship between biological rhythms of BP and resilience was cross-sectionally assessed by 7-day/24-hour chronobiologic screening in a rural Japanese community (Tosa), with focus on the 12-hour component and the "circadian-circasemidian coupling" of systolic (S) BP. Subjects and Methods Tosa residents (N = 239, 147 women, 23-74 years), free of anti-hypertensive medication, completed 7-day/24-hour ambulatory BP monitoring. The circadian-circasemidian coupling was determined individually by computing the difference between the circadian phase and the circasemidian morning-phase of SBP. Participants were classified into three groups: those with a short coupling interval of about 4.5 hours (Group A), those with an intermediate coupling interval of about 6.0 hours (Group B), and those with a long coupling interval of about 8.0 hours (Group C). Results Residents of Group B who showed optimal circadian-circasemidian coordination had less pronounced morning and evening SBP surges, as compared to residents of Group A (10.82 vs 14.29 mmHg, P < 0.0001) and Group C (11.86 vs 15.21 mmHg, P < 0.0001), respectively. The incidence of morning or evening SBP surge was less in Group B than in Group A (P < 0.0001) or Group C (P < 0.0001). Group B residents showed highest measures of wellbeing and psychological resilience, assessed by good relation with friends (P < 0.05), life satisfaction (P < 0.05), and subjective happiness (P < 0.05). A disturbed circadian-circasemidian coupling was associated with elevated BP, dyslipidemia, arteriosclerosis and a depressive mood. Conclusion The circadian-circasemidian coupling of SBP could serve as a new biomarker in clinical practice to guide precision medicine interventions aimed at achieving properly timed rhythms, and thereby resilience and wellbeing.
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Affiliation(s)
- Kuniaki Otsuka
- Tokyo Women’s Medical University, Tokyo, Japan
- Halberg Chronobiology Center, University of Minnesota, Minneapolis, MN, USA
| | - Shougo Murakami
- Department of Cardiovascular Medicine, Soseikai General Hospital, Kyoto, Japan
| | - Kiyotaka Okajima
- Cardiovascular Internal Medicine, Higashi Omiya General Hospital, Saitama, Japan
| | | | - Yutaka Kubo
- Department of Medicine, Machida Keisen Hospital, Tokyo, Japan
| | - Denis G Gubin
- Laboratory for Chronobiology and Chronomedicine, Research Institute of Biomedicine and Biomedical Technologies, Medical University, Tyumen, 625023, Russia
- Department of Biology, Medical University, Tyumen, 625023, Russia
- Tyumen Cardiology Research Center, Tomsk National Research Medical Center, Russian Academy of Science, Tomsk, Russia
| | - Larry A Beaty
- Halberg Chronobiology Center, University of Minnesota, Minneapolis, MN, USA
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Asher G, Zhu B. Beyond circadian rhythms: emerging roles of ultradian rhythms in control of liver functions. Hepatology 2023; 77:1022-1035. [PMID: 35591797 PMCID: PMC9674798 DOI: 10.1002/hep.32580] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 04/26/2022] [Accepted: 04/28/2022] [Indexed: 12/08/2022]
Abstract
The mammalian liver must cope with various metabolic and physiological changes that normally recur every day and primarily stem from daily cycles of rest-activity and fasting-feeding. Although a large body of evidence supports the reciprocal regulation of circadian rhythms and liver function, the research on the hepatic ultradian rhythms have largely been lagging behind. However, with the advent of more cost-effective high-throughput omics technologies, high-resolution time-lapse imaging, and more robust and powerful mathematical tools, several recent studies have shed new light on the presence and functions of hepatic ultradian rhythms. In this review, we will first very briefly discuss the basic principles of circadian rhythms, and then cover in greater details the recent literature related to ultradian rhythms. Specifically, we will highlight the prevalence and mechanisms of hepatic 12-h rhythms, and 8-h rhythms, which cycle at the second and third harmonics of circadian frequency. Finally, we also refer to ultradian rhythms with other frequencies and examine the limitations of the current approaches as well as the challenges related to identifying ultradian rhythm and addressing their molecular underpinnings.
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Affiliation(s)
- Gad Asher
- Department of Biomolecular Sciences, Weizmann Institute of Science, 7610001, Rehovot, Israel
| | - Bokai Zhu
- Aging Institute of UPMC, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Pittsburgh Liver Research Center, University of Pittsburgh, Pennsylvania, USA
- Division of Endocrinology and Metabolism, Department of Medicine, University of Pittsburgh, School of Medicine, Pittsburgh, Pennsylvania, USA
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Obodo D, Outland EH, Hughey JJ. Sex Inclusion in Transcriptome Studies of Daily Rhythms. J Biol Rhythms 2023; 38:3-14. [PMID: 36419398 PMCID: PMC9903005 DOI: 10.1177/07487304221134160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Biomedical research on mammals has traditionally neglected females, raising the concern that some scientific findings may generalize poorly to half the population. Although this lack of sex inclusion has been broadly documented, its extent within circadian genomics remains undescribed. To address this gap, we examined sex inclusion practices in a comprehensive collection of publicly available transcriptome studies on daily rhythms. Among 148 studies having samples from mammals in vivo, we found strong underrepresentation of females across organisms and tissues. Overall, only 23 of 123 studies in mice, 0 of 10 studies in rats, and 9 of 15 studies in humans included samples from females. In addition, studies having samples from both sexes tended to have more samples from males than from females. These trends appear to have changed little over time, including since 2016, when the US National Institutes of Health began requiring investigators to consider sex as a biological variable. Our findings highlight an opportunity to dramatically improve representation of females in circadian research and to explore sex differences in daily rhythms at the genome level.
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Affiliation(s)
- Dora Obodo
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee,Program in Chemical and Physical Biology, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Elliot H. Outland
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Jacob J. Hughey
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee,Program in Chemical and Physical Biology, Vanderbilt University School of Medicine, Nashville, Tennessee,Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee,Jacob J. Hughey, Department of Biomedical Informatics, Vanderbilt University Medical Center, 2525 West End Ave., Suite 1475, Nashville, TN 37232, USA; e-mail:
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10
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Liu X, Chiu JC. Nutrient-sensitive protein O-GlcNAcylation shapes daily biological rhythms. Open Biol 2022; 12:220215. [PMID: 36099933 PMCID: PMC9470261 DOI: 10.1098/rsob.220215] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 08/17/2022] [Indexed: 11/12/2022] Open
Abstract
O-linked-N-acetylglucosaminylation (O-GlcNAcylation) is a nutrient-sensitive protein modification that alters the structure and function of a wide range of proteins involved in diverse cellular processes. Similar to phosphorylation, another protein modification that targets serine and threonine residues, O-GlcNAcylation occupancy on cellular proteins exhibits daily rhythmicity and has been shown to play critical roles in regulating daily rhythms in biology by modifying circadian clock proteins and downstream effectors. We recently reported that daily rhythm in global O-GlcNAcylation observed in Drosophila tissues is regulated via the integration of circadian and metabolic signals. Significantly, mistimed feeding, which disrupts coordination of these signals, is sufficient to dampen daily O-GlcNAcylation rhythm and is predicted to negatively impact animal biological rhythms and health span. In this review, we provide an overview of published and potential mechanisms by which metabolic and circadian signals regulate hexosamine biosynthetic pathway metabolites and enzymes, as well as O-GlcNAc processing enzymes to shape daily O-GlcNAcylation rhythms. We also discuss the significance of functional interactions between O-GlcNAcylation and other post-translational modifications in regulating biological rhythms. Finally, we highlight organ/tissue-specific cellular processes and molecular pathways that could be modulated by rhythmic O-GlcNAcylation to regulate time-of-day-specific biology.
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Affiliation(s)
- Xianhui Liu
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California Davis, Davis, CA, USA
- Department of Pharmacology, School of Medicine, University of California Davis, Davis, CA, USA
| | - Joanna C. Chiu
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California Davis, Davis, CA, USA
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11
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Unconscious mind activates central cardiovascular network and promotes adaptation to microgravity possibly anti-aging during 1-year-long spaceflight. Sci Rep 2022; 12:11862. [PMID: 35831420 PMCID: PMC9279338 DOI: 10.1038/s41598-022-14858-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 06/14/2022] [Indexed: 12/12/2022] Open
Abstract
The intrinsic cardiovascular regulatory system (β, 0.00013–0.02 Hz) did not adapt to microgravity after a 6-month spaceflight. The infraslow oscillation (ISO, 0.01–0.10 Hz) coordinating brain dynamics via thalamic astrocytes plays a key role in the adaptation to novel environments. We investigate the adaptive process of a healthy astronaut during a 12-month-long spaceflight by analyzing heart rate variability (HRV) in the LF (0.01–0.05 Hz) and MF1 (0.05–0.10 Hz) bands for two consecutive days on four occasions: before launch, at 1-month (ISS01) and 11-month (ISS02) in space, and after return to Earth. Alteration of β during ISS01 improved during ISS02 (P = 0.0167). During ISS01, LF and MF1 bands, reflecting default mode network (DMN) activity, started to increase at night (by 43.1% and 32.0%, respectively), when suprachiasmatic astrocytes are most active, followed by a 25.9% increase in MF1-band throughout the entire day during ISS02, larger at night (47.4%) than during daytime. Magnetic declination correlated positively with β during ISS01 (r = 0.6706, P < 0.0001) and ISS02 (r = 0.3958, P = 0.0095). Magnetic fluctuations may affect suprachiasmatic astrocytes, and the DMN involving ISOs and thalamic astrocytes may then be activated, first at night, then during the entire day, a mechanism that could perhaps promote an anti-aging effect noted in other investigations.
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12
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Hunter AL, Pelekanou CE, Barron NJ, Northeast RC, Grudzien M, Adamson AD, Downton P, Cornfield T, Cunningham PS, Billaud JN, Hodson L, Loudon ASI, Unwin RD, Iqbal M, Ray DW, Bechtold DA. Adipocyte NR1D1 dictates adipose tissue expansion during obesity. eLife 2021; 10:e63324. [PMID: 34350828 PMCID: PMC8360653 DOI: 10.7554/elife.63324] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 07/30/2021] [Indexed: 12/13/2022] Open
Abstract
The circadian clock component NR1D1 (REVERBα) is considered a dominant regulator of lipid metabolism, with global Nr1d1 deletion driving dysregulation of white adipose tissue (WAT) lipogenesis and obesity. However, a similar phenotype is not observed under adipocyte-selective deletion (Nr1d1Flox2-6:AdipoqCre), and transcriptional profiling demonstrates that, under basal conditions, direct targets of NR1D1 regulation are limited, and include the circadian clock and collagen dynamics. Under high-fat diet (HFD) feeding, Nr1d1Flox2-6:AdipoqCre mice do manifest profound obesity, yet without the accompanying WAT inflammation and fibrosis exhibited by controls. Integration of the WAT NR1D1 cistrome with differential gene expression reveals broad control of metabolic processes by NR1D1 which is unmasked in the obese state. Adipocyte NR1D1 does not drive an anticipatory daily rhythm in WAT lipogenesis, but rather modulates WAT activity in response to alterations in metabolic state. Importantly, NR1D1 action in adipocytes is critical to the development of obesity-related WAT pathology and insulin resistance.
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Affiliation(s)
- Ann Louise Hunter
- Centre for Biological Timing, Faculty of Biology, Medicine and Health, University of ManchesterManchesterUnited Kingdom
| | - Charlotte E Pelekanou
- Centre for Biological Timing, Faculty of Biology, Medicine and Health, University of ManchesterManchesterUnited Kingdom
| | - Nichola J Barron
- Centre for Biological Timing, Faculty of Biology, Medicine and Health, University of ManchesterManchesterUnited Kingdom
| | - Rebecca C Northeast
- Centre for Biological Timing, Faculty of Biology, Medicine and Health, University of ManchesterManchesterUnited Kingdom
| | - Magdalena Grudzien
- Centre for Biological Timing, Faculty of Biology, Medicine and Health, University of ManchesterManchesterUnited Kingdom
| | - Antony D Adamson
- Centre for Biological Timing, Faculty of Biology, Medicine and Health, University of ManchesterManchesterUnited Kingdom
| | - Polly Downton
- Centre for Biological Timing, Faculty of Biology, Medicine and Health, University of ManchesterManchesterUnited Kingdom
| | - Thomas Cornfield
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, and NIHR Oxford Biomedical Research Centre, John Radcliffe HospitalOxfordUnited Kingdom
| | - Peter S Cunningham
- Centre for Biological Timing, Faculty of Biology, Medicine and Health, University of ManchesterManchesterUnited Kingdom
| | | | - Leanne Hodson
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, and NIHR Oxford Biomedical Research Centre, John Radcliffe HospitalOxfordUnited Kingdom
| | - Andrew SI Loudon
- Centre for Biological Timing, Faculty of Biology, Medicine and Health, University of ManchesterManchesterUnited Kingdom
| | - Richard D Unwin
- Stoller Biomarker Discovery Centre, Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of ManchesterManchesterUnited Kingdom
| | - Mudassar Iqbal
- Division of Informatics, Imaging and Data Sciences, Faculty of Biology, Medicine and Health, University of ManchesterManchesterUnited Kingdom
| | - David W Ray
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, and NIHR Oxford Biomedical Research Centre, John Radcliffe HospitalOxfordUnited Kingdom
| | - David A Bechtold
- Centre for Biological Timing, Faculty of Biology, Medicine and Health, University of ManchesterManchesterUnited Kingdom
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13
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Ness-Cohn E, Braun R. TimeCycle: Topology Inspired MEthod for the Detection of Cycling Transcripts in Circadian Time-Series Data. Bioinformatics 2021; 37:4405-4413. [PMID: 34175927 PMCID: PMC8652031 DOI: 10.1093/bioinformatics/btab476] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 05/05/2021] [Accepted: 06/25/2021] [Indexed: 11/15/2022] Open
Abstract
MOTIVATION The circadian rhythm drives the oscillatory expression of thousands of genes across all tissues. The recent revolution in high-throughput transcriptomics, coupled with the significant implications of the circadian clock for human health, has sparked an interest in circadian profiling studies to discover genes under circadian control. RESULT We present TimeCycle: a topology-based rhythm detection method designed to identify cycling transcripts. For a given time-series, the method reconstructs the state space using time-delay embedding, a data transformation technique from dynamical systems theory. In the embedded space, Takens' theorem proves that the dynamics of a rhythmic signal will exhibit circular patterns. The degree of circularity of the embedding is calculated as a persistence score using persistent homology, an algebraic method for discerning the topological features of data. By comparing the persistence scores to a bootstrapped null distribution, cycling genes are identified. Results in both synthetic and biological data highlight TimeCycle's ability to identify cycling genes across a range of sampling schemes, number of replicates, and missing data. Comparison to competing methods highlights their relative strengths, providing guidance as to the optimal choice of cycling detection method. AVAILABILITY A fully documented open-source R package implementing TimeCycle is available at: https://nesscoder.github.io/TimeCycle/. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Elan Ness-Cohn
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA.,Biostatistics Division, Department of Preventive Medicine, Northwestern University, Chicago, IL 60611, USA.,NSF-Simons Center for Quantitative Biology, Northwestern University, Evanston, IL 60208, USA
| | - Rosemary Braun
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA.,Biostatistics Division, Department of Preventive Medicine, Northwestern University, Chicago, IL 60611, USA.,NSF-Simons Center for Quantitative Biology, Northwestern University, Evanston, IL 60208, USA.,Department of Engineering Sciences and Applied Mathematics, Northwestern University, Evanston, IL 60208, USA.,Department of Physics and Astronomy, Northwestern University, Evanston, IL 60208, USA.,Northwestern Instutute on Complex Systems, Northwestern University, Evanston, IL 60208, USA
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14
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Revealing the hidden reality of the mammalian 12-h ultradian rhythms. Cell Mol Life Sci 2021; 78:3127-3140. [PMID: 33449146 DOI: 10.1007/s00018-020-03730-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 11/18/2020] [Accepted: 12/04/2020] [Indexed: 12/29/2022]
Abstract
Biological oscillations often cycle at different harmonics of the 24-h circadian rhythms, a phenomenon we coined "Musica Universalis" in 2017. Like the circadian rhythm, the 12-h oscillation is also evolutionarily conserved, robust, and has recently gained new traction in the field of chronobiology. Originally thought to be regulated by the circadian clock and/or environmental cues, recent new evidences support the notion that the majority of 12-h rhythms are regulated by a distinct and cell-autonomous pacemaker that includes the unfolded protein response (UPR) transcription factor spliced form of XBP1 (XBP1s). 12-h cycle of XBP1s level in turn transcriptionally generates robust 12-h rhythms of gene expression enriched in the central dogma information flow (CEDIF) pathway. Given the regulatory and functional separation of the 12-h and circadian clocks, in this review, we will focus our attention on the mammalian 12-h pacemaker, and discuss our current understanding of its prevalence, evolutionary origin, regulation, and functional roles in both physiological and pathological processes.
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15
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Zhu B. Decoding the function and regulation of the mammalian 12-h clock. J Mol Cell Biol 2020; 12:752-758. [PMID: 32384155 PMCID: PMC7816679 DOI: 10.1093/jmcb/mjaa021] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 04/16/2020] [Accepted: 04/24/2020] [Indexed: 11/26/2022] Open
Affiliation(s)
- Bokai Zhu
- Aging Institute of UPMC, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.,Pittsburgh Liver Research Center, University of Pittsburgh, Pittsburgh, PA, USA.,Division of Endocrinology and Metabolism, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
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16
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Mei W, Jiang Z, Chen Y, Chen L, Sancar A, Jiang Y. Genome-wide circadian rhythm detection methods: systematic evaluations and practical guidelines. Brief Bioinform 2020; 22:5872170. [PMID: 32672832 DOI: 10.1093/bib/bbaa135] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 05/18/2020] [Accepted: 06/04/2020] [Indexed: 12/31/2022] Open
Abstract
Circadian rhythms are oscillations of behavior, physiology and metabolism in many organisms. Recent advancements in omics technology make it possible for genome-wide profiling of circadian rhythms. Here, we conducted a comprehensive analysis of seven existing algorithms commonly used for circadian rhythm detection. Using gold-standard circadian and non-circadian genes, we systematically evaluated the accuracy and reproducibility of the algorithms on empirical datasets generated from various omics platforms under different experimental designs. We also carried out extensive simulation studies to test each algorithm's robustness to key variables, including sampling patterns, replicates, waveforms, signal-to-noise ratios, uneven samplings and missing values. Furthermore, we examined the distributions of the nominal $P$-values under the null and raised issues with multiple testing corrections using traditional approaches. With our assessment, we provide method selection guidelines for circadian rhythm detection, which are applicable to different types of high-throughput omics data.
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Affiliation(s)
- Wenwen Mei
- Department of Biostatistics, University of North Carolina at Chapel Hill
| | - Zhiwen Jiang
- Department of Biostatistics, University of North Carolina at Chapel Hill
| | - Yang Chen
- Department of Statistics and the Michigan Institute of Data Science, University of Michigan
| | - Li Chen
- Department of Medicine and a member of the Center for Computational Biology and Bioinformatics, Indiana University School of Medicine
| | - Aziz Sancar
- Biochemistry and Biophysics at the University of North Carolina School of Medicine
| | - Yuchao Jiang
- Department of Biostatistics and the Department of Genetics, University of North Carolina at Chapel Hill and a member of UNC Lineberger Comprehensive Cancer Center
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17
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Genome-wide circadian regulation: A unique system for computational biology. Comput Struct Biotechnol J 2020; 18:1914-1924. [PMID: 32774786 PMCID: PMC7385043 DOI: 10.1016/j.csbj.2020.07.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Revised: 06/30/2020] [Accepted: 07/02/2020] [Indexed: 01/20/2023] Open
Abstract
Circadian rhythms are 24-hour oscillations affecting an organism at multiple levels from gene expression all the way to tissues and organs. They have been observed in organisms across the kingdom of life, spanning from cyanobacteria to humans. In mammals, the master circadian pacemaker is located in the hypothalamic suprachiasmatic nuclei (SCN) in the brain where it synchronizes the peripheral oscillators that exist in other tissues. This system regulates the circadian activity of a large part of the transcriptome and recent findings indicate that almost every cell in the body has this clock at the molecular level. In this review, we briefly summarize the different factors that can influence the circadian transcriptome, including light, temperature, and food intake. We then summarize recently identified general principles governing genome-scale circadian regulation, as well as future lines of research. Genome-scale circadian activity represents a fascinating study model for computational biology. For this purpose, systems biology methods are promising exploratory tools to decode the global regulatory principles of circadian regulation.
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Key Words
- ABSR, Autoregressive Bayesian spectral regression
- AMPK, AMP-activated protein kinase
- AR, Arrhythmic feeding
- ARSER, Harmonic regression based on autoregressive spectral estimation
- BMAL1, The aryl hydrocarbon receptor nuclear translocator-like (ARNTL)
- CCD, Cortical collecting duct
- CR, Calorie-restricted diet
- CRY, Cryptochrome
- Circadian regulatory network
- Circadian rhythms
- Circadian transcriptome
- Cycling genes
- DCT/CNT, Distal convoluted tubule and connecting tubule
- DD, Dark: dark
- Energetic cost
- HF, High fat diet
- JTK_CYCLE, Jonckheere-Terpstra-Kendall (JTK) cycle
- KD, Ketogenic diet
- LB, Ad libitum
- LD, Light:dark
- LS, Lomb-Scargle
- Liver-RE, Liver clock reconstituted BMAL1-deficient mice
- NAD, Nicotinamide adenine dinucleotides
- ND, Normal diet
- NR, Night-restricted feeding
- PAS, PER-ARNT-SIM
- PER, Period
- RAIN, Rhythmicity Analysis Incorporating Nonparametric methods
- RF, Restricted feeding
- SCN, Suprachiasmatic nucleus
- SREBP, The sterol regulatory element binding protein
- TTFL, Transcriptional-translational feedback loop
- WT, Wild type
- eJTK_CYCLE, Empirical JTK_CYCLE
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18
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Ness-Cohn E, Iwanaszko M, Kath WL, Allada R, Braun R. TimeTrial: An Interactive Application for Optimizing the Design and Analysis of Transcriptomic Time-Series Data in Circadian Biology Research. J Biol Rhythms 2020; 35:439-451. [PMID: 32613882 PMCID: PMC7534021 DOI: 10.1177/0748730420934672] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The circadian rhythm drives the oscillatory expression of thousands of genes across all tissues, coordinating physiological processes. The effect of this rhythm on health has generated increasing interest in discovering genes under circadian control by searching for periodic patterns in transcriptomic time-series experiments. While algorithms for detecting cycling transcripts have advanced, there remains little guidance quantifying the effect of experimental design and analysis choices on cycling detection accuracy. We present TimeTrial, a user-friendly benchmarking framework using both real and synthetic data to investigate cycle detection algorithms’ performance and improve circadian experimental design. Results show that the optimal choice of analysis method depends on the sampling scheme, noise level, and shape of the waveform of interest and provides guidance on the impact of sampling frequency and duration on cycling detection accuracy. The TimeTrial software is freely available for download and may also be accessed through a web interface. By supplying a tool to vary and optimize experimental design considerations, TimeTrial will enhance circadian transcriptomics studies.
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Affiliation(s)
- Elan Ness-Cohn
- Biostatistics Division, Department of Preventive Medicine, Northwestern University, Chicago, Illinois, USA.,NSF-Simons Center for Quantitative Biology, Northwestern University, Evanston, Illinois, USA
| | - Marta Iwanaszko
- Biostatistics Division, Department of Preventive Medicine, Northwestern University, Chicago, Illinois, USA.,NSF-Simons Center for Quantitative Biology, Northwestern University, Evanston, Illinois, USA.,Silesian University of Technology, Department of Systems Biology and Engineering, Gliwice, Poland
| | - William L Kath
- NSF-Simons Center for Quantitative Biology, Northwestern University, Evanston, Illinois, USA.,Department of Engineering Sciences and Applied Mathematics, Northwestern University, Evanston, IL, USA.,Department of Neurobiology, Northwestern University, Evanston, IL, USA
| | - Ravi Allada
- NSF-Simons Center for Quantitative Biology, Northwestern University, Evanston, Illinois, USA.,Department of Neurobiology, Northwestern University, Evanston, IL, USA
| | - Rosemary Braun
- Biostatistics Division, Department of Preventive Medicine, Northwestern University, Chicago, Illinois, USA.,NSF-Simons Center for Quantitative Biology, Northwestern University, Evanston, Illinois, USA.,Department of Engineering Sciences and Applied Mathematics, Northwestern University, Evanston, IL, USA.,Department of Physics and Astronomy, Northwestern University, Evanston, Illinois, USA
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19
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Smith LM, Motta FC, Chopra G, Moch JK, Nerem RR, Cummins B, Roche KE, Kelliher CM, Leman AR, Harer J, Gedeon T, Waters NC, Haase SB. An intrinsic oscillator drives the blood stage cycle of the malaria parasite Plasmodium falciparum. Science 2020; 368:754-759. [PMID: 32409472 DOI: 10.1126/science.aba4357] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 02/11/2020] [Accepted: 04/06/2020] [Indexed: 12/14/2022]
Abstract
The blood stage of the infection of the malaria parasite Plasmodium falciparum exhibits a 48-hour developmental cycle that culminates in the synchronous release of parasites from red blood cells, which triggers 48-hour fever cycles in the host. This cycle could be driven extrinsically by host circadian processes or by a parasite-intrinsic oscillator. To distinguish between these hypotheses, we examine the P. falciparum cycle in an in vitro culture system and show that the parasite has molecular signatures associated with circadian and cell cycle oscillators. Each of the four strains examined has a different period, which indicates strain-intrinsic period control. Finally, we demonstrate that parasites have low cell-to-cell variance in cycle period, on par with a circadian oscillator. We conclude that an intrinsic oscillator maintains Plasmodium's rhythmic life cycle.
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Affiliation(s)
| | - Francis C Motta
- Department of Mathematical Sciences, Florida Atlantic University, Boca Raton, FL, USA
| | - Garima Chopra
- Malaria Biologics Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - J Kathleen Moch
- Malaria Biologics Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Robert R Nerem
- Department of Mathematical Sciences, Montana State University, Bozeman, MT, USA
| | - Bree Cummins
- Department of Mathematical Sciences, Montana State University, Bozeman, MT, USA
| | - Kimberly E Roche
- Program in Computational Biology and Bioinformatics, Duke University, Durham, NC, USA
| | | | - Adam R Leman
- Department of Biology, Duke University, Durham, NC, USA
| | - John Harer
- Department of Mathematics, Duke University, Durham, NC, USA
| | - Tomas Gedeon
- Department of Mathematical Sciences, Montana State University, Bozeman, MT, USA
| | - Norman C Waters
- Malaria Biologics Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Steven B Haase
- Department of Biology, Duke University, Durham, NC, USA. .,Department of Medicine, Duke University, Durham, NC, USA
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20
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Abstract
Circadian rhythms are daily cycles in biological function that are ubiquitous in nature. Understood as a means for organisms to anticipate daily environmental changes, circadian rhythms are also important for orchestrating complex biological processes such as immunity. Nowhere is this more evident than in the respiratory system, where circadian rhythms in inflammatory lung disease have been appreciated since ancient times. In this focused review we examine how emerging research on circadian rhythms is being applied to the study of fundamental lung biology and respiratory disease. We begin with a general introduction to circadian rhythms and the molecular circadian clock that underpins them. We then focus on emerging data tying circadian clock function to immunologic activities within the respiratory system. We conclude by considering outstanding questions about biological timing in the lung and how a better command of chronobiology could inform our understanding of complex lung diseases.
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Affiliation(s)
- Charles Nosal
- Division of Pulmonary and Critical Care Medicine, Washington University School of Medicine, St. Louis, Missouri 63110, USA;
| | - Anna Ehlers
- Division of Pulmonary and Critical Care Medicine, Washington University School of Medicine, St. Louis, Missouri 63110, USA;
| | - Jeffrey A Haspel
- Division of Pulmonary and Critical Care Medicine, Washington University School of Medicine, St. Louis, Missouri 63110, USA;
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21
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Abstract
Group 3 innate lymphoid cells (ILC3s) are critical for maintaining gut epithelial integrity and tissue repair. Recent research identifies mechanisms by which circadian machinery and feeding behavior regulate enteric ILC3s to maintain gut homeostasis.
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Affiliation(s)
- Gitalee Sarker
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK
| | - Chelsea M Larabee
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK
| | - Ana I Domingos
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK.
- The Howard Hughes Medical Institute (HHMI), New York, NY, USA.
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22
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Pan Y, Ballance H, Meng H, Gonzalez N, Kim SM, Abdurehman L, York B, Chen X, Schnytzer Y, Levy O, Dacso CC, McClung CA, O’Malley BW, Liu S, Zhu B. 12-h clock regulation of genetic information flow by XBP1s. PLoS Biol 2020; 18:e3000580. [PMID: 31935211 PMCID: PMC6959563 DOI: 10.1371/journal.pbio.3000580] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 12/11/2019] [Indexed: 12/15/2022] Open
Abstract
Our group recently characterized a cell-autonomous mammalian 12-h clock independent from the circadian clock, but its function and mechanism of regulation remain poorly understood. Here, we show that in mouse liver, transcriptional regulation significantly contributes to the establishment of 12-h rhythms of mRNA expression in a manner dependent on Spliced Form of X-box Binding Protein 1 (XBP1s). Mechanistically, the motif stringency of XBP1s promoter binding sites dictates XBP1s’s ability to drive 12-h rhythms of nascent mRNA transcription at dawn and dusk, which are enriched for basal transcription regulation, mRNA processing and export, ribosome biogenesis, translation initiation, and protein processing/sorting in the Endoplasmic Reticulum (ER)-Golgi in a temporal order consistent with the progressive molecular processing sequence described by the central dogma information flow (CEDIF). We further identified GA-binding proteins (GABPs) as putative novel transcriptional regulators driving 12-h rhythms of gene expression with more diverse phases. These 12-h rhythms of gene expression are cell autonomous and evolutionarily conserved in marine animals possessing a circatidal clock. Our results demonstrate an evolutionarily conserved, intricate network of transcriptional control of the mammalian 12-h clock that mediates diverse biological pathways. We speculate that the 12-h clock is coopted to accommodate elevated gene expression and processing in mammals at the two rush hours, with the particular genes processed at each rush hour regulated by the circadian and/or tissue-specific pathways. Distinct from the well-known 24-hour circadian clock, this study shows that the mammalian 12-hour clock upregulates genetic information flow capacity during the two "rush hours" (dawn and dusk) in a manner dependent on the transcription factor XBP1s.
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Affiliation(s)
- Yinghong Pan
- UPMC Genome Center, Pittsburgh, Pennsylvania, United States of America
| | - Heather Ballance
- Aging Institute of UPMC, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Huan Meng
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Naomi Gonzalez
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Sam-Moon Kim
- Translational Neuroscience Program, Department of Psychiatry, Center for Neuroscience, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Leymaan Abdurehman
- Aging Institute of UPMC, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Brian York
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Xi Chen
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Yisrael Schnytzer
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Oren Levy
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Clifford C. Dacso
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Colleen A. McClung
- Translational Neuroscience Program, Department of Psychiatry, Center for Neuroscience, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Bert W. O’Malley
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Silvia Liu
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
- Pittsburgh Liver Research Center, University of Pittsburgh, Pennsylvania, United States of America
- * E-mail: (SL); (BZ)
| | - Bokai Zhu
- Aging Institute of UPMC, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
- Pittsburgh Liver Research Center, University of Pittsburgh, Pennsylvania, United States of America
- Division of Endocrinology and Metabolism, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
- * E-mail: (SL); (BZ)
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23
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Logan RW, Parekh PK, Kaplan G, Becker-Krail D, Williams W, Yamaguchi S, Yoshino J, Shelton MA, Zhu X, Zhang H, Waplinger S, Fitzgerald E, Oliver-Smith J, Sundarvelu P, Enwright JF, Huang YH, McClung CA. NAD+ cellular redox and SIRT1 regulate the diurnal rhythms of tyrosine hydroxylase and conditioned cocaine reward. Mol Psychiatry 2019; 24:1668-1684. [PMID: 29728703 PMCID: PMC6215755 DOI: 10.1038/s41380-018-0061-1] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Revised: 01/12/2018] [Accepted: 02/19/2018] [Indexed: 12/21/2022]
Abstract
The diurnal regulation of dopamine is important for normal physiology and diseases such as addiction. Here we find a novel role for the CLOCK protein to antagonize CREB-mediated transcriptional activity at the tyrosine hydroxylase (TH) promoter, which is mediated by the interaction with the metabolic sensing protein, Sirtuin 1 (SIRT1). Additionally, we demonstrate that the transcriptional activity of TH is modulated by the cellular redox state, and daily rhythms of redox balance in the ventral tegmental area (VTA), along with TH transcription, are highly disrupted following chronic cocaine administration. Furthermore, CLOCK and SIRT1 are important for regulating cocaine reward and dopaminergic (DAergic) activity, with interesting differences depending on whether DAergic activity is in a heightened state and if there is a functional CLOCK protein. Taken together, we find that rhythms in cellular metabolism and circadian proteins work together to regulate dopamine synthesis and the reward value for drugs of abuse.
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Affiliation(s)
- Ryan W. Logan
- Translational Neuroscience Program, Department of Psychiatry, University of Pittsburgh Medical School, Pittsburgh, PA, 15219, USA,Center for Neuroscience, University of Pittsburgh, Pittsburgh, PA, 15260, USA,Center for Systems Neurogenetics of Addiction, The Jackson Laboratory, Bar Harbor, ME, 04609
| | - Puja K. Parekh
- Translational Neuroscience Program, Department of Psychiatry, University of Pittsburgh Medical School, Pittsburgh, PA, 15219, USA,Center for Neuroscience, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Gabrielle Kaplan
- Translational Neuroscience Program, Department of Psychiatry, University of Pittsburgh Medical School, Pittsburgh, PA, 15219, USA,Center for Neuroscience, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Darius Becker-Krail
- Translational Neuroscience Program, Department of Psychiatry, University of Pittsburgh Medical School, Pittsburgh, PA, 15219, USA,Center for Neuroscience, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Wilbur Williams
- Translational Neuroscience Program, Department of Psychiatry, University of Pittsburgh Medical School, Pittsburgh, PA, 15219, USA
| | - Shintaro Yamaguchi
- Center for Systems Neurogenetics of Addiction, The Jackson Laboratory, Bar Harbor, ME, 04609
| | - Jun Yoshino
- Center for Systems Neurogenetics of Addiction, The Jackson Laboratory, Bar Harbor, ME, 04609
| | - Micah A. Shelton
- Translational Neuroscience Program, Department of Psychiatry, University of Pittsburgh Medical School, Pittsburgh, PA, 15219, USA
| | - Xiyu Zhu
- Translational Neuroscience Program, Department of Psychiatry, University of Pittsburgh Medical School, Pittsburgh, PA, 15219, USA,Center for Neuroscience, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Hui Zhang
- Translational Neuroscience Program, Department of Psychiatry, University of Pittsburgh Medical School, Pittsburgh, PA, 15219, USA,School of Medicine, Peking Union Medical College, Tsinghua University, Beijing, China
| | - Spencer Waplinger
- Translational Neuroscience Program, Department of Psychiatry, University of Pittsburgh Medical School, Pittsburgh, PA, 15219, USA
| | - Ethan Fitzgerald
- Translational Neuroscience Program, Department of Psychiatry, University of Pittsburgh Medical School, Pittsburgh, PA, 15219, USA
| | - Jeffrey Oliver-Smith
- Translational Neuroscience Program, Department of Psychiatry, University of Pittsburgh Medical School, Pittsburgh, PA, 15219, USA
| | - Poornima Sundarvelu
- Translational Neuroscience Program, Department of Psychiatry, University of Pittsburgh Medical School, Pittsburgh, PA, 15219, USA
| | - John F. Enwright
- Translational Neuroscience Program, Department of Psychiatry, University of Pittsburgh Medical School, Pittsburgh, PA, 15219, USA
| | | | - Colleen A. McClung
- Translational Neuroscience Program, Department of Psychiatry, University of Pittsburgh Medical School, Pittsburgh, PA, 15219, USA,Center for Neuroscience, University of Pittsburgh, Pittsburgh, PA, 15260, USA,Center for Systems Neurogenetics of Addiction, The Jackson Laboratory, Bar Harbor, ME, 04609,Correspondence: (C.A.M.)
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24
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Cedernaes J, Waldeck N, Bass J. Neurogenetic basis for circadian regulation of metabolism by the hypothalamus. Genes Dev 2019; 33:1136-1158. [PMID: 31481537 PMCID: PMC6719618 DOI: 10.1101/gad.328633.119] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Circadian rhythms are driven by a transcription-translation feedback loop that separates anabolic and catabolic processes across the Earth's 24-h light-dark cycle. Central pacemaker neurons that perceive light entrain a distributed clock network and are closely juxtaposed with hypothalamic neurons involved in regulation of sleep/wake and fast/feeding states. Gaps remain in identifying how pacemaker and extrapacemaker neurons communicate with energy-sensing neurons and the distinct role of circuit interactions versus transcriptionally driven cell-autonomous clocks in the timing of organismal bioenergetics. In this review, we discuss the reciprocal relationship through which the central clock drives appetitive behavior and metabolic homeostasis and the pathways through which nutrient state and sleep/wake behavior affect central clock function.
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Affiliation(s)
- Jonathan Cedernaes
- Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
| | - Nathan Waldeck
- Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
| | - Joseph Bass
- Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
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25
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Gendron CM, Chakraborty TS, Chung BY, Harvanek ZM, Holme KJ, Johnson JC, Lyu Y, Munneke AS, Pletcher SD. Neuronal Mechanisms that Drive Organismal Aging Through the Lens of Perception. Annu Rev Physiol 2019; 82:227-249. [PMID: 31635526 DOI: 10.1146/annurev-physiol-021119-034440] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Sensory neurons provide organisms with data about the world in which they live, for the purpose of successfully exploiting their environment. The consequences of sensory perception are not simply limited to decision-making behaviors; evidence suggests that sensory perception directly influences physiology and aging, a phenomenon that has been observed in animals across taxa. Therefore, understanding the neural mechanisms by which sensory input influences aging may uncover novel therapeutic targets for aging-related physiologies. In this review, we examine different perceptive experiences that have been most clearly linked to aging or age-related disease: food perception, social perception, time perception, and threat perception. For each, the sensory cues, receptors, and/or pathways that influence aging as well as the individual or groups of neurons involved, if known, are discussed. We conclude with general thoughts about the potential impact of this line of research on human health and aging.
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Affiliation(s)
- Christi M Gendron
- Department of Molecular and Integrative Physiology and the Geriatrics Center, University of Michigan, Ann Arbor, Michigan 48109, USA;
| | - Tuhin S Chakraborty
- Department of Molecular and Integrative Physiology and the Geriatrics Center, University of Michigan, Ann Arbor, Michigan 48109, USA;
| | - Brian Y Chung
- Department of Molecular and Integrative Physiology and the Geriatrics Center, University of Michigan, Ann Arbor, Michigan 48109, USA;
| | - Zachary M Harvanek
- Department of Molecular and Integrative Physiology and the Geriatrics Center, University of Michigan, Ann Arbor, Michigan 48109, USA;
| | - Kristina J Holme
- Department of Molecular and Integrative Physiology and the Geriatrics Center, University of Michigan, Ann Arbor, Michigan 48109, USA;
| | - Jacob C Johnson
- Department of Molecular and Integrative Physiology and the Geriatrics Center, University of Michigan, Ann Arbor, Michigan 48109, USA;
| | - Yang Lyu
- Department of Molecular and Integrative Physiology and the Geriatrics Center, University of Michigan, Ann Arbor, Michigan 48109, USA;
| | - Allyson S Munneke
- Program in Cellular and Molecular Biology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Scott D Pletcher
- Department of Molecular and Integrative Physiology and the Geriatrics Center, University of Michigan, Ann Arbor, Michigan 48109, USA; .,Program in Cellular and Molecular Biology, University of Michigan, Ann Arbor, Michigan 48109, USA
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26
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Lugena AB, Zhang Y, Menet JS, Merlin C. Genome-wide discovery of the daily transcriptome, DNA regulatory elements and transcription factor occupancy in the monarch butterfly brain. PLoS Genet 2019; 15:e1008265. [PMID: 31335862 PMCID: PMC6677324 DOI: 10.1371/journal.pgen.1008265] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 08/02/2019] [Accepted: 06/21/2019] [Indexed: 12/20/2022] Open
Abstract
The Eastern North American monarch butterfly, Danaus plexippus, is famous for its spectacular seasonal long-distance migration. In recent years, it has also emerged as a novel system to study how animal circadian clocks keep track of time and regulate ecologically relevant daily rhythmic activities and seasonal behavioral outputs. However, unlike in Drosophila and the mouse, little work has been undertaken in the monarch to identify rhythmic genes at the genome-wide level and elucidate the regulation of their diurnal expression. Here, we used RNA-sequencing and Assay for Transposase-Accessible Chromatin (ATAC)-sequencing to profile the diurnal transcriptome, open chromatin regions, and transcription factor (TF) footprints in the brain of wild-type monarchs and of monarchs with impaired clock function, including Cryptochrome 2 (Cry2), Clock (Clk), and Cycle-like loss-of-function mutants. We identified 217 rhythmically expressed genes in the monarch brain; many of them were involved in the regulation of biological processes key to brain function, such as glucose metabolism and neurotransmission. Surprisingly, we found no significant time-of-day and genotype-dependent changes in chromatin accessibility in the brain. Instead, we found the existence of a temporal regulation of TF occupancy within open chromatin regions in the vicinity of rhythmic genes in the brains of wild-type monarchs, which is disrupted in clock deficient mutants. Together, this work identifies for the first time the rhythmic genes and modes of regulation by which diurnal transcription rhythms are regulated in the monarch brain. It also illustrates the power of ATAC-sequencing to profile genome-wide regulatory elements and TF binding in a non-model organism for which TF-specific antibodies are not yet available. With a rich biology that includes a clock-regulated migratory behavior and a circadian clock possessing mammalian clock orthologues, the monarch butterfly is an unconventional system with broad appeal to study circadian and seasonal rhythms. While clockwork mechanisms and rhythmic behavioral outputs have been studied in this species, the rhythmic genes that regulate rhythmic daily and seasonal activities remain largely unknown. Likewise, the mechanisms regulating rhythmic gene expression have not been explored in the monarch. Here, we applied genome-wide sequencing approaches to identify genes with rhythmic diurnal expression in the monarch brain, revealing the coordination of key pathways for brain function. We also identified the monarch brain open chromatin regions and provide evidence that regulation of rhythmic gene expression does not occur through temporal regulation of chromatin opening but rather by the time-of-day dependent binding of transcription factors in cis-regulatory elements. Together, our data extend our knowledge of the molecular rhythmic pathways, which may prove important in understanding the mechanisms underlying the daily and seasonal biology of the migratory monarch butterflies.
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Affiliation(s)
- Aldrin B. Lugena
- Department of Biology and Center for Biological Clocks Research, Texas A&M University, College Station, Texas, United States of America
| | - Ying Zhang
- Department of Biology and Center for Biological Clocks Research, Texas A&M University, College Station, Texas, United States of America
| | - Jerome S. Menet
- Department of Biology and Center for Biological Clocks Research, Texas A&M University, College Station, Texas, United States of America
| | - Christine Merlin
- Department of Biology and Center for Biological Clocks Research, Texas A&M University, College Station, Texas, United States of America
- * E-mail:
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27
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Chikamoto A, Sekizawa SI, Tochinai R, Kuwahara M. Early attenuation of autonomic nervous function in senescence accelerated mouse-prone 8 (SAMP8). Exp Anim 2019; 68:511-517. [PMID: 31168043 PMCID: PMC6842801 DOI: 10.1538/expanim.19-0032] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The senescence-accelerated mouse (SAM) strain has been established as an inbred strain with an accelerated aging phenotype. SAM prone-8 (SAMP8), one of the SAM strain, exhibits learning disability, immune deficiency, and circadian rhythm loss at a relatively young age. However, it has not been clarified whether aging affects the autonomic nervous activity in SAMP8. The aim of this study was to clarify the utility of SAMP8 in age-related studies of autonomic nervous function. Electrocardiogram (ECG), body temperature, and locomotor activity were recorded to evaluate bio-behavioral activities. Autonomic nervous activity was evaluated via power spectral analysis of heart rate variability from ECG recordings. SAMP8 significantly decreased both biological and autonomic nervous functions, and the animals exhibited circadian rhythm loss of locomotive activity at as early as 40 weeks of age compared with a control strain at the same age. We concluded that the SAMP8 strain can be used as an animal model for age-related studies of autonomic nervous function.
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Affiliation(s)
- Akitoshi Chikamoto
- Laboratory of Veterinary Pathophysiology and Animal Health, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Shin-Ichi Sekizawa
- Laboratory of Veterinary Pathophysiology and Animal Health, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Ryota Tochinai
- Laboratory of Veterinary Pathophysiology and Animal Health, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Masayoshi Kuwahara
- Laboratory of Veterinary Pathophysiology and Animal Health, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
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28
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Leite Góes Gitai D, de Andrade TG, Dos Santos YDR, Attaluri S, Shetty AK. Chronobiology of limbic seizures: Potential mechanisms and prospects of chronotherapy for mesial temporal lobe epilepsy. Neurosci Biobehav Rev 2019; 98:122-134. [PMID: 30629979 PMCID: PMC7023906 DOI: 10.1016/j.neubiorev.2019.01.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 12/20/2018] [Accepted: 01/06/2019] [Indexed: 12/11/2022]
Abstract
Mesial Temporal Lobe Epilepsy (mTLE) characterized by progressive development of complex partial seizures originating from the hippocampus is the most prevalent and refractory type of epilepsy. One of the remarkable features of mTLE is the rhythmic pattern of occurrence of spontaneous seizures, implying a dependence on the endogenous clock system for seizure threshold. Conversely, circadian rhythms are affected by epilepsy too. Comprehending how the circadian system and seizures interact with each other is essential for understanding the pathophysiology of epilepsy as well as for developing innovative therapies that are efficacious for better seizure control. In this review, we confer how the temporal dysregulation of the circadian clock in the hippocampus combined with multiple uncoupled oscillators could lead to periodic seizure occurrences and comorbidities. Unraveling these associations with additional research would help in developing chronotherapy for mTLE, based on the chronobiology of spontaneous seizures. Notably, differential dosing of antiepileptic drugs over the circadian period and/or strategies that resynchronize biological rhythms may substantially improve the management of seizures in mTLE patients.
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Affiliation(s)
- Daniel Leite Góes Gitai
- Institute for Regenerative Medicine, Department of Molecular and Cellular Medicine, Texas A&M University, College Station, Texas, USA; Institute of Biological Sciences and Health, Federal University of Alagoas, Maceio, Alagoas, Brazil
| | | | | | - Sahithi Attaluri
- Institute for Regenerative Medicine, Department of Molecular and Cellular Medicine, Texas A&M University, College Station, Texas, USA
| | - Ashok K Shetty
- Institute for Regenerative Medicine, Department of Molecular and Cellular Medicine, Texas A&M University, College Station, Texas, USA; Research Service, Olin E. Teague Veterans' Medical Center, Central Texas Veterans Health Care System, Temple, Texas, USA.
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29
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Hong HK, Maury E, Ramsey KM, Perelis M, Marcheva B, Omura C, Kobayashi Y, Guttridge DC, Barish GD, Bass J. Requirement for NF-κB in maintenance of molecular and behavioral circadian rhythms in mice. Genes Dev 2018; 32:1367-1379. [PMID: 30366905 PMCID: PMC6217733 DOI: 10.1101/gad.319228.118] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 09/13/2018] [Indexed: 12/12/2022]
Abstract
The mammalian circadian clock is encoded by an autoregulatory transcription feedback loop that drives rhythmic behavior and gene expression in the brain and peripheral tissues. Transcriptomic analyses indicate cell type-specific effects of circadian cycles on rhythmic physiology, although how clock cycles respond to environmental stimuli remains incompletely understood. Here, we show that activation of the inducible transcription factor NF-κB in response to inflammatory stimuli leads to marked inhibition of clock repressors, including the Period, Cryptochrome, and Rev-erb genes, within the negative limb. Furthermore, activation of NF-κB relocalizes the clock components CLOCK/BMAL1 genome-wide to sites convergent with those bound by NF-κB, marked by acetylated H3K27, and enriched in RNA polymerase II. Abrogation of NF-κB during adulthood alters the expression of clock repressors, disrupts clock-controlled gene cycles, and impairs rhythmic activity behavior, revealing a role for NF-κB in both unstimulated and activated conditions. Together, these data highlight NF-κB-mediated transcriptional repression of the clock feedback limb as a cause of circadian disruption in response to inflammation.
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Affiliation(s)
- Hee-Kyung Hong
- Department of Medicine, Division of Endocrinology, Metabolism, and Molecular Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
- Department of Neurobiology, Northwestern University, Evanston, Illinois 60208, USA
| | - Eleonore Maury
- Department of Medicine, Division of Endocrinology, Metabolism, and Molecular Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
- Department of Neurobiology, Northwestern University, Evanston, Illinois 60208, USA
- Unit of Endocrinology, Diabetes, and Nutrition, Université Catholique de Louvain (UCL), Brussels B-1200, Belgium
| | - Kathryn Moynihan Ramsey
- Department of Medicine, Division of Endocrinology, Metabolism, and Molecular Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
- Department of Neurobiology, Northwestern University, Evanston, Illinois 60208, USA
| | - Mark Perelis
- Department of Medicine, Division of Endocrinology, Metabolism, and Molecular Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
- Department of Neurobiology, Northwestern University, Evanston, Illinois 60208, USA
| | - Biliana Marcheva
- Department of Medicine, Division of Endocrinology, Metabolism, and Molecular Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
- Department of Neurobiology, Northwestern University, Evanston, Illinois 60208, USA
| | - Chiaki Omura
- Department of Medicine, Division of Endocrinology, Metabolism, and Molecular Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
- Department of Neurobiology, Northwestern University, Evanston, Illinois 60208, USA
| | - Yumiko Kobayashi
- Department of Medicine, Division of Endocrinology, Metabolism, and Molecular Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
- Department of Neurobiology, Northwestern University, Evanston, Illinois 60208, USA
| | - Denis C Guttridge
- Darby Children's Research Institute, Medical University of South Carolina, Charleston, South Carolina 29425, USA
| | - Grant D Barish
- Department of Medicine, Division of Endocrinology, Metabolism, and Molecular Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, Illinois 60611, USA
| | - Joseph Bass
- Department of Medicine, Division of Endocrinology, Metabolism, and Molecular Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
- Department of Neurobiology, Northwestern University, Evanston, Illinois 60208, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, Illinois 60611, USA
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30
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Yeung J, Naef F. Rhythms of the Genome: Circadian Dynamics from Chromatin Topology, Tissue-Specific Gene Expression, to Behavior. Trends Genet 2018; 34:915-926. [PMID: 30309754 DOI: 10.1016/j.tig.2018.09.005] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Revised: 08/31/2018] [Accepted: 09/10/2018] [Indexed: 11/18/2022]
Abstract
Circadian rhythms in physiology and behavior evolved to resonate with daily cycles in the external environment. In mammals, organs orchestrate temporal physiology over the 24-h day, which requires extensive gene expression rhythms targeted to the right tissue. Although a core set of gene products oscillates across virtually all cell types, gene expression profiling across tissues over the 24-h day showed that rhythmic gene expression programs are tissue specific. We highlight recent progress in uncovering how the circadian clock interweaves with tissue-specific gene regulatory networks involving functions such as xenobiotic metabolism, glucose homeostasis, and sleep. This progress hinges on not only comprehensive experimental approaches but also computational methods for multivariate analysis of periodic functional genomics data. We emphasize dynamic chromatin interactions as a novel regulatory layer underlying circadian gene transcription, core clock functions, and ultimately behavior. Finally, we discuss perspectives on extending the knowledge of the circadian clock in animals to human chronobiology.
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Affiliation(s)
- Jake Yeung
- The Institute of Bioengineering (IBI), School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Felix Naef
- The Institute of Bioengineering (IBI), School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
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31
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Top D, Young MW. Coordination between Differentially Regulated Circadian Clocks Generates Rhythmic Behavior. Cold Spring Harb Perspect Biol 2018; 10:a033589. [PMID: 28893860 PMCID: PMC6028074 DOI: 10.1101/cshperspect.a033589] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Specialized groups of neurons in the brain are key mediators of circadian rhythms, receiving daily environmental cues and communicating those signals to other tissues in the organism for entrainment and to organize circadian physiology. In Drosophila, the "circadian clock" is housed in seven neuronal clusters, which are defined by their expression of the main circadian proteins, Period, Timeless, Clock, and Cycle. These clusters are distributed across the fly brain and are thereby subject to the respective environments associated with their anatomical locations. While these core components are universally expressed in all neurons of the circadian network, additional regulatory proteins that act on these components are differentially expressed, giving rise to "local clocks" within the network that nonetheless converge to regulate coherent behavioral rhythms. In this review, we describe the communication between the neurons of the circadian network and the molecular differences within neurons of this network. We focus on differences in protein-expression patterns and discuss how such variation can impart functional differences in each local clock. Finally, we summarize our current understanding of how communication within the circadian network intersects with intracellular biochemical mechanisms to ultimately specify behavioral rhythms. We propose that additional efforts are required to identify regulatory mechanisms within each neuronal cluster to understand the molecular basis of circadian behavior.
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Affiliation(s)
- Deniz Top
- Laboratory of Genetics, The Rockefeller University, New York, New York 10065
| | - Michael W Young
- Laboratory of Genetics, The Rockefeller University, New York, New York 10065
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32
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Zhu B, Dacso CC, O’Malley BW. Unveiling "Musica Universalis" of the Cell: A Brief History of Biological 12-Hour Rhythms. J Endocr Soc 2018; 2:727-752. [PMID: 29978151 PMCID: PMC6025213 DOI: 10.1210/js.2018-00113] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 06/01/2018] [Indexed: 12/18/2022] Open
Abstract
"Musica universalis" is an ancient philosophical concept claiming the movements of celestial bodies follow mathematical equations and resonate to produce an inaudible harmony of music, and the harmonious sounds that humans make were an approximation of this larger harmony of the universe. Besides music, electromagnetic waves such as light and electric signals also are presented as harmonic resonances. Despite the seemingly universal theme of harmonic resonance in various disciplines, it was not until recently that the same harmonic resonance was discovered also to exist in biological systems. Contrary to traditional belief that a biological system is either at stead-state or cycles with a single frequency, it is now appreciated that most biological systems have no homeostatic "set point," but rather oscillate as composite rhythms consisting of superimposed oscillations. These oscillations often cycle at different harmonics of the circadian rhythm, and among these, the ~12-hour oscillation is most prevalent. In this review, we focus on these 12-hour oscillations, with special attention to their evolutionary origin, regulation, and functions in mammals, as well as their relationship to the circadian rhythm. We further discuss the potential roles of the 12-hour clock in regulating hepatic steatosis, aging, and the possibility of 12-hour clock-based chronotherapy. Finally, we posit that biological rhythms are also musica universalis: whereas the circadian rhythm is synchronized to the 24-hour light/dark cycle coinciding with the Earth's rotation, the mammalian 12-hour clock may have evolved from the circatidal clock, which is entrained by the 12-hour tidal cues orchestrated by the moon.
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Affiliation(s)
- Bokai Zhu
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas
| | - Clifford C Dacso
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas
- Department of Medicine, Baylor College of Medicine, Houston, Texas
- Dan L. Duncan Cancer Center, 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
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33
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Yeung J, Mermet J, Jouffe C, Marquis J, Charpagne A, Gachon F, Naef F. Transcription factor activity rhythms and tissue-specific chromatin interactions explain circadian gene expression across organs. Genome Res 2018; 28:182-191. [PMID: 29254942 PMCID: PMC5793782 DOI: 10.1101/gr.222430.117] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 12/11/2017] [Indexed: 11/28/2022]
Abstract
Temporal control of physiology requires the interplay between gene networks involved in daily timekeeping and tissue function across different organs. How the circadian clock interweaves with tissue-specific transcriptional programs is poorly understood. Here, we dissected temporal and tissue-specific regulation at multiple gene regulatory layers by examining mouse tissues with an intact or disrupted clock over time. Integrated analysis uncovered two distinct regulatory modes underlying tissue-specific rhythms: tissue-specific oscillations in transcription factor (TF) activity, which were linked to feeding-fasting cycles in liver and sodium homeostasis in kidney; and colocalized binding of clock and tissue-specific transcription factors at distal enhancers. Chromosome conformation capture (4C-seq) in liver and kidney identified liver-specific chromatin loops that recruited clock-bound enhancers to promoters to regulate liver-specific transcriptional rhythms. Furthermore, this looping was remarkably promoter-specific on the scale of less than 10 kilobases (kb). Enhancers can contact a rhythmic promoter while looping out nearby nonrhythmic alternative promoters, confining rhythmic enhancer activity to specific promoters. These findings suggest that chromatin folding enables the clock to regulate rhythmic transcription of specific promoters to output temporal transcriptional programs tailored to different tissues.
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Affiliation(s)
- Jake Yeung
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, CH-1015, Switzerland
| | - Jérôme Mermet
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, CH-1015, Switzerland
| | - Céline Jouffe
- Department of Diabetes and Circadian Rhythms, Nestlé Institute of Health Sciences, CH-1015 Lausanne, Switzerland
| | - Julien Marquis
- Functional Genomics, Nestlé Institute of Health Sciences, CH-1015 Lausanne, Switzerland
| | - Aline Charpagne
- Functional Genomics, Nestlé Institute of Health Sciences, CH-1015 Lausanne, Switzerland
| | - Frédéric Gachon
- Department of Diabetes and Circadian Rhythms, Nestlé Institute of Health Sciences, CH-1015 Lausanne, Switzerland
- Faculty of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Felix Naef
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, CH-1015, Switzerland
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34
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O'Callaghan EK, Green EW, Franken P, Mongrain V. Omics Approaches in Sleep-Wake Regulation. Handb Exp Pharmacol 2018; 253:59-81. [PMID: 29796779 DOI: 10.1007/164_2018_125] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Although sleep seems an obvious and simple behaviour, it is extremely complex involving numerous interactions both at the neuronal and the molecular levels. While we have gained detailed insight into the molecules and neuronal networks responsible for the circadian organization of sleep and wakefulness, the molecular underpinnings of the homeostatic aspect of sleep regulation are still unknown and the focus of a considerable research effort. In the last 20 years, the development of techniques allowing the simultaneous measurement of hundreds to thousands of molecular targets (i.e. 'omics' approaches) has enabled the unbiased study of the molecular pathways regulated by and regulating sleep. In this chapter, we will review how the different omics approaches, including transcriptomics, epigenomics, proteomics, and metabolomics, have advanced sleep research. We present relevant data in the framework of the two-process model in which circadian and homeostatic processes interact to regulate sleep. The integration of the different omics levels, known as 'systems genetics', will eventually lead to a better understanding of how information flows from the genome, to molecules, to networks, and finally to sleep both in health and disease.
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Affiliation(s)
- Emma K O'Callaghan
- Center for Advanced Research in Sleep Medicine and Research Center, Hôpital du Sacré-Coeur de Montréal, Montreal, QC, Canada.,Department of Neuroscience, Université de Montréal, Montreal, QC, Canada
| | - Edward W Green
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Paul Franken
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Valérie Mongrain
- Center for Advanced Research in Sleep Medicine and Research Center, Hôpital du Sacré-Coeur de Montréal, Montreal, QC, Canada. .,Department of Neuroscience, Université de Montréal, Montreal, QC, Canada.
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35
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Perelis M, Ramsey KM, Marcheva B, Bass J. Circadian Transcription from Beta Cell Function to Diabetes Pathophysiology. J Biol Rhythms 2017; 31:323-36. [PMID: 27440914 DOI: 10.1177/0748730416656949] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The mammalian circadian clock plays a central role in the temporal coordination of physiology across the 24-h light-dark cycle. A major function of the clock is to maintain energy constancy in anticipation of alternating periods of fasting and feeding that correspond with sleep and wakefulness. While it has long been recognized that humans exhibit robust variation in glucose tolerance and insulin sensitivity across the sleep-wake cycle, experimental genetic analysis has now revealed that the clock transcription cycle plays an essential role in insulin secretion and metabolic function within pancreatic beta cells. This review addresses how studies of the beta cell clock may elucidate the etiology of subtypes of diabetes associated with circadian and sleep cycle disruption, in addition to more general forms of the disease.
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Affiliation(s)
- Mark Perelis
- Department of Medicine, Division of Endocrinology, Metabolism and Molecular Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Kathryn Moynihan Ramsey
- Department of Medicine, Division of Endocrinology, Metabolism and Molecular Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Biliana Marcheva
- Department of Medicine, Division of Endocrinology, Metabolism and Molecular Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Joseph Bass
- Department of Medicine, Division of Endocrinology, Metabolism and Molecular Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
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36
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Fontenot MR, Berto S, Liu Y, Werthmann G, Douglas C, Usui N, Gleason K, Tamminga CA, Takahashi JS, Konopka G. Novel transcriptional networks regulated by CLOCK in human neurons. Genes Dev 2017; 31:2121-2135. [PMID: 29196536 PMCID: PMC5749161 DOI: 10.1101/gad.305813.117] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Accepted: 11/07/2017] [Indexed: 01/01/2023]
Abstract
Fontenot et al. show that CLOCK regulates the expression of genes involved in neuronal migration. Dysregulation of CLOCK disrupts coexpressed networks of genes implicated in neuropsychiatric disorders, and the expression of these networks is driven by hub genes with human-specific patterns of expression. The molecular mechanisms underlying human brain evolution are not fully understood; however, previous work suggested that expression of the transcription factor CLOCK in the human cortex might be relevant to human cognition and disease. In this study, we investigated this novel transcriptional role for CLOCK in human neurons by performing chromatin immunoprecipitation sequencing for endogenous CLOCK in adult neocortices and RNA sequencing following CLOCK knockdown in differentiated human neurons in vitro. These data suggested that CLOCK regulates the expression of genes involved in neuronal migration, and a functional assay showed that CLOCK knockdown increased neuronal migratory distance. Furthermore, dysregulation of CLOCK disrupts coexpressed networks of genes implicated in neuropsychiatric disorders, and the expression of these networks is driven by hub genes with human-specific patterns of expression. These data support a role for CLOCK-regulated transcriptional cascades involved in human brain evolution and function.
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Affiliation(s)
- Miles R Fontenot
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Stefano Berto
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Yuxiang Liu
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Gordon Werthmann
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Connor Douglas
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Noriyoshi Usui
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Kelly Gleason
- Department of Psychiatry, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Carol A Tamminga
- Department of Psychiatry, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Joseph S Takahashi
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA.,Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Genevieve Konopka
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
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Acuña-Castroviejo D, Rahim I, Acuña-Fernández C, Fernández-Ortiz M, Solera-Marín J, Sayed RKA, Díaz-Casado ME, Rusanova I, López LC, Escames G. Melatonin, clock genes and mitochondria in sepsis. Cell Mol Life Sci 2017; 74:3965-3987. [PMID: 28785808 PMCID: PMC11107653 DOI: 10.1007/s00018-017-2610-1] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 08/03/2017] [Indexed: 12/22/2022]
Abstract
After the characterization of the central pacemaker in the suprachiasmatic nucleus, the expression of clock genes was identified in several peripheral tissues including the immune system. The hierarchical control from the central clock to peripheral clocks extends to other functions including endocrine, metabolic, immune, and mitochondrial responses. Increasing evidence links the disruption of the clock genes expression with multiple diseases and aging. Chronodisruption is associated with alterations of the immune system, immunosenescence, impairment of energy metabolism, and reduction of pineal and extrapineal melatonin production. Regarding sepsis, a condition coursing with an exaggerated response of innate immunity, experimental and clinical data showed an alteration of circadian rhythms that reflects the loss of the normal oscillation of the clock. Moreover, recent data point to that some mediators of the immune system affects the normal function of the clock. Under specific conditions, this control disappears reactivating the immune response. So, it seems that clock gene disruption favors the innate immune response, which in turn induces the expression of proinflammatory mediators, causing a further alteration of the clock. Here, the clock control of the mitochondrial function turns off, leading to a bioenergetic decay and formation of reactive oxygen species that, in turn, activate the inflammasome. This arm of the innate immunity is responsible for the huge increase of interleukin-1β and entrance into a vicious cycle that could lead to the death of the patient. The broken clock is recovered by melatonin administration, that is accompanied by the normalization of the innate immunity and mitochondrial homeostasis. Thus, this review emphasizes the connection between clock genes, innate immunity and mitochondria in health and sepsis, and the role of melatonin to maintain clock homeostasis.
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Affiliation(s)
- Darío Acuña-Castroviejo
- Departamento de Fisiología, Facultad de Medicina, Instituto de Biotecnología, Centro de Investigación Biomédica, Parque Tecnológico de Ciencias de la Salud, Universidad de Granada, Avenida del Conocimiento s/n, 18016, Granada, Spain.
- CIBERfes, Ibs.Granada, and UGC de Laboratorios Clínicos, Complejo Hospitalario de Granada, Granada, Spain.
| | - Ibtissem Rahim
- Departamento de Fisiología, Facultad de Medicina, Instituto de Biotecnología, Centro de Investigación Biomédica, Parque Tecnológico de Ciencias de la Salud, Universidad de Granada, Avenida del Conocimiento s/n, 18016, Granada, Spain
- Département de Biologie et Physiologie Cellulaire, Faculté des Sciences de la Nature et de la Vie, Université Blida 1, Blida, Algeria
| | - Carlos Acuña-Fernández
- Unidad of Anestesiología y Reanimación, Hospital Universitario de Canarias, San Cristóbal de La Laguna, Santa Cruz de Tenerife, Spain
| | - Marisol Fernández-Ortiz
- Departamento de Fisiología, Facultad de Medicina, Instituto de Biotecnología, Centro de Investigación Biomédica, Parque Tecnológico de Ciencias de la Salud, Universidad de Granada, Avenida del Conocimiento s/n, 18016, Granada, Spain
| | - Jorge Solera-Marín
- Unidad of Anestesiología y Reanimación, Hospital Universitario de Canarias, San Cristóbal de La Laguna, Santa Cruz de Tenerife, Spain
| | - Ramy K A Sayed
- Departamento de Fisiología, Facultad de Medicina, Instituto de Biotecnología, Centro de Investigación Biomédica, Parque Tecnológico de Ciencias de la Salud, Universidad de Granada, Avenida del Conocimiento s/n, 18016, Granada, Spain
- Department of Anatomy and Embryology, Faculty of Veterinary Medicine, Sohag University, Sohâg, Egypt
| | - María E Díaz-Casado
- Departamento de Fisiología, Facultad de Medicina, Instituto de Biotecnología, Centro de Investigación Biomédica, Parque Tecnológico de Ciencias de la Salud, Universidad de Granada, Avenida del Conocimiento s/n, 18016, Granada, Spain
| | - Iryna Rusanova
- Departamento de Fisiología, Facultad de Medicina, Instituto de Biotecnología, Centro de Investigación Biomédica, Parque Tecnológico de Ciencias de la Salud, Universidad de Granada, Avenida del Conocimiento s/n, 18016, Granada, Spain
- CIBERfes, Ibs.Granada, and UGC de Laboratorios Clínicos, Complejo Hospitalario de Granada, Granada, Spain
| | - Luis C López
- Departamento de Fisiología, Facultad de Medicina, Instituto de Biotecnología, Centro de Investigación Biomédica, Parque Tecnológico de Ciencias de la Salud, Universidad de Granada, Avenida del Conocimiento s/n, 18016, Granada, Spain
- CIBERfes, Ibs.Granada, and UGC de Laboratorios Clínicos, Complejo Hospitalario de Granada, Granada, Spain
| | - Germaine Escames
- Departamento de Fisiología, Facultad de Medicina, Instituto de Biotecnología, Centro de Investigación Biomédica, Parque Tecnológico de Ciencias de la Salud, Universidad de Granada, Avenida del Conocimiento s/n, 18016, Granada, Spain
- CIBERfes, Ibs.Granada, and UGC de Laboratorios Clínicos, Complejo Hospitalario de Granada, Granada, Spain
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Zhu B, Zhang Q, Pan Y, Mace EM, York B, Antoulas AC, Dacso CC, O'Malley BW. A Cell-Autonomous Mammalian 12 hr Clock Coordinates Metabolic and Stress Rhythms. Cell Metab 2017; 25:1305-1319.e9. [PMID: 28591634 PMCID: PMC5526350 DOI: 10.1016/j.cmet.2017.05.004] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 12/11/2016] [Accepted: 05/18/2017] [Indexed: 02/08/2023]
Abstract
Besides circadian rhythms, oscillations cycling with a 12 hr period exist. However, the prevalence, origin, regulation, and function of mammalian 12 hr rhythms remain elusive. Utilizing an unbiased mathematical approach identifying all superimposed oscillations, we uncovered prevalent 12 hr gene expression and metabolic rhythms in mouse liver, coupled with a physiological 12 hr unfolded protein response oscillation. The mammalian 12 hr rhythm is cell autonomous, driven by a dedicated 12 hr pacemaker distinct from the circadian clock, and can be entrained in vitro by metabolic and ER stress cues. Mechanistically, we identified XBP1s as a transcriptional regulator of the mammalian 12 hr clock. Downregulation of the 12 hr gene expression strongly correlates with human hepatic steatosis and steatohepatitis, implying its importance in maintaining metabolic homeostasis. The mammalian 12 hr rhythm of gene expression also is conserved in nematodes and crustaceans, indicating an ancient origin of the 12 hr clock. Our work sheds new light on how perturbed biological rhythms contribute to human disease.
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Affiliation(s)
- Bokai Zhu
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Qiang Zhang
- Department of Electrical and Computer Engineering, Rice University, Houston, TX 77005, USA
| | - Yinghong Pan
- Department of Biology and Biochemistry, University of Houston, Houston, TX 77004, USA
| | - Emily M Mace
- Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Brian York
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Athanasios C Antoulas
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Department of Electrical and Computer Engineering, Rice University, Houston, TX 77005, USA; Max Planck Fellow Group for Data-Driven System Reduction and Identification, Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg 39106, Germany
| | - Clifford C Dacso
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Electrical and Computer Engineering, Rice University, Houston, TX 77005, USA
| | - Bert W O'Malley
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA.
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39
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McAlpine CS, Swirski FK. Circadian Influence on Metabolism and Inflammation in Atherosclerosis. Circ Res 2017; 119:131-41. [PMID: 27340272 DOI: 10.1161/circresaha.116.308034] [Citation(s) in RCA: 89] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Accepted: 03/11/2016] [Indexed: 11/16/2022]
Abstract
Many aspects of human health and disease display daily rhythmicity. The brain's suprachiasmic nucleus, which interprets recurring external stimuli, and autonomous molecular networks in peripheral cells together, set our biological circadian clock. Disrupted or misaligned circadian rhythms promote multiple pathologies including chronic inflammatory and metabolic diseases such as atherosclerosis. Here, we discuss studies suggesting that circadian fluctuations in the vessel wall and in the circulation contribute to atherogenesis. Data from humans and mice indicate that an impaired molecular clock, disturbed sleep, and shifting light-dark patterns influence leukocyte and lipid supply in the circulation and alter cellular behavior in atherosclerotic lesions. We propose that a better understanding of both local and systemic circadian rhythms in atherosclerosis will enhance clinical management, treatment, and public health policy.
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Affiliation(s)
- Cameron S McAlpine
- From the Center for Systems Biology, Massachusetts General Hospital and Harvard Medical School, Boston.
| | - Filip K Swirski
- From the Center for Systems Biology, Massachusetts General Hospital and Harvard Medical School, Boston
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40
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Krishnaiah SY, Wu G, Altman BJ, Growe J, Rhoades SD, Coldren F, Venkataraman A, Olarerin-George AO, Francey LJ, Mukherjee S, Girish S, Selby CP, Cal S, Er U, Sianati B, Sengupta A, Anafi RC, Kavakli IH, Sancar A, Baur JA, Dang CV, Hogenesch JB, Weljie AM. Clock Regulation of Metabolites Reveals Coupling between Transcription and Metabolism. Cell Metab 2017; 25:961-974.e4. [PMID: 28380384 PMCID: PMC5479132 DOI: 10.1016/j.cmet.2017.03.019] [Citation(s) in RCA: 107] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Revised: 01/12/2017] [Accepted: 03/22/2017] [Indexed: 01/09/2023]
Abstract
The intricate connection between the circadian clock and metabolism remains poorly understood. We used high temporal resolution metabolite profiling to explore clock regulation of mouse liver and cell-autonomous metabolism. In liver, ∼50% of metabolites were circadian, with enrichment of nucleotide, amino acid, and methylation pathways. In U2 OS cells, 28% were circadian, including amino acids and NAD biosynthesis metabolites. Eighteen metabolites oscillated in both systems and a subset of these in primary hepatocytes. These 18 metabolites were enriched in methylation and amino acid pathways. To assess clock dependence of these rhythms, we used genetic perturbation. BMAL1 knockdown diminished metabolite rhythms, while CRY1 or CRY2 perturbation generally shortened or lengthened rhythms, respectively. Surprisingly, CRY1 knockdown induced 8 hr rhythms in amino acid, methylation, and vitamin metabolites, decoupling metabolite from transcriptional rhythms, with potential impact on nutrient sensing in vivo. These results provide the first comprehensive views of circadian liver and cell-autonomous metabolism.
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Affiliation(s)
- Saikumari Y Krishnaiah
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute of Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Gang Wu
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Brian J Altman
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jacqueline Growe
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Seth D Rhoades
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute of Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Faith Coldren
- Institute of Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Anand Venkataraman
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Anthony O Olarerin-George
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Lauren J Francey
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Sarmistha Mukherjee
- Department of Physiology and Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Saiveda Girish
- Department of Physiology and Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Christopher P Selby
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Sibel Cal
- Chemical and Biological Engineering and Molecular Biology and Genetics, Koc University, Rumeli Feneri Yolu, 34450 Sariyer, Istanbul, Turkey
| | - Ubeydullah Er
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute of Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Bahareh Sianati
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute of Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Arjun Sengupta
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute of Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ron C Anafi
- Department of Medicine and Center for Sleep and Circadian Neurobiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - I Halil Kavakli
- Chemical and Biological Engineering and Molecular Biology and Genetics, Koc University, Rumeli Feneri Yolu, 34450 Sariyer, Istanbul, Turkey
| | - Aziz Sancar
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Joseph A Baur
- Department of Physiology and Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Chi V Dang
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - John B Hogenesch
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.
| | - Aalim M Weljie
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute of Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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41
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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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Ben-Moshe Livne Z, Alon S, Vallone D, Bayleyen Y, Tovin A, Shainer I, Nisembaum LG, Aviram I, Smadja-Storz S, Fuentes M, Falcón J, Eisenberg E, Klein DC, Burgess HA, Foulkes NS, Gothilf Y. Genetically Blocking the Zebrafish Pineal Clock Affects Circadian Behavior. PLoS Genet 2016; 12:e1006445. [PMID: 27870848 PMCID: PMC5147766 DOI: 10.1371/journal.pgen.1006445] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Accepted: 10/24/2016] [Indexed: 01/10/2023] Open
Abstract
The master circadian clock in fish has been considered to reside in the pineal gland. This dogma is challenged, however, by the finding that most zebrafish tissues contain molecular clocks that are directly reset by light. To further examine the role of the pineal gland oscillator in the zebrafish circadian system, we generated a transgenic line in which the molecular clock is selectively blocked in the melatonin-producing cells of the pineal gland by a dominant-negative strategy. As a result, clock-controlled rhythms of melatonin production in the adult pineal gland were disrupted. Moreover, transcriptome analysis revealed that the circadian expression pattern of the majority of clock-controlled genes in the adult pineal gland is abolished. Importantly, circadian rhythms of behavior in zebrafish larvae were affected: rhythms of place preference under constant darkness were eliminated, and rhythms of locomotor activity under constant dark and constant dim light conditions were markedly attenuated. On the other hand, global peripheral molecular oscillators, as measured in whole larvae, were unaffected in this model. In conclusion, characterization of this novel transgenic model provides evidence that the molecular clock in the melatonin-producing cells of the pineal gland plays a key role, possibly as part of a multiple pacemaker system, in modulating circadian rhythms of behavior.
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Affiliation(s)
- Zohar Ben-Moshe Livne
- Department of Neurobiology, George S. Wise Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv, Israel
| | - Shahar Alon
- Department of Neurobiology, George S. Wise Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv, Israel
- Sagol School of Neuroscience, Tel-Aviv University, Tel-Aviv, Israel
| | - Daniela Vallone
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany
| | - Yared Bayleyen
- Unit on Behavioral Neurogenetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Adi Tovin
- Department of Neurobiology, George S. Wise Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv, Israel
| | - Inbal Shainer
- Department of Neurobiology, George S. Wise Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv, Israel
| | - Laura G. Nisembaum
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Biologie Intégrative des Organismes Marins, Observatoire Océanologique, Banyuls/Mer, France
| | - Idit Aviram
- Department of Neurobiology, George S. Wise Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv, Israel
| | - Sima Smadja-Storz
- Department of Neurobiology, George S. Wise Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv, Israel
| | - Michael Fuentes
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Biologie Intégrative des Organismes Marins, Observatoire Océanologique, Banyuls/Mer, France
| | - Jack Falcón
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Biologie Intégrative des Organismes Marins, Observatoire Océanologique, Banyuls/Mer, France
| | - Eli Eisenberg
- Sagol School of Neuroscience, Tel-Aviv University, Tel-Aviv, Israel
- Raymond and Beverly Sackler School of Physics and Astronomy, Tel-Aviv University, Tel-Aviv, Israel
| | - David C. Klein
- Section on Neuroendocrinology and Office of the Scientific Directory, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Harold A. Burgess
- Unit on Behavioral Neurogenetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Nicholas S. Foulkes
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany
| | - Yoav Gothilf
- Department of Neurobiology, George S. Wise Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv, Israel
- Sagol School of Neuroscience, Tel-Aviv University, Tel-Aviv, Israel
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Polidarová L, Houdek P, Sládek M, Novosadová Z, Pácha J, Sumová A. Mechanisms of hormonal regulation of the peripheral circadian clock in the colon. Chronobiol Int 2016; 34:1-16. [PMID: 27661138 DOI: 10.1080/07420528.2016.1231198] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Colonic function is controlled by an endogenous clock that allows the colon to optimize its function on the daytime basis. For the first time, this study provided evidence that the clock is synchronized by rhythmic hormonal signals. In rat colon, adrenalectomy decreased and repeated applications of dexamethasone selectively rescued circadian rhythm in the expression of the clock gene Per1. Dexamethasone entrained the colonic clock in explants from mPer2Luc mice in vitro. In contrast, pinealectomy had no effect on the rat colonic clock, and repeated melatonin injections were not able to rescue the clock in animals maintained in constant light. Additionally, melatonin did not entrain the clock in colonic explants from mPer2Luc mice in vitro. However, melatonin affected rhythmic regulation of Nr1d1 gene expression in vivo. The findings provide novel insight into possible beneficial effects of glucocorticoids in the treatment of digestive tract-related diseases, greatly exceeding their anti-inflammatory action.
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Affiliation(s)
| | | | | | | | - Jiří Pácha
- b Department of Epithelial Function, Institute of Physiology , The Czech Academy of Sciences , Videnska , Prague , Czech Republic
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Steidle-Kloc E, Schönfelder M, Müller E, Sixt S, Schuler G, Patsch W, Niebauer J. Does exercise training impact clock genes in patients with coronary artery disease and type 2 diabetes mellitus? Eur J Prev Cardiol 2016; 23:1375-82. [DOI: 10.1177/2047487316639682] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Accepted: 02/27/2016] [Indexed: 11/17/2022]
Affiliation(s)
- Eva Steidle-Kloc
- University Institute of Sports Medicine, Prevention and Rehabilitation, Paracelsus Medical University, Austria
| | - Martin Schönfelder
- Research Institute of Molecular Sports Medicine and Rehabilitation, Paracelsus Medical University, Austria
| | - Edith Müller
- Research Institute of Molecular Sports Medicine and Rehabilitation, Paracelsus Medical University, Austria
| | | | - Gerhard Schuler
- Heart Center, Department of Cardiology, University of Leipzig, Germany
| | - Wolfgang Patsch
- Institute of Pharmacology and Toxicology, Paracelsus Medical University, Salzburg, Austria
| | - Josef Niebauer
- University Institute of Sports Medicine, Prevention and Rehabilitation, Paracelsus Medical University, Austria
- Research Institute of Molecular Sports Medicine and Rehabilitation, Paracelsus Medical University, Austria
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45
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Xu C, Ochi H, Fukuda T, Sato S, Sunamura S, Takarada T, Hinoi E, Okawa A, Takeda S. Circadian Clock Regulates Bone Resorption in Mice. J Bone Miner Res 2016; 31:1344-55. [PMID: 26841172 DOI: 10.1002/jbmr.2803] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Revised: 01/20/2016] [Accepted: 02/01/2016] [Indexed: 01/06/2023]
Abstract
The circadian clock controls many behavioral and physiological processes beyond daily rhythms. Circadian dysfunction increases the risk of cancer, obesity, and cardiovascular and metabolic diseases. Although clinical studies have shown that bone resorption is controlled by circadian rhythm, as indicated by diurnal variations in bone resorption, the molecular mechanism of circadian clock-dependent bone resorption remains unknown. To clarify the role of circadian rhythm in bone resorption, aryl hydrocarbon receptor nuclear translocator-like (Bmal1), a prototype circadian gene, was knocked out specifically in osteoclasts. Osteoclast-specific Bmal1-knockout mice showed a high bone mass phenotype due to reduced osteoclast differentiation. A cell-based assay revealed that BMAL1 upregulated nuclear factor of activated T cells, cytoplasmic, calcineurin-dependent 1 (Nfatc1) transcription through its binding to an E-box element located on the Nfatc1 promoter in cooperation with circadian locomotor output cycles kaput (CLOCK), a heterodimer partner of BMAL1. Moreover, steroid receptor coactivator (SRC) family members were shown to interact with and upregulate BMAL1:CLOCK transcriptional activity. Collectively, these data suggest that bone resorption is controlled by osteoclastic BMAL1 through interactions with the SRC family and binding to the Nfatc1 promoter. © 2016 American Society for Bone and Mineral Research.
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Affiliation(s)
- Cheng Xu
- Department of Physiology and Cell Biology, Tokyo Medical and Dental University, Tokyo, Japan
- Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, Tokyo, Japan
- Department of Orthopedic Surgery and Global Center of Excellence (GCOE) Program, International Research Center for Molecular Science in Tooth and Bone Diseases, Tokyo Medical and Dental University, Tokyo, Japan
| | - Hiroki Ochi
- Department of Physiology and Cell Biology, Tokyo Medical and Dental University, Tokyo, Japan
- Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, Tokyo, Japan
| | - Toru Fukuda
- Department of Physiology and Cell Biology, Tokyo Medical and Dental University, Tokyo, Japan
- Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, Tokyo, Japan
| | - Shingo Sato
- Department of Physiology and Cell Biology, Tokyo Medical and Dental University, Tokyo, Japan
- Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, Tokyo, Japan
| | - Satoko Sunamura
- Department of Physiology and Cell Biology, Tokyo Medical and Dental University, Tokyo, Japan
- Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, Tokyo, Japan
| | - Takeshi Takarada
- Laboratory of Molecular Pharmacology, Division of Pharmaceutical Sciences, Kanazawa University Graduate School, Ishikawa, Japan
| | - Eiichi Hinoi
- Laboratory of Molecular Pharmacology, Division of Pharmaceutical Sciences, Kanazawa University Graduate School, Ishikawa, Japan
| | - Atsushi Okawa
- Department of Orthopedic Surgery and Global Center of Excellence (GCOE) Program, International Research Center for Molecular Science in Tooth and Bone Diseases, Tokyo Medical and Dental University, Tokyo, Japan
| | - Shu Takeda
- Department of Physiology and Cell Biology, Tokyo Medical and Dental University, Tokyo, Japan
- Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, Tokyo, Japan
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46
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Finding Clocks in Genes: A Bayesian Approach to Estimate Periodicity. BIOMED RESEARCH INTERNATIONAL 2016; 2016:3017475. [PMID: 27340654 PMCID: PMC4909896 DOI: 10.1155/2016/3017475] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 04/28/2016] [Indexed: 11/20/2022]
Abstract
Identification of rhythmic gene expression from metabolic cycles to circadian rhythms is crucial for understanding the gene regulatory networks and functions of these biological processes. Recently, two algorithms, JTK_CYCLE and ARSER, have been developed to estimate periodicity of rhythmic gene expression. JTK_CYCLE performs well for long or less noisy time series, while ARSER performs well for detecting a single rhythmic category. However, observing gene expression at high temporal resolution is not always feasible, and many scientists are interested in exploring both ultradian and circadian rhythmic categories simultaneously. In this paper, a new algorithm, named autoregressive Bayesian spectral regression (ABSR), is proposed. It estimates the period of time-course experimental data and classifies gene expression profiles into multiple rhythmic categories simultaneously. Through the simulation studies, it is shown that ABSR substantially improves the accuracy of periodicity estimation and clustering of rhythmic categories as compared to JTK_CYCLE and ARSER for the data with low temporal resolution. Moreover, ABSR is insensitive to rhythmic patterns. This new scheme is applied to existing time-course mouse liver data to estimate period of rhythms and classify the genes into ultradian, circadian, and arrhythmic categories. It is observed that 49.2% of the circadian profiles detected by JTK_CYCLE with 1-hour resolution are also detected by ABSR with only 4-hour resolution.
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47
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Thaben PF, Westermark PO. Differential rhythmicity: detecting altered rhythmicity in biological data. Bioinformatics 2016; 32:2800-8. [DOI: 10.1093/bioinformatics/btw309] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 05/11/2016] [Indexed: 11/14/2022] Open
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48
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Erion R, King AN, Wu G, Hogenesch JB, Sehgal A. Neural clocks and Neuropeptide F/Y regulate circadian gene expression in a peripheral metabolic tissue. eLife 2016; 5. [PMID: 27077948 PMCID: PMC4862751 DOI: 10.7554/elife.13552] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2015] [Accepted: 04/07/2016] [Indexed: 11/23/2022] Open
Abstract
Metabolic homeostasis requires coordination between circadian clocks in different tissues. Also, systemic signals appear to be required for some transcriptional rhythms in the mammalian liver and the Drosophila fat body. Here we show that free-running oscillations of the fat body clock require clock function in the PDF-positive cells of the fly brain. Interestingly, rhythmic expression of the cytochrome P450 transcripts, sex-specific enzyme 1 (sxe1) and Cyp6a21, which cycle in the fat body independently of the local clock, depends upon clocks in neurons expressing neuropeptide F (NPF). NPF signaling itself is required to drive cycling of sxe1 and Cyp6a21 in the fat body, and its mammalian ortholog, Npy, functions similarly to regulate cycling of cytochrome P450 genes in the mouse liver. These data highlight the importance of neuronal clocks for peripheral rhythms, particularly in a specific detoxification pathway, and identify a novel and conserved role for NPF/Npy in circadian rhythms. DOI:http://dx.doi.org/10.7554/eLife.13552.001 Many processes in the body follow rhythms that repeat over 24 hours and are synchronized to the cycle of day and night. Our sleep pattern is a well-known example, but others include daily fluctuations in body temperature and the production of several hormones. Internal clocks located in the brain and other organs drive these rhythms by altering the activity of certain genes depending on the time of day. Animals have specific organs that contain enzymes needed to break down toxic molecules in the body, and the levels of several of these enzymes rise and fall over each 24-hour period. In mammals, these enzymes are found in the liver, but in insects they are found in an organ called the fat body. Here, Erion, King et al. set out to determine the extent to which the internal clock in the brain influences the daily rhythms of these enzymes. The experiments show that a hormone released by the nervous system is required for the levels of the detoxifying enzymes to change in 24-hour cycles. This hormone – termed Neuropeptide F in fruit flies and Neuropeptide Y in mice – is also known to stimulate both mice and fruit flies to eat. Since toxic molecules often enter the body during feeding, Erion, King et al. speculate that it may be beneficial to link the detoxification process to feeding by using the same mechanism to control both processes. The next step following on from this work would be to find out exactly how neuropeptide F drives the 24-hour rhythms in the fat body and other organs. DOI:http://dx.doi.org/10.7554/eLife.13552.002
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Affiliation(s)
- Renske Erion
- Howard Hughes Medical Institute, University of Pennsylvania, Philadelphia, United States
| | - Anna N King
- Howard Hughes Medical Institute, University of Pennsylvania, Philadelphia, United States
| | - Gang Wu
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, United States
| | - John B Hogenesch
- Department of Molecular and Cellular Physiology, University of Cincinnati, Cincinnati, United States
| | - Amita Sehgal
- Howard Hughes Medical Institute, University of Pennsylvania, Philadelphia, United States
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Dallmann R, Okyar A, Lévi F. Dosing-Time Makes the Poison: Circadian Regulation and Pharmacotherapy. Trends Mol Med 2016; 22:430-445. [PMID: 27066876 DOI: 10.1016/j.molmed.2016.03.004] [Citation(s) in RCA: 162] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Accepted: 03/17/2016] [Indexed: 12/14/2022]
Abstract
Daily rhythms in physiology significantly modulate drug pharmacokinetics and pharmacodynamics according to the time-of-day, a finding that has led to the concept of chronopharmacology. The importance of biological clocks for xenobiotic metabolism has gained increased attention with the discovery of the molecular circadian clockwork. Mechanistic understanding of the cell-autonomous molecular circadian oscillator and the circadian timing system as a whole has opened new conceptual and methodological lines of investigation to understand first, the clock's impact on a specific drug's daily variations or the effects/side effects of environmental substances, and second, how clock-controlled pathways are coordinated within a given tissue or organism. Today, there is an increased understanding of the circadian modulation of drug effects. Moreover, several molecular strategies are being developed to treat disease-dependent and drug-induced clock disruptions in humans.
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Affiliation(s)
- Robert Dallmann
- Warwick Medical School, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, UK; Warwick Systems Biology Centre, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, UK.
| | - Alper Okyar
- Department of Pharmacology, Faculty of Pharmacy, Istanbul University, Beyazit-Istanbul, Turkey
| | - Francis Lévi
- Warwick Medical School, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, UK; Warwick Systems Biology Centre, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, UK
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50
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Takahashi JS. Molecular Architecture of the Circadian Clock in Mammals. RESEARCH AND PERSPECTIVES IN ENDOCRINE INTERACTIONS 2016. [DOI: 10.1007/978-3-319-27069-2_2] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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