1
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Zeng Y, Guo Z, Wu M, Chen F, Chen L. Circadian rhythm regulates the function of immune cells and participates in the development of tumors. Cell Death Discov 2024; 10:199. [PMID: 38678017 PMCID: PMC11055927 DOI: 10.1038/s41420-024-01960-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 04/02/2024] [Accepted: 04/11/2024] [Indexed: 04/29/2024] Open
Abstract
Circadian rhythms are present in almost all cells and play a crucial role in regulating various biological processes. Maintaining a stable circadian rhythm is essential for overall health. Disruption of this rhythm can alter the expression of clock genes and cancer-related genes, and affect many metabolic pathways and factors, thereby affecting the function of the immune system and contributing to the occurrence and progression of tumors. This paper aims to elucidate the regulatory effects of BMAL1, clock and other clock genes on immune cells, and reveal the molecular mechanism of circadian rhythm's involvement in tumor and its microenvironment regulation. A deeper understanding of circadian rhythms has the potential to provide new strategies for the treatment of cancer and other immune-related diseases.
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Affiliation(s)
- Yuen Zeng
- Department of Immunology, School of Basic Medical Sciences, Air Force Medical University, Xi'an, China
| | - Zichan Guo
- Faculty of Life Sciences, Northwest University, Xi'an, China
| | - Mengqi Wu
- Department of Immunology, School of Basic Medical Sciences, Air Force Medical University, Xi'an, China
| | - Fulin Chen
- Faculty of Life Sciences, Northwest University, Xi'an, China
| | - Lihua Chen
- Department of Immunology, School of Basic Medical Sciences, Air Force Medical University, Xi'an, China.
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2
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Ono D, Weaver DR, Hastings MH, Honma KI, Honma S, Silver R. The Suprachiasmatic Nucleus at 50: Looking Back, Then Looking Forward. J Biol Rhythms 2024; 39:135-165. [PMID: 38366616 PMCID: PMC7615910 DOI: 10.1177/07487304231225706] [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] [Indexed: 02/18/2024]
Abstract
It has been 50 years since the suprachiasmatic nucleus (SCN) was first identified as the central circadian clock and 25 years since the last overview of developments in the field was published in the Journal of Biological Rhythms. Here, we explore new mechanisms and concepts that have emerged in the subsequent 25 years. Since 1997, methodological developments, such as luminescent and fluorescent reporter techniques, have revealed intricate relationships between cellular and network-level mechanisms. In particular, specific neuropeptides such as arginine vasopressin, vasoactive intestinal peptide, and gastrin-releasing peptide have been identified as key players in the synchronization of cellular circadian rhythms within the SCN. The discovery of multiple oscillators governing behavioral and physiological rhythms has significantly advanced our understanding of the circadian clock. The interaction between neurons and glial cells has been found to play a crucial role in regulating these circadian rhythms within the SCN. Furthermore, the properties of the SCN network vary across ontogenetic stages. The application of cell type-specific genetic manipulations has revealed components of the functional input-output system of the SCN and their correlation with physiological functions. This review concludes with the high-risk effort of identifying open questions and challenges that lie ahead.
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Affiliation(s)
- Daisuke Ono
- Stress Recognition and Response, Research Institute of Environmental Medicine, Nagoya University, Nagoya, Japan
- Department of Neural Regulation, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - David R Weaver
- Department of Neurobiology and NeuroNexus Institute, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Michael H Hastings
- Division of Neurobiology, MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Ken-Ichi Honma
- Research and Education Center for Brain Science, Hokkaido University, Sapporo, Japan
- Center for Sleep and Circadian Rhythm Disorders, Sapporo Hanazono Hospital, Sapporo, Japan
| | - Sato Honma
- Research and Education Center for Brain Science, Hokkaido University, Sapporo, Japan
- Center for Sleep and Circadian Rhythm Disorders, Sapporo Hanazono Hospital, Sapporo, Japan
| | - Rae Silver
- Stress Recognition and Response, Research Institute of Environmental Medicine, Nagoya University, Nagoya, Japan
- Department of Neural Regulation, Nagoya University Graduate School of Medicine, Nagoya, Japan
- Department of Neuroscience & Behavior, Barnard College and Department of Psychology, Columbia University, New York City, New York, USA
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3
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Zhang H, Zhou Z, Guo J. The Function, Regulation, and Mechanism of Protein Turnover in Circadian Systems in Neurospora and Other Species. Int J Mol Sci 2024; 25:2574. [PMID: 38473819 DOI: 10.3390/ijms25052574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 02/18/2024] [Accepted: 02/20/2024] [Indexed: 03/14/2024] Open
Abstract
Circadian clocks drive a large array of physiological and behavioral activities. At the molecular level, circadian clocks are composed of positive and negative elements that form core oscillators generating the basic circadian rhythms. Over the course of the circadian period, circadian negative proteins undergo progressive hyperphosphorylation and eventually degrade, and their stability is finely controlled by complex post-translational pathways, including protein modifications, genetic codon preference, protein-protein interactions, chaperon-dependent conformation maintenance, degradation, etc. The effects of phosphorylation on the stability of circadian clock proteins are crucial for precisely determining protein function and turnover, and it has been proposed that the phosphorylation of core circadian clock proteins is tightly correlated with the circadian period. Nonetheless, recent studies have challenged this view. In this review, we summarize the research progress regarding the function, regulation, and mechanism of protein stability in the circadian clock systems of multiple model organisms, with an emphasis on Neurospora crassa, in which circadian mechanisms have been extensively investigated. Elucidation of the highly complex and dynamic regulation of protein stability in circadian clock networks would greatly benefit the integrated understanding of the function, regulation, and mechanism of protein stability in a wide spectrum of other biological processes.
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Affiliation(s)
- Haoran Zhang
- MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Zengxuan Zhou
- MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Jinhu Guo
- MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
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4
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Agriesti F, Cela O, Capitanio N. "Time Is out of Joint" in Pluripotent Stem Cells: How and Why. Int J Mol Sci 2024; 25:2063. [PMID: 38396740 PMCID: PMC10889767 DOI: 10.3390/ijms25042063] [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: 01/10/2024] [Revised: 02/02/2024] [Accepted: 02/06/2024] [Indexed: 02/25/2024] Open
Abstract
The circadian rhythm is necessary for the homeostasis and health of living organisms. Molecular clocks interconnected by transcription/translation feedback loops exist in most cells of the body. A puzzling exemption to this, otherwise, general biological hallmark is given by the cell physiology of pluripotent stem cells (PSCs) that lack circadian oscillations gradually acquired following their in vivo programmed differentiation. This process can be nicely phenocopied following in vitro commitment and reversed during the reprogramming of somatic cells to induce PSCs. The current understanding of how and why pluripotency is "time-uncoupled" is largely incomplete. A complex picture is emerging where the circadian core clockwork is negatively regulated in PSCs at the post-transcriptional/translational, epigenetic, and other-clock-interaction levels. Moreover, non-canonical functions of circadian core-work components in the balance between pluripotency identity and metabolic-driven cell reprogramming are emerging. This review selects and discusses results of relevant recent investigations providing major insights into this context.
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Affiliation(s)
- Francesca Agriesti
- Department of Clinical and Experimental Medicine, University of Foggia, 71122 Foggia, Italy; (O.C.); (N.C.)
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5
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Jiang H, Wang X, Ma J, Xu G. The fine-tuned crosstalk between lysine acetylation and the circadian rhythm. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2023; 1866:194958. [PMID: 37453648 DOI: 10.1016/j.bbagrm.2023.194958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Accepted: 07/03/2023] [Indexed: 07/18/2023]
Abstract
Circadian rhythm is a roughly 24-h wake and sleep cycle that almost all of the organisms on the earth follow when they execute their biological functions and physiological activities. The circadian clock is mainly regulated by the transcription-translation feedback loop (TTFL), consisting of the core clock proteins, including BMAL1, CLOCK, PERs, CRYs, and a series of accessory factors. The circadian clock and the downstream gene expression are not only controlled at the transcriptional and translational levels but also precisely regulated at the post-translational modification level. Recently, it has been discovered that CLOCK exhibits lysine acetyltransferase activities and could acetylate protein substrates. Core clock proteins are also acetylated, thereby altering their biological functions in the regulation of the expression of downstream genes. Studies have revealed that many protein acetylation events exhibit oscillation behavior. However, the biological function of acetylation on circadian rhythm has only begun to explore. This review will briefly introduce the acetylation and deacetylation of the core clock proteins and summarize the proteins whose acetylation is regulated by CLOCK and circadian rhythm. Then, we will also discuss the crosstalk between lysine acetylation and the circadian clock or other post-translational modifications. Finally, we will briefly describe the possible future perspectives in the field.
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Affiliation(s)
- Honglv Jiang
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Suzhou Key Laboratory of Drug Research for Prevention and Treatment of Hyperlipidemic Diseases, Soochow University, Suzhou, Jiangsu 215123, China
| | - Xiaohui Wang
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Suzhou Key Laboratory of Drug Research for Prevention and Treatment of Hyperlipidemic Diseases, Soochow University, Suzhou, Jiangsu 215123, China
| | - Jingjing Ma
- Department of Pharmacy, Medical Center of Soochow University, Dushu Lake Hospital Affiliated to Soochow University, Suzhou, Jiangsu 215123, China.
| | - Guoqiang Xu
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Suzhou Key Laboratory of Drug Research for Prevention and Treatment of Hyperlipidemic Diseases, Soochow University, Suzhou, Jiangsu 215123, China.
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6
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Schmal C, Maier B, Ashwal-Fluss R, Bartok O, Finger AM, Bange T, Koutsouli S, Robles MS, Kadener S, Herzel H, Kramer A. Alternative polyadenylation factor CPSF6 regulates temperature compensation of the mammalian circadian clock. PLoS Biol 2023; 21:e3002164. [PMID: 37379316 DOI: 10.1371/journal.pbio.3002164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 05/15/2023] [Indexed: 06/30/2023] Open
Abstract
A defining property of circadian clocks is temperature compensation, characterized by the resilience of their near 24-hour free-running periods against changes in environmental temperature within the physiological range. While temperature compensation is evolutionary conserved across different taxa of life and has been studied within many model organisms, its molecular underpinnings remain elusive. Posttranscriptional regulations such as temperature-sensitive alternative splicing or phosphorylation have been described as underlying reactions. Here, we show that knockdown of cleavage and polyadenylation specificity factor subunit 6 (CPSF6), a key regulator of 3'-end cleavage and polyadenylation, significantly alters circadian temperature compensation in human U-2 OS cells. We apply a combination of 3'-end-RNA-seq and mass spectrometry-based proteomics to globally quantify changes in 3' UTR length as well as gene and protein expression between wild-type and CPSF6 knockdown cells and their dependency on temperature. Since changes in temperature compensation behavior should be reflected in alterations of temperature responses within one or all of the 3 regulatory layers, we statistically assess differential responses upon changes in ambient temperature between wild-type and CPSF6 knockdown cells. By this means, we reveal candidate genes underlying circadian temperature compensation, including eukaryotic translation initiation factor 2 subunit 1 (EIF2S1).
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Affiliation(s)
- Christoph Schmal
- Institute for Theoretical Biology, Humboldt-Universität zu Berlin and Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Bert Maier
- Laboratory of Chronobiology, Institute for Medical immunology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Reut Ashwal-Fluss
- Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Osnat Bartok
- Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Anna-Marie Finger
- Laboratory of Chronobiology, Institute for Medical immunology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Tanja Bange
- Institute of Medical Psychology, Faculty of Medicine, Ludwig-Maximilians-Universität München, München, Germany
| | - Stella Koutsouli
- Institute of Medical Psychology, Faculty of Medicine, Ludwig-Maximilians-Universität München, München, Germany
| | - Maria S Robles
- Institute of Medical Psychology, Faculty of Medicine, Ludwig-Maximilians-Universität München, München, Germany
| | - Sebastian Kadener
- Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
- Department of Biology, Brandeis University, Waltham, Massachusetts, United States of America
| | - Hanspeter Herzel
- Institute for Theoretical Biology, Humboldt-Universität zu Berlin and Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Achim Kramer
- Laboratory of Chronobiology, Institute for Medical immunology, Charité-Universitätsmedizin Berlin, Berlin, Germany
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7
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Lee K, Lee C. Generation of CRISPR-Cas9-mediated knockin mutant models in mice and MEFs for studies of polymorphism in clock genes. Sci Rep 2023; 13:8109. [PMID: 37208532 DOI: 10.1038/s41598-023-35203-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 05/14/2023] [Indexed: 05/21/2023] Open
Abstract
The creation of mutant mice has been invaluable for advancing biomedical science, but is too time- and resource-intensive for investigating the full range of mutations and polymorphisms. Cell culture models are therefore an invaluable complement to mouse models, especially for cell-autonomous pathways like the circadian clock. In this study, we quantitatively assessed the use of CRISPR to create cell models in mouse embryonic fibroblasts (MEFs) as compared to mouse models. We generated two point mutations in the clock genes Per1 and Per2 in mice and in MEFs using the same sgRNAs and repair templates for HDR and quantified the frequency of the mutations by digital PCR. The frequency was about an order of magnitude higher in mouse zygotes compared to that in MEFs. However, the mutation frequency in MEFs was still high enough for clonal isolation by simple screening of a few dozen individual cells. The Per mutant cells that we generated provide important new insights into the role of the PAS domain in regulating PER phosphorylation, a key aspect of the circadian clock mechanism. Quantification of the mutation frequency in bulk MEF populations provides a valuable basis for optimizing CRISPR protocols and time/resource planning for generating cell models for further studies.
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Affiliation(s)
- Kwangjun Lee
- Program in Neuroscience, Department of Biomedical Sciences, College of Medicine, Florida State University, 1115 West Call Street, Tallahassee, FL, 32306, USA
| | - Choogon Lee
- Program in Neuroscience, Department of Biomedical Sciences, College of Medicine, Florida State University, 1115 West Call Street, Tallahassee, FL, 32306, USA.
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8
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Endogenous circadian reporters reveal functional differences of PERIOD paralogs and the significance of PERIOD:CK1 stable interaction. Proc Natl Acad Sci U S A 2023; 120:e2212255120. [PMID: 36724252 PMCID: PMC9962996 DOI: 10.1073/pnas.2212255120] [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: 02/03/2023] Open
Abstract
Adverse consequences from having a faulty circadian clock include compromised sleep quality and poor performance in the short-term, and metabolic diseases and cancer in the long-term. However, our understanding of circadian disorders is limited by the incompleteness of our molecular models and our dearth of defined mutant models. Because it would be prohibitively expensive to develop live animal models to study the full range of complicated clock mechanisms, we developed PER1-luc and PER2-luc endogenous circadian reporters in a validated clock cell model, U-2 OS, where the genome can be easily manipulated, and functional consequences of mutations can be accurately studied. When major clock genes were knocked out in these cells, circadian rhythms were modulated similarly compared with corresponding mutant mice, validating the platform for genetics studies. Using these reporter cells, we uncovered critical differences between two paralogs of PER. Although PER1 and PER2 are considered redundant and either one can serve as a pacemaker alone, they were dramatically different in biochemical parameters such as stability and phosphorylation kinetics. Consistently, circadian phase was dramatically different between PER1 and PER2 knockout reporter cells. We further showed that the stable binding of casein kinase1δ/ε to PER is not required for PER phosphorylation itself, but is critical for delayed timing of phosphorylation. Our system can be used as an efficient platform to study circadian disorders associated with pathogenic mutations and their underlying molecular mechanisms.
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9
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Katsioudi G, Dreos R, Arpa ES, Gaspari S, Liechti A, Sato M, Gabriel CH, Kramer A, Brown SA, Gatfield D. A conditional Smg6 mutant mouse model reveals circadian clock regulation through the nonsense-mediated mRNA decay pathway. SCIENCE ADVANCES 2023; 9:eade2828. [PMID: 36638184 PMCID: PMC9839329 DOI: 10.1126/sciadv.ade2828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 12/15/2022] [Indexed: 06/17/2023]
Abstract
Nonsense-mediated messenger RNA (mRNA) decay (NMD) has been intensively studied as a surveillance pathway that degrades erroneous transcripts arising from mutations or RNA processing errors. While additional roles in physiological control of mRNA stability have emerged, possible functions in mammalian physiology in vivo remain unclear. Here, we created a conditional mouse allele that allows converting the NMD effector nuclease SMG6 from wild-type to nuclease domain-mutant protein. We find that NMD down-regulation affects the function of the circadian clock, a system known to require rapid mRNA turnover. Specifically, we uncover strong lengthening of free-running circadian periods for liver and fibroblast clocks and direct NMD regulation of Cry2 mRNA, encoding a key transcriptional repressor within the rhythm-generating feedback loop. Transcriptome-wide changes in daily mRNA accumulation patterns in the entrained liver, as well as an altered response to food entrainment, expand the known scope of NMD regulation in mammalian gene expression and physiology.
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Affiliation(s)
- Georgia Katsioudi
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - René Dreos
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Enes S. Arpa
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Sevasti Gaspari
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Angelica Liechti
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Miho Sato
- Chronobiology and Sleep Research Group, Institute of Pharmacology and Toxicology, University of Zürich, Zürich, Switzerland
| | - Christian H. Gabriel
- Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Laboratory of Chronobiology, Berlin, Germany
| | - Achim Kramer
- Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Laboratory of Chronobiology, Berlin, Germany
| | - Steven A. Brown
- Chronobiology and Sleep Research Group, Institute of Pharmacology and Toxicology, University of Zürich, Zürich, Switzerland
| | - David Gatfield
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
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10
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Gao D, Ma T, Gao L, Zhang J, Zhang H, Zhang L, Dong H, Li Y, Zhao L, Liu W, Zhao H, Li D, Zhou D, Wang A, Jin Y, Chen H. Autophagy activation attenuates the circadian clock oscillators in U2OS cells via the ATG5 pathway. Cell Signal 2023; 101:110502. [PMID: 36280090 DOI: 10.1016/j.cellsig.2022.110502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 09/30/2022] [Accepted: 10/17/2022] [Indexed: 11/28/2022]
Abstract
The circadian clock and autophagy are essential biological mechanisms involved in regulating many physiological processes. Accumulating evidence has revealed that autophagic activity is regulated by the circadian clock system. However, whether autophagy regulates the circadian clock system remains unclear. In this study, rapamycin and AICAR, two classical activators of autophagy, were used to create autophagy activation models in BMAL1-dLuc U2OS cell line. The results showed that the mRNA expression of MAP1LC3B and ATG5 were significantly upregulated after autophagy activation, whereas the mRNA expression of circadian clock genes (BMAL1, PER2, REV-ERBα, and DBP) were significantly decreased. Consistent with these data, the relative ratio of LC3-II/LC3-I and the protein level of ATG5 were increased after rapamycin or AICAR treatment. In contrast, BMAL1 and REV-ERBα levels were decreased. Notably, the mRNA expression of circadian clock genes (BMAL1, PER2, REV-ERBα, and DBP) and autophagy-related genes (MAP1LC3B and ATG5) showed rhythmic expression patterns in both untreated and rapamycin/AICAR-treated U2OS cells. Moreover, the autophagy inhibitor 3-methyladenine partially reversed the inhibitory effects of autophagy on circadian clock genes expression and BMAL1-Luc oscillations. Another critical finding was that ATG5 knockout alleviates the inhibitory effect of rapamycin-mediated autophagy activation on the circadian clock oscillators in U2OS cells. Collectively, our data indicate that autophagy activation attenuates the circadian clock oscillators in U2OS cells via the ATG5 pathway.
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Affiliation(s)
- Dengke Gao
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling 712100, Shaanxi, China; Key Laboratory of Animal Biotechnology of the Ministry of Agriculture and Rural Affairs, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Tiantian Ma
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling 712100, Shaanxi, China; Key Laboratory of Animal Biotechnology of the Ministry of Agriculture and Rural Affairs, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Lei Gao
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling 712100, Shaanxi, China; Key Laboratory of Animal Biotechnology of the Ministry of Agriculture and Rural Affairs, Northwest A&F University, Yangling 712100, Shaanxi, China; College of Agriculture and Animal Husbandry, Qing Hai University, Xining, Qinghai, China
| | - Jing Zhang
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling 712100, Shaanxi, China; Key Laboratory of Animal Biotechnology of the Ministry of Agriculture and Rural Affairs, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Haisen Zhang
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling 712100, Shaanxi, China; Key Laboratory of Animal Biotechnology of the Ministry of Agriculture and Rural Affairs, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Linlin Zhang
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling 712100, Shaanxi, China; Key Laboratory of Animal Biotechnology of the Ministry of Agriculture and Rural Affairs, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Hao Dong
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling 712100, Shaanxi, China; Key Laboratory of Animal Biotechnology of the Ministry of Agriculture and Rural Affairs, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Yating Li
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling 712100, Shaanxi, China; Key Laboratory of Animal Biotechnology of the Ministry of Agriculture and Rural Affairs, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Lijia Zhao
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling 712100, Shaanxi, China; Key Laboratory of Animal Biotechnology of the Ministry of Agriculture and Rural Affairs, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Wei Liu
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling 712100, Shaanxi, China; Key Laboratory of Animal Biotechnology of the Ministry of Agriculture and Rural Affairs, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Hongcong Zhao
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling 712100, Shaanxi, China; Key Laboratory of Animal Biotechnology of the Ministry of Agriculture and Rural Affairs, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Dan Li
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling 712100, Shaanxi, China; Key Laboratory of Animal Biotechnology of the Ministry of Agriculture and Rural Affairs, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Dong Zhou
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling 712100, Shaanxi, China; Key Laboratory of Animal Biotechnology of the Ministry of Agriculture and Rural Affairs, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Aihua Wang
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture and Rural Affairs, Northwest A&F University, Yangling 712100, Shaanxi, China; Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Yaping Jin
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling 712100, Shaanxi, China; Key Laboratory of Animal Biotechnology of the Ministry of Agriculture and Rural Affairs, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Huatao Chen
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling 712100, Shaanxi, China; Key Laboratory of Animal Biotechnology of the Ministry of Agriculture and Rural Affairs, Northwest A&F University, Yangling 712100, Shaanxi, China.
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11
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Kelliher CM, Stevenson EL, Loros JJ, Dunlap JC. Nutritional compensation of the circadian clock is a conserved process influenced by gene expression regulation and mRNA stability. PLoS Biol 2023; 21:e3001961. [PMID: 36603054 PMCID: PMC9848017 DOI: 10.1371/journal.pbio.3001961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 01/18/2023] [Accepted: 12/15/2022] [Indexed: 01/06/2023] Open
Abstract
Compensation is a defining principle of a true circadian clock, where its approximately 24-hour period length is relatively unchanged across environmental conditions. Known compensation effectors directly regulate core clock factors to buffer the oscillator's period length from variables in the environment. Temperature Compensation mechanisms have been experimentally addressed across circadian model systems, but much less is known about the related process of Nutritional Compensation, where circadian period length is maintained across physiologically relevant nutrient levels. Using the filamentous fungus Neurospora crassa, we performed a genetic screen under glucose and amino acid starvation conditions to identify new regulators of Nutritional Compensation. Our screen uncovered 16 novel mutants, and together with 4 mutants characterized in prior work, a model emerges where Nutritional Compensation of the fungal clock is achieved at the levels of transcription, chromatin regulation, and mRNA stability. However, eukaryotic circadian Nutritional Compensation is completely unstudied outside of Neurospora. To test for conservation in cultured human cells, we selected top hits from our fungal genetic screen, performed siRNA knockdown experiments of the mammalian orthologs, and characterized the cell lines with respect to compensation. We find that the wild-type mammalian clock is also compensated across a large range of external glucose concentrations, as observed in Neurospora, and that knocking down the mammalian orthologs of the Neurospora compensation-associated genes CPSF6 or SETD2 in human cells also results in nutrient-dependent period length changes. We conclude that, like Temperature Compensation, Nutritional Compensation is a conserved circadian process in fungal and mammalian clocks and that it may share common molecular determinants.
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Affiliation(s)
- Christina M. Kelliher
- Department of Molecular & Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, United States of America
- Department of Biology, University of Massachusetts Boston, Boston, Massachusetts, United States of America
| | - Elizabeth-Lauren Stevenson
- Department of Molecular & Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, United States of America
| | - Jennifer J. Loros
- Department of Biochemistry & Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, United States of America
| | - Jay C. Dunlap
- Department of Molecular & Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, United States of America
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12
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Sun C, Li C, Liu W, Schiöth HB. Generation of Endogenous Promoter-Driven Luciferase Reporter System Using CRISPR/Cas9 for Investigating Transcriptional Regulation of the Core Clock Gene BMAL1. Biomedicines 2022; 10:biomedicines10123108. [PMID: 36551864 PMCID: PMC9775583 DOI: 10.3390/biomedicines10123108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 11/22/2022] [Accepted: 11/28/2022] [Indexed: 12/04/2022] Open
Abstract
Humans and other organisms are continuously exposed to thousands of chemicals through the atmosphere, drinking water, food, or direct contact. A large proportion of such chemicals are present in very low concentrations and may have synergistic effects, even at their no-observed-adverse-effect level (NOAEL). Complex mixtures of contaminants are very difficult to assess by traditional toxicological methods. There is increasing attention on how different pollutants induce adverse physiological functions in the human body through effects on the circadian rhythm. However, it is very difficult to screen for compounds with circadian-rhythm-disrupting effects from a large number of chemicals or their complex mixtures. We established a stable firefly luciferase reporter gene knock-in U2-OS cell line by CRISPR/Cas9 to screen circadian-rhythm-disrupting pollutants. The luciferase gene was inserted downstream of the core clock gene BMAL1 and controlled by an endogenous promoter. Compared to detection systems using exogenous promoters, these cells enable the detection of compounds that interfere with the circadian rhythm system mediated by BMAL1 gene expression. The U2-OS knock-in cells showed BMAL1 and luciferase activity had parallel changes when treated with BMAL1 inhibitor and activator. Furthermore, the luciferase reporter gene has high sensitivity and is faster and more cost-effective than classic toxicology methods. The knock-in cell line can be used for high-throughput and efficient screening of circadian-rhythm-disrupting chemicals such as drugs and pollutants.
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Affiliation(s)
- Chengxi Sun
- Department of Surgical Sciences, Uppsala University, 751 24 Uppsala, Sweden
- Department of Clinical Laboratory, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Chen Li
- Department of Medical Biochemistry and Microbiology, Uppsala University, 752 36 Uppsala, Sweden
| | - Wen Liu
- Department of Surgical Sciences, Uppsala University, 751 24 Uppsala, Sweden
| | - Helgi B. Schiöth
- Department of Surgical Sciences, Uppsala University, 751 24 Uppsala, Sweden
- Correspondence:
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13
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Gul S, Akyel YK, Gul ZM, Isin S, Ozcan O, Korkmaz T, Selvi S, Danis I, Ipek OS, Aygenli F, Taskin AC, Akarlar BA, Ozlu N, Ozturk N, Ozturk N, Ünal DÖ, Guzel M, Turkay M, Okyar A, Kavakli IH. Discovery of a small molecule that selectively destabilizes Cryptochrome 1 and enhances life span in p53 knockout mice. Nat Commun 2022; 13:6742. [PMID: 36347873 PMCID: PMC9643396 DOI: 10.1038/s41467-022-34582-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Accepted: 10/31/2022] [Indexed: 11/09/2022] Open
Abstract
Cryptochromes are negative transcriptional regulators of the circadian clock in mammals. It is not clear how reducing the level of endogenous CRY1 in mammals will affect circadian rhythm and the relation of such a decrease with apoptosis. Here, we discovered a molecule (M47) that destabilizes Cryptochrome 1 (CRY1) both in vitro and in vivo. The M47 selectively enhanced the degradation rate of CRY1 by increasing its ubiquitination and resulted in increasing the circadian period length of U2OS Bmal1-dLuc cells. In addition, subcellular fractionation studies from mice liver indicated that M47 increased degradation of the CRY1 in the nucleus. Furthermore, M47-mediated CRY1 reduction enhanced oxaliplatin-induced apoptosis in Ras-transformed p53 null fibroblast cells. Systemic repetitive administration of M47 increased the median lifespan of p53-/- mice by ~25%. Collectively our data suggest that M47 is a promising molecule to treat forms of cancer depending on the p53 mutation.
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Affiliation(s)
- Seref Gul
- grid.15876.3d0000000106887552Department of Chemical and Biological Engineering, Koc University, 34450 Sariyer-Istanbul, Turkey ,grid.9601.e0000 0001 2166 6619Present Address: Department of Biology, Biotechnology Division, İstanbul University, TR-34116 Beyazit-Istanbul, Turkey
| | - Yasemin Kubra Akyel
- grid.9601.e0000 0001 2166 6619Faculty of Pharmacy, Department of Pharmacology, İstanbul University, TR-34116 Beyazit-Istanbul, Turkey ,grid.411781.a0000 0004 0471 9346Present Address: School of Medicine, Department of Medical Pharmacology, Istanbul Medipol University, Istanbul, Turkey
| | - Zeynep Melis Gul
- grid.15876.3d0000000106887552Department of Molecular Biology and Genetics, Koc University, İstanbul, Turkey
| | - Safak Isin
- grid.15876.3d0000000106887552Department of Molecular Biology and Genetics, Koc University, İstanbul, Turkey
| | - Onur Ozcan
- grid.15876.3d0000000106887552Department of Molecular Biology and Genetics, Koc University, İstanbul, Turkey
| | - Tuba Korkmaz
- grid.448834.70000 0004 0595 7127Department of Molecular Biology and Genetics, Gebze Technical University, Gebze, 41400 Kocaeli, Turkey
| | - Saba Selvi
- grid.448834.70000 0004 0595 7127Department of Molecular Biology and Genetics, Gebze Technical University, Gebze, 41400 Kocaeli, Turkey
| | - Ibrahim Danis
- grid.9601.e0000 0001 2166 6619Faculty of Pharmacy, Department of Analytical Chemistry, İstanbul University, TR-34116 Beyazit-Istanbul, Turkey ,grid.9601.e0000 0001 2166 6619İstanbul University Drug Research and Application Center (ILAM), TR-34116 Beyazıt-Istanbul, Turkey
| | - Ozgecan Savlug Ipek
- grid.411781.a0000 0004 0471 9346Regenerative and Restorative Medicine Research Center (REMER), İstanbul Medipol University, Kavacik Campus, Kavacik-Beykoz/Istanbul, 34810 Turkey ,grid.38575.3c0000 0001 2337 3561Department of Chemistry, Graduate School of Natural and Applied Sciences, Yildiz Technical University, Besiktas/Istanbul, 34349 Turkey
| | - Fatih Aygenli
- grid.448834.70000 0004 0595 7127Department of Molecular Biology and Genetics, Gebze Technical University, Gebze, 41400 Kocaeli, Turkey
| | - Ali Cihan Taskin
- grid.15876.3d0000000106887552Animal Research Facility, Research Center for Translational Medicine, Koc University, Rumelifeneri yolu, 34450 Sariyer-Istanbul, Turkey
| | - Büşra Aytül Akarlar
- grid.15876.3d0000000106887552Department of Molecular Biology and Genetics, Koc University, İstanbul, Turkey
| | - Nurhan Ozlu
- grid.15876.3d0000000106887552Department of Molecular Biology and Genetics, Koc University, İstanbul, Turkey
| | - Nuri Ozturk
- grid.448834.70000 0004 0595 7127Department of Molecular Biology and Genetics, Gebze Technical University, Gebze, 41400 Kocaeli, Turkey
| | - Narin Ozturk
- grid.9601.e0000 0001 2166 6619Faculty of Pharmacy, Department of Pharmacology, İstanbul University, TR-34116 Beyazit-Istanbul, Turkey
| | - Durişehvar Özer Ünal
- grid.9601.e0000 0001 2166 6619Faculty of Pharmacy, Department of Analytical Chemistry, İstanbul University, TR-34116 Beyazit-Istanbul, Turkey ,grid.9601.e0000 0001 2166 6619İstanbul University Drug Research and Application Center (ILAM), TR-34116 Beyazıt-Istanbul, Turkey
| | - Mustafa Guzel
- grid.411781.a0000 0004 0471 9346Regenerative and Restorative Medicine Research Center (REMER), İstanbul Medipol University, Kavacik Campus, Kavacik-Beykoz/Istanbul, 34810 Turkey ,grid.411781.a0000 0004 0471 9346International School of Medicine, Department of Medical Pharmacology, Kavacik Campus, İstanbul Medipol University, Kavacik-Beykoz/Istanbul, 34810 Turkey
| | - Metin Turkay
- grid.15876.3d0000000106887552Department of Industrial Engineering, Koc University, Istanbul, Turkey
| | - Alper Okyar
- grid.9601.e0000 0001 2166 6619Faculty of Pharmacy, Department of Pharmacology, İstanbul University, TR-34116 Beyazit-Istanbul, Turkey
| | - Ibrahim Halil Kavakli
- grid.15876.3d0000000106887552Department of Chemical and Biological Engineering, Koc University, 34450 Sariyer-Istanbul, Turkey ,grid.15876.3d0000000106887552Department of Molecular Biology and Genetics, Koc University, İstanbul, Turkey
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14
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CRY2 isoform selectivity of a circadian clock modulator with antiglioblastoma efficacy. Proc Natl Acad Sci U S A 2022; 119:e2203936119. [PMID: 36161947 PMCID: PMC9546630 DOI: 10.1073/pnas.2203936119] [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: 11/18/2022] Open
Abstract
The mammalian cryptochrome isoforms, CRY1 and CRY2, are core circadian clock regulators that work redundantly. Recent studies revealed distinct roles of these closely related homologs in clock output pathways. Isoform-selective control of CRY1 and CRY2 is critical for further understanding their redundant and distinct roles. KL001 was the first identified small-molecule CRY modulator that activates both CRY1 and CRY2. SHP656 is an orally available KL001 derivative and has shown efficacy in blood glucose control and inhibition of glioblastoma stem cell (GSC) growth in animal models. However, CRY isoform selectivity of SHP656 was uncharacterized, limiting understanding of the roles of CRY1 and CRY2. Here, we report the elucidation of CRY2 selectivity of SHP656. SHP656 lengthened cellular circadian period in a CRY2-dependent manner and selectively interacted with CRY2. By determining the X-ray crystal structure of CRY2 in complex with SHP656 and performing molecular dynamics simulations, we elucidated compound interaction mechanisms. SHP656 binding was compatible with the intrinsic CRY2 gatekeeper W417 "in" orientation and also a close "further in" conformation. Perturbation of W417 interaction with the lid loop resulted in a reduced effect of SHP656 on CRY2, supporting an important role of gatekeeper orientation in isoform selectivity. We also identified the R form of SHP656 (called SHP1703) as the active isomer. Treatment with SHP1703 effectively reduced GSC viability. Our results suggest a direct role of CRY2 in glioblastoma antitumorigenesis and provide a rationale for the selective modulation of CRY isoforms in the therapeutic treatment of glioblastoma and other circadian clock-related diseases.
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15
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An Y, Yuan B, Xie P, Gu Y, Liu Z, Wang T, Li Z, Xu Y, Liu Y. Decoupling PER phosphorylation, stability and rhythmic expression from circadian clock function by abolishing PER-CK1 interaction. Nat Commun 2022; 13:3991. [PMID: 35810166 PMCID: PMC9271041 DOI: 10.1038/s41467-022-31715-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 06/29/2022] [Indexed: 11/09/2022] Open
Abstract
Robust rhythms of abundances and phosphorylation profiles of PERIOD proteins were thought be the master rhythms that drive mammalian circadian clock functions. PER stability was proposed to be a major determinant of period length. In mammals, CK1 forms stable complexes with PER. Here we identify the PER residues essential for PER-CK1 interaction. In cells and in mice, their mutation abolishes PER phosphorylation and CLOCK hyperphosphorylation, resulting in PER stabilization, arrhythmic PER abundance and impaired negative feedback process, indicating that PER acts as the CK1 scaffold in circadian feedback mechanism. Surprisingly, the mutant mice exhibit robust short period locomotor activity and other physiological rhythms but low amplitude molecular rhythms. PER-CK1 interaction has two opposing roles in regulating CLOCK-BMAL1 activity. These results indicate that the circadian clock can function independently of PER phosphorylation and abundance rhythms due to another PER-CRY-dependent feedback mechanism and that period length can be uncoupled from PER stability.
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Affiliation(s)
- Yang An
- Model Animal Research Center, Nanjing University, 12 Xuefu Road, Pukou District, Nanjing, 210061, China.,Cambridge-Su Genomic Resource Center, Soochow University, Suzhou, Jiangsu, 215123, China
| | - Baoshi Yuan
- Cambridge-Su Genomic Resource Center, Soochow University, Suzhou, Jiangsu, 215123, China
| | - Pancheng Xie
- Cambridge-Su Genomic Resource Center, Soochow University, Suzhou, Jiangsu, 215123, China.,Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Yue Gu
- Cambridge-Su Genomic Resource Center, Soochow University, Suzhou, Jiangsu, 215123, China
| | - Zhiwei Liu
- Cambridge-Su Genomic Resource Center, Soochow University, Suzhou, Jiangsu, 215123, China
| | - Tao Wang
- Cambridge-Su Genomic Resource Center, Soochow University, Suzhou, Jiangsu, 215123, China
| | - Zhihao Li
- Cambridge-Su Genomic Resource Center, Soochow University, Suzhou, Jiangsu, 215123, China
| | - Ying Xu
- Cambridge-Su Genomic Resource Center, Soochow University, Suzhou, Jiangsu, 215123, China.
| | - Yi Liu
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
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16
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Srimani S, Schmidt CX, Gómez-Serranillos MP, Oster H, Divakar PK. Modulation of Cellular Circadian Rhythms by Secondary Metabolites of Lichens. Front Cell Neurosci 2022; 16:907308. [PMID: 35813500 PMCID: PMC9260025 DOI: 10.3389/fncel.2022.907308] [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: 04/08/2022] [Accepted: 05/20/2022] [Indexed: 12/14/2022] Open
Abstract
Background Most mammalian cells harbor molecular circadian clocks that synchronize physiological functions with the 24-h day-night cycle. Disruption of circadian rhythms, through genetic or environmental changes, promotes the development of disorders like obesity, cardiovascular diseases, and cancer. At the cellular level, circadian, mitotic, and redox cycles are functionally coupled. Evernic (EA) and usnic acid (UA), two lichen secondary metabolites, show various pharmacological activities including anti-oxidative, anti-inflammatory, and neuroprotective action. All these effects have likewise been associated with a functional circadian clock. Hypothesis/Purpose To test, if the lichen compounds EA and UA modulate circadian clock function at the cellular level. Methods We used three different cell lines and two circadian luminescence reporter systems for evaluating dose- and time-dependent effects of EA/UA treatment on cellular clock regulation at high temporal resolution. Output parameters studied were circadian luminescence rhythm period, amplitude, phase, and dampening rate. Results Both compounds had marked effects on clock rhythm amplitudes and dampening independent of cell type, with UA generally showing a higher efficiency than EA. Only in fibroblast cells, significant effects on clock period were observed for UA treated cells showing shorter and EA treated cells showing longer period lengths. Transient treatment of mouse embryonic fibroblasts at different phases had only minor clock resetting effects for both compounds. Conclusion Secondary metabolites of lichen alter cellular circadian clocks through amplitude reduction and increased rhythm dampening.
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Affiliation(s)
- Soumi Srimani
- Institute of Neurobiology, Center of Brain, Behavior & Metabolism (CBBM), University of Lübeck, Lübeck, Germany
- Department of Pharmacology, Pharmacognosy and Botany, Faculty of Pharmacy, Complutense University of Madrid, Madrid, Spain
| | - Cosima Xenia Schmidt
- Institute of Neurobiology, Center of Brain, Behavior & Metabolism (CBBM), University of Lübeck, Lübeck, Germany
| | - Maria Pilar Gómez-Serranillos
- Department of Pharmacology, Pharmacognosy and Botany, Faculty of Pharmacy, Complutense University of Madrid, Madrid, Spain
| | - Henrik Oster
- Institute of Neurobiology, Center of Brain, Behavior & Metabolism (CBBM), University of Lübeck, Lübeck, Germany
| | - Pradeep K. Divakar
- Department of Pharmacology, Pharmacognosy and Botany, Faculty of Pharmacy, Complutense University of Madrid, Madrid, Spain
- *Correspondence: Pradeep K. Divakar
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17
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Mammalian PERIOD2 regulates H2A.Z incorporation in chromatin to orchestrate circadian negative feedback. Nat Struct Mol Biol 2022; 29:549-562. [PMID: 35606517 DOI: 10.1038/s41594-022-00777-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 04/11/2022] [Indexed: 11/08/2022]
Abstract
Mammalian circadian oscillators are built on a feedback loop in which the activity of the transcription factor CLOCK-BMAL1 is repressed by the PER-CRY complex. Here, we show that murine Per-/- fibroblasts display aberrant nucleosome occupancy around transcription start sites (TSSs) and at promoter-proximal and distal CTCF sites due to impaired histone H2A.Z deposition. Knocking out H2A.Z mimicked the Per null chromatin state and disrupted cellular rhythms. We found that endogenous mPER2 complexes retained CTCF as well as the specific H2A.Z-deposition chaperone YL1-a component of the ATP-dependent remodeler SRCAP and p400-TIP60 complex. While depleting YL1 or mutating chaperone-binding sites on H2A.Z lengthened the circadian period, H2A.Z deletion abrogated BMAL1 chromatin recruitment and promoted its proteasomal degradation. We propose that a PER2-mediated H2A.Z deposition pathway (1) compacts CLOCK-BMAL1 binding sites to establish negative feedback, (2) organizes circadian chromatin landscapes using CTCF and (3) bookmarks genomic loci for BMAL1 binding to impinge on the positive arm of the subsequent cycle.
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18
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Abdo AN, Rintisch C, Gabriel CH, Kramer A. Mutational scanning identified amino acids of the CLOCK exon 19-domain essential for circadian rhythms. Acta Physiol (Oxf) 2022; 234:e13794. [PMID: 35112498 DOI: 10.1111/apha.13794] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 01/28/2022] [Accepted: 01/29/2022] [Indexed: 12/21/2022]
Abstract
AIM In the mammalian circadian clock, the CLOCK/BMAL1 heterodimer binds to E-box enhancer elements in the promoters of its target genes to activate transcription. The classical Clock mice, the first circadian mouse mutant discovered, are behaviourally arrhythmic. In this mutant, CLOCK lacks a 51 amino acid domain corresponding to exon 19 (CLOCKΔ19), which is required for normal transactivation. While the importance of this CLOCK domain for circadian rhythms is well established, the exact molecular mechanism is still unclear. METHODS Using CRISPR/Cas9 technology, we created a CLOCK knockout - CLOCK rescue system in human circadian reporter cells and performed systematic mutational scanning to assess the functionality of individual amino acids within the CLOCK exon 19-domain. RESULTS CLOCK knockout cells were arrhythmic, and circadian rhythms could be rescued by introducing wild-type CLOCK, but not CLOCKΔ19. In addition, we identified several residues, whose mutation failed to rescue rhythms in CLOCK knockout cells. Many of these are part of the hydrophobic binding interface of the predicted dimer of the CLOCK exon 19-domain. CONCLUSION Our data not only indicate that CLOCK/BMAL1 oligomerization mediated by the exon 19-domain is important for circadian dynamics but also suggest that the exon 19-domain provides a platform for binding coactivators and repressors, which in turn is required for normal circadian rhythms.
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Affiliation(s)
- Ashraf N Abdo
- Laboratory of Chronobiology, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Carola Rintisch
- Laboratory of Chronobiology, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Christian H Gabriel
- Laboratory of Chronobiology, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Achim Kramer
- Laboratory of Chronobiology, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Charité-Universitätsmedizin Berlin, Berlin, Germany
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19
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Minami Y, Yuan Y, Ueda HR. High-throughput Genetically Modified Animal Experiments Achieved by Next-generation Mammalian Genetics. J Biol Rhythms 2022; 37:135-151. [PMID: 35137623 DOI: 10.1177/07487304221075002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Animal models are essential tools for modern scientists to conduct biological experiments and investigate their hypotheses in vivo. However, for the past decade, raising the throughput of such animal experiments has been a great challenge. Conventionally, in vivo high-throughput assay was achieved through large-scale mutagen-driven forward genetic screening, which took years to find causal genes. In contrast, reverse genetics accelerated the causal gene identification process, but its throughput was also limited by 2 barriers, that is, the genome modification step and the time-consuming crossing step. Defined as genetics without crossing, next-generation genetics is able to produce gene-modified animals that can be analyzed at the founder generation (F0). This method is or can be accomplished through recent technological advances in gene editing and virus-based efficient gene modifications. Notably, next-generation genetics has accelerated the process of cross-species studies, and it will be a useful technique during animal experiments as it can provide genetic perturbation at an individual level without crossing. In this review, we begin by introducing the history of animal-based high-throughput analysis, with a specific focus on chronobiology. We then describe ways that gene modification efficiency during animal experiments was enhanced and why crossing remained a barrier to reaching higher efficiency. Moreover, we mention the Triple CRISPR as a critical technique for achieving next-generation genetics. Finally, we discuss the potential applications and limitations of next-generation mammalian genetics.
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Affiliation(s)
- Yoichi Minami
- Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yufei Yuan
- Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Hiroki R Ueda
- Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research, Suita, Japan
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20
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Finger AM. In Vitro Assays for Measuring Intercellular Coupling Among Peripheral Circadian Oscillators. Methods Mol Biol 2022; 2482:153-167. [PMID: 35610425 DOI: 10.1007/978-1-0716-2249-0_10] [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] [Indexed: 06/15/2023]
Abstract
Circadian clocks can be found in nearly all eukaryotic organisms, as well as certain bacterial strains, including commensal microbiota. Exploring intercellular coupling among cell-autonomous circadian oscillators is crucial for understanding how cellular ensembles generate and sustain coherent circadian rhythms on the tissue level, and thus, rhythmic organ functions. Here we describe a protocol for studying intercellular coupling among peripheral circadian oscillators using three-dimensional spheroid cultures in order to measure coupling strength within peripheral clock networks. We use cell spheroids to simulate in vivo tissue integrity, as well as to increase complexity of cell-cell interactions and the abundance of potential coupling factors. Circadian rhythms are monitored using live-cell imaging of spheroids equipped with circadian reporters over several days.
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Affiliation(s)
- Anna-Marie Finger
- Charité Universitätsmedizin Berlin, Institute for Medical Immunology, Laboratory of Chronobiology, Berlin, Germany.
- Freie Universität Berlin, Berlin, Germany.
- Humboldt-Universität zu Berlin, Berlin, Germany.
- Berlin Institute of Health (BIH), Berlin, Germany.
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21
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Krahmer J, Hindle M, Perby LK, Mogensen HK, Nielsen TH, Halliday KJ, VanOoijen G, LeBihan T, Millar AJ. The circadian clock gene circuit controls protein and phosphoprotein rhythms in Arabidopsis thaliana. Mol Cell Proteomics 2021; 21:100172. [PMID: 34740825 PMCID: PMC8733343 DOI: 10.1016/j.mcpro.2021.100172] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 09/27/2021] [Accepted: 11/01/2021] [Indexed: 11/29/2022] Open
Abstract
Twenty-four-hour, circadian rhythms control many eukaryotic mRNA levels, whereas the levels of their more stable proteins are not expected to reflect the RNA rhythms, emphasizing the need to test the circadian regulation of protein abundance and modification. Here we present circadian proteomic and phosphoproteomic time series from Arabidopsis thaliana plants under constant light conditions, estimating that just 0.4% of quantified proteins but a much larger proportion of quantified phospho-sites were rhythmic. Approximately half of the rhythmic phospho-sites were most phosphorylated at subjective dawn, a pattern we term the “phospho-dawn.” Members of the SnRK/CDPK family of protein kinases are candidate regulators. A CCA1-overexpressing line that disables the clock gene circuit lacked most circadian protein phosphorylation. However, the few phospho-sites that fluctuated despite CCA1-overexpression still tended to peak in abundance close to subjective dawn, suggesting that the canonical clock mechanism is necessary for most but perhaps not all protein phosphorylation rhythms. To test the potential functional relevance of our datasets, we conducted phosphomimetic experiments using the bifunctional enzyme fructose-6-phosphate-2-kinase/phosphatase (F2KP), as an example. The rhythmic phosphorylation of diverse protein targets is controlled by the clock gene circuit, implicating posttranslational mechanisms in the transmission of circadian timing information in plants. Circadian (phospho)proteomics time courses of plants with or without functional clock. Most protein abundance/phosphorylation rhythms require a transcriptional oscillator. The majority of rhythmic phosphosites peak around subjective dawn (“phospho-dawn”). A phosphorylated serine of the metabolic enzyme F2KP has functional relevance.
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Affiliation(s)
- Johanna Krahmer
- SynthSys and School of Biological Sciences, CH Waddington Building, Max Born Crescent, Kings Buildings, University of Edinburgh, Edinburgh, EH9 3BF, United Kingdom; Institute for Molecular Plant Science, School of Biological Sciences, Daniel Rutherford Building, Building, Max Born Crescent, Kings Buildings, University of Edinburgh, Edinburgh, EH9 3BF, United Kingdom.
| | - Matthew Hindle
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, Easter Bush, Edinburgh, EH25 9RG, United Kingdom
| | - Laura K Perby
- Department of Plant and Environmental Sciences, University of Copenhagen, Section for Molecular Plant Biology, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Denmark
| | - Helle K Mogensen
- Department of Plant and Environmental Sciences, University of Copenhagen, Section for Molecular Plant Biology, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Denmark
| | - Tom H Nielsen
- Department of Plant and Environmental Sciences, University of Copenhagen, Section for Molecular Plant Biology, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Denmark
| | - Karen J Halliday
- Institute for Molecular Plant Science, School of Biological Sciences, Daniel Rutherford Building, Building, Max Born Crescent, Kings Buildings, University of Edinburgh, Edinburgh, EH9 3BF, United Kingdom
| | - Gerben VanOoijen
- Institute for Molecular Plant Science, School of Biological Sciences, Daniel Rutherford Building, Building, Max Born Crescent, Kings Buildings, University of Edinburgh, Edinburgh, EH9 3BF, United Kingdom
| | - Thierry LeBihan
- SynthSys and School of Biological Sciences, CH Waddington Building, Max Born Crescent, Kings Buildings, University of Edinburgh, Edinburgh, EH9 3BF, United Kingdom
| | - Andrew J Millar
- SynthSys and School of Biological Sciences, CH Waddington Building, Max Born Crescent, Kings Buildings, University of Edinburgh, Edinburgh, EH9 3BF, United Kingdom.
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22
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Healy KL, Morris AR, Liu AC. Circadian Synchrony: Sleep, Nutrition, and Physical Activity. FRONTIERS IN NETWORK PHYSIOLOGY 2021; 1:732243. [PMID: 35156088 PMCID: PMC8830366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 09/20/2021] [Indexed: 11/11/2022]
Abstract
The circadian clock in mammals regulates the sleep/wake cycle and many associated behavioral and physiological processes. The cellular clock mechanism involves a transcriptional negative feedback loop that gives rise to circadian rhythms in gene expression with an approximately 24-h periodicity. To maintain system robustness, clocks throughout the body must be synchronized and their functions coordinated. In mammals, the master clock is located in the suprachiasmatic nucleus (SCN) of the hypothalamus. The SCN is entrained to the light/dark cycle through photic signal transduction and subsequent induction of core clock gene expression. The SCN in turn relays the time-of-day information to clocks in peripheral tissues. While the SCN is highly responsive to photic cues, peripheral clocks are more sensitive to non-photic resetting cues such as nutrients, body temperature, and neuroendocrine hormones. For example, feeding/fasting and physical activity can entrain peripheral clocks through signaling pathways and subsequent regulation of core clock genes and proteins. As such, timing of food intake and physical activity matters. In an ideal world, the sleep/wake and feeding/fasting cycles are synchronized to the light/dark cycle. However, asynchronous environmental cues, such as those experienced by shift workers and frequent travelers, often lead to misalignment between the master and peripheral clocks. Emerging evidence suggests that the resulting circadian disruption is associated with various diseases and chronic conditions that cause further circadian desynchrony and accelerate disease progression. In this review, we discuss how sleep, nutrition, and physical activity synchronize circadian clocks and how chronomedicine may offer novel strategies for disease intervention.
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Affiliation(s)
| | | | - Andrew C. Liu
- Department of Physiology and Functional Genomics, University of Florida College of Medicine, Gainesville, FL, United States
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Healy KL, Morris AR, Liu AC. Circadian Synchrony: Sleep, Nutrition, and Physical Activity. FRONTIERS IN NETWORK PHYSIOLOGY 2021; 1:732243. [PMID: 35156088 PMCID: PMC8830366 DOI: 10.3389/fnetp.2021.732243] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 09/20/2021] [Indexed: 08/01/2023]
Abstract
The circadian clock in mammals regulates the sleep/wake cycle and many associated behavioral and physiological processes. The cellular clock mechanism involves a transcriptional negative feedback loop that gives rise to circadian rhythms in gene expression with an approximately 24-h periodicity. To maintain system robustness, clocks throughout the body must be synchronized and their functions coordinated. In mammals, the master clock is located in the suprachiasmatic nucleus (SCN) of the hypothalamus. The SCN is entrained to the light/dark cycle through photic signal transduction and subsequent induction of core clock gene expression. The SCN in turn relays the time-of-day information to clocks in peripheral tissues. While the SCN is highly responsive to photic cues, peripheral clocks are more sensitive to non-photic resetting cues such as nutrients, body temperature, and neuroendocrine hormones. For example, feeding/fasting and physical activity can entrain peripheral clocks through signaling pathways and subsequent regulation of core clock genes and proteins. As such, timing of food intake and physical activity matters. In an ideal world, the sleep/wake and feeding/fasting cycles are synchronized to the light/dark cycle. However, asynchronous environmental cues, such as those experienced by shift workers and frequent travelers, often lead to misalignment between the master and peripheral clocks. Emerging evidence suggests that the resulting circadian disruption is associated with various diseases and chronic conditions that cause further circadian desynchrony and accelerate disease progression. In this review, we discuss how sleep, nutrition, and physical activity synchronize circadian clocks and how chronomedicine may offer novel strategies for disease intervention.
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24
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Tuvia N, Pivovarova-Ramich O, Murahovschi V, Lück S, Grudziecki A, Ost AC, Kruse M, Nikiforova VJ, Osterhoff M, Gottmann P, Gögebakan Ö, Sticht C, Gretz N, Schupp M, Schürmann A, Rudovich N, Pfeiffer AFH, Kramer A. Insulin Directly Regulates the Circadian Clock in Adipose Tissue. Diabetes 2021; 70:1985-1999. [PMID: 34226282 DOI: 10.2337/db20-0910] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 06/15/2021] [Indexed: 11/13/2022]
Abstract
Adipose tissue (AT) is a key metabolic organ which functions are rhythmically regulated by an endogenous circadian clock. Feeding is a "zeitgeber" aligning the clock in AT with the external time, but mechanisms of this regulation remain largely unclear. We tested the hypothesis that postprandial changes of the hormone insulin directly entrain circadian clocks in AT and investigated a transcriptional-dependent mechanism of this regulation. We analyzed gene expression in subcutaneous AT (SAT) of obese subjects collected before and after the hyperinsulinemic-euglycemic clamp or control saline infusion (SC). The expressions of core clock genes PER2, PER3, and NR1D1 in SAT were differentially changed upon insulin and saline infusion, suggesting insulin-dependent clock regulation. In human stem cell-derived adipocytes, mouse 3T3-L1 cells, and AT explants from mPer2Luc knockin mice, insulin induced a transient increase of the Per2 mRNA and protein expression, leading to the phase shift of circadian oscillations, with similar effects for Per1 Insulin effects were dependent on the region between -64 and -43 in the Per2 promoter but not on CRE and E-box elements. Our results demonstrate that insulin directly regulates circadian clocks in AT and isolated adipocytes, thus representing a primary mechanism of feeding-induced AT clock entrainment.
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Affiliation(s)
- Neta Tuvia
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Laboratory of Chronobiology, Berlin, Germany
| | - Olga Pivovarova-Ramich
- Reseach Group Molecular Nutritional Medicine, Department of Molecular Toxicology, German Institute of Human Nutrition Potsdam-Rehbruecke, Nuthetal, Germany
- Department of Clinical Nutrition, German Institute of Human Nutrition Potsdam-Rehbruecke, Nuthetal, Germany
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Endocrinology, Diabetes and Nutrition, Berlin, Germany
- German Center for Diabetes Research (DZD), München-Neuherberg, Germany
| | - Veronica Murahovschi
- Department of Clinical Nutrition, German Institute of Human Nutrition Potsdam-Rehbruecke, Nuthetal, Germany
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Endocrinology, Diabetes and Nutrition, Berlin, Germany
| | - Sarah Lück
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Laboratory of Chronobiology, Berlin, Germany
| | - Astrid Grudziecki
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Laboratory of Chronobiology, Berlin, Germany
| | - Anne-Catrin Ost
- Department of Clinical Nutrition, German Institute of Human Nutrition Potsdam-Rehbruecke, Nuthetal, Germany
| | - Michael Kruse
- Department of Clinical Nutrition, German Institute of Human Nutrition Potsdam-Rehbruecke, Nuthetal, Germany
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Endocrinology, Diabetes and Nutrition, Berlin, Germany
| | - Victoria J Nikiforova
- Department of Molecular Physiology, Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Martin Osterhoff
- Department of Clinical Nutrition, German Institute of Human Nutrition Potsdam-Rehbruecke, Nuthetal, Germany
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Endocrinology, Diabetes and Nutrition, Berlin, Germany
| | - Pascal Gottmann
- German Center for Diabetes Research (DZD), München-Neuherberg, Germany
- Department of Experimental Diabetology, German Institute of Human Nutrition Potsdam-Rehbruecke (DIfE), Nuthetal, Germany
| | - Özlem Gögebakan
- Department of Clinical Nutrition, German Institute of Human Nutrition Potsdam-Rehbruecke, Nuthetal, Germany
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Endocrinology, Diabetes and Nutrition, Berlin, Germany
| | - Carsten Sticht
- Medical Research Center, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Norbert Gretz
- Medical Research Center, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Michael Schupp
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Pharmacology, Berlin, Germany
| | - Annette Schürmann
- German Center for Diabetes Research (DZD), München-Neuherberg, Germany
- Department of Experimental Diabetology, German Institute of Human Nutrition Potsdam-Rehbruecke (DIfE), Nuthetal, Germany
- Institute of Nutritional Science, University of Potsdam, Nuthetal, Germany
| | - Natalia Rudovich
- Department of Clinical Nutrition, German Institute of Human Nutrition Potsdam-Rehbruecke, Nuthetal, Germany
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Endocrinology, Diabetes and Nutrition, Berlin, Germany
- German Center for Diabetes Research (DZD), München-Neuherberg, Germany
- Division of Endocrinology and Diabetes, Department of Internal Medicine, Spital Bülach, Bülach, Switzerland
| | - Andreas F H Pfeiffer
- Department of Clinical Nutrition, German Institute of Human Nutrition Potsdam-Rehbruecke, Nuthetal, Germany
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Endocrinology, Diabetes and Nutrition, Berlin, Germany
- German Center for Diabetes Research (DZD), München-Neuherberg, Germany
| | - Achim Kramer
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Laboratory of Chronobiology, Berlin, Germany
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Klemz S, Wallach T, Korge S, Rosing M, Klemz R, Maier B, Fiorenza NC, Kaymak I, Fritzsche AK, Herzog ED, Stanewsky R, Kramer A. Protein phosphatase 4 controls circadian clock dynamics by modulating CLOCK/BMAL1 activity. Genes Dev 2021; 35:1161-1174. [PMID: 34301769 PMCID: PMC8336894 DOI: 10.1101/gad.348622.121] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Accepted: 06/14/2021] [Indexed: 12/15/2022]
Abstract
In all organisms with circadian clocks, post-translational modifications of clock proteins control the dynamics of circadian rhythms, with phosphorylation playing a dominant role. All major clock proteins are highly phosphorylated, and many kinases have been described to be responsible. In contrast, it is largely unclear whether and to what extent their counterparts, the phosphatases, play an equally crucial role. To investigate this, we performed a systematic RNAi screen in human cells and identified protein phosphatase 4 (PPP4) with its regulatory subunit PPP4R2 as critical components of the circadian system in both mammals and Drosophila Genetic depletion of PPP4 shortens the circadian period, whereas overexpression lengthens it. PPP4 inhibits CLOCK/BMAL1 transactivation activity by binding to BMAL1 and counteracting its phosphorylation. This leads to increased CLOCK/BMAL1 DNA occupancy and decreased transcriptional activity, which counteracts the "kamikaze" properties of CLOCK/BMAL1. Through this mechanism, PPP4 contributes to the critical delay of negative feedback by retarding PER/CRY/CK1δ-mediated inhibition of CLOCK/BMAL1.
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Affiliation(s)
- Sabrina Klemz
- Laboratory of Chronobiology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin,10117 Berlin, Germany
| | - Thomas Wallach
- Laboratory of Chronobiology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin,10117 Berlin, Germany
| | - Sandra Korge
- Laboratory of Chronobiology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin,10117 Berlin, Germany
| | - Mechthild Rosing
- Institute of Neuro and Behavioral Biology, Westfälische Wilhelms University, Münster 48149, Germany
| | - Roman Klemz
- Laboratory of Chronobiology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin,10117 Berlin, Germany
| | - Bert Maier
- Laboratory of Chronobiology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin,10117 Berlin, Germany
| | - Nicholas C Fiorenza
- Laboratory of Chronobiology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin,10117 Berlin, Germany
| | - Irem Kaymak
- Laboratory of Chronobiology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin,10117 Berlin, Germany
| | - Anna K Fritzsche
- Laboratory of Chronobiology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin,10117 Berlin, Germany
| | - Erik D Herzog
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri 63130, USA
| | - Ralf Stanewsky
- Institute of Neuro and Behavioral Biology, Westfälische Wilhelms University, Münster 48149, Germany
| | - Achim Kramer
- Laboratory of Chronobiology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin,10117 Berlin, Germany
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Finger AM, Jäschke S, Del Olmo M, Hurwitz R, Granada AE, Herzel H, Kramer A. Intercellular coupling between peripheral circadian oscillators by TGF-β signaling. SCIENCE ADVANCES 2021; 7:7/30/eabg5174. [PMID: 34301601 PMCID: PMC8302137 DOI: 10.1126/sciadv.abg5174] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 06/08/2021] [Indexed: 05/04/2023]
Abstract
Coupling between cell-autonomous circadian oscillators is crucial to prevent desynchronization of cellular networks and disruption of circadian tissue functions. While neuronal oscillators within the mammalian central clock, the suprachiasmatic nucleus, couple intercellularly, coupling among peripheral oscillators is controversial and the molecular mechanisms are unknown. Using two- and three-dimensional mammalian culture models in vitro (mainly human U-2 OS cells) and ex vivo, we show that peripheral oscillators couple via paracrine pathways. We identify transforming growth factor-β (TGF-β) as peripheral coupling factor that mediates paracrine phase adjustment of molecular clocks through transcriptional regulation of core-clock genes. Disruption of TGF-β signaling causes desynchronization of oscillator networks resulting in reduced amplitude and increased sensitivity toward external zeitgebers. Our findings reveal an unknown mechanism for peripheral clock synchrony with implications for rhythmic organ functions and circadian health.
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Affiliation(s)
- Anna-Marie Finger
- Charité Universitätsmedizin Berlin, Institute for Medical Immunology, Laboratory of Chronobiology, Charitéplatz 1, 10117 Berlin, Germany.
- Berlin Institute of Health (BIH), Berlin, Germany
| | - Sebastian Jäschke
- Charité Universitätsmedizin Berlin, Institute for Medical Immunology, Laboratory of Chronobiology, Charitéplatz 1, 10117 Berlin, Germany
- Berlin Institute of Health (BIH), Berlin, Germany
| | - Marta Del Olmo
- Charité and Humboldt Universität zu Berlin, Institute for Theoretical Biology, Laboratory of Theoretical Chronobiology, Philippstraße 13, 10115 Berlin, Germany
| | - Robert Hurwitz
- Max Planck Institute for Infection Biology, Biochemistry-Protein Purification Core Facility, Charitéplatz 1, 10117 Berlin, Germany
| | - Adrián E Granada
- Charité-Universitätsmedizin, Charité Comprehensive Cancer Center, Laboratory of Systems Oncology, Charitéplatz 1, 10117 Berlin, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center, Partner Site Berlin, 69120, Heidelberg, Germany
| | - Hanspeter Herzel
- Charité and Humboldt Universität zu Berlin, Institute for Theoretical Biology, Laboratory of Theoretical Chronobiology, Philippstraße 13, 10115 Berlin, Germany
| | - Achim Kramer
- Charité Universitätsmedizin Berlin, Institute for Medical Immunology, Laboratory of Chronobiology, Charitéplatz 1, 10117 Berlin, Germany.
- Berlin Institute of Health (BIH), Berlin, Germany
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Gabriel CH, Del Olmo M, Zehtabian A, Jäger M, Reischl S, van Dijk H, Ulbricht C, Rakhymzhan A, Korte T, Koller B, Grudziecki A, Maier B, Herrmann A, Niesner R, Zemojtel T, Ewers H, Granada AE, Herzel H, Kramer A. Live-cell imaging of circadian clock protein dynamics in CRISPR-generated knock-in cells. Nat Commun 2021; 12:3796. [PMID: 34145278 PMCID: PMC8213786 DOI: 10.1038/s41467-021-24086-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 05/25/2021] [Indexed: 02/06/2023] Open
Abstract
The cell biology of circadian clocks is still in its infancy. Here, we describe an efficient strategy for generating knock-in reporter cell lines using CRISPR technology that is particularly useful for genes expressed transiently or at low levels, such as those coding for circadian clock proteins. We generated single and double knock-in cells with endogenously expressed PER2 and CRY1 fused to fluorescent proteins allowing us to simultaneously monitor the dynamics of CRY1 and PER2 proteins in live single cells. Both proteins are highly rhythmic in the nucleus of human cells with PER2 showing a much higher amplitude than CRY1. Surprisingly, CRY1 protein is nuclear at all circadian times indicating the absence of circadian gating of nuclear import. Furthermore, in the nucleus of individual cells CRY1 abundance rhythms are phase-delayed (~5 hours), and CRY1 levels are much higher (>5 times) compared to PER2 questioning the current model of the circadian oscillator.
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Affiliation(s)
- Christian H Gabriel
- Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Laboratory of Chronobiology, Berlin, Germany
- Berlin Institute of Health (BIH), Berlin, Germany
| | - Marta Del Olmo
- Institute for Theoretical Biology, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Amin Zehtabian
- Institute for Chemistry and Biochemistry, Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Berlin, Germany
| | - Marten Jäger
- Berlin Institute of Health (BIH) Core Genomics Facility, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Silke Reischl
- Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Laboratory of Chronobiology, Berlin, Germany
- Berlin Institute of Health (BIH), Berlin, Germany
| | - Hannah van Dijk
- Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Laboratory of Chronobiology, Berlin, Germany
- Berlin Institute of Health (BIH), Berlin, Germany
| | - Carolin Ulbricht
- Immune Dynamics, Rheumatology and Clinical Immunology, Charité - Universitätsmedizin Berlin, Berlin, Germany
- Immune Dynamics, Deutsches Rheuma-Forschungszentrum (DRFZ), a Leibniz Institute, Berlin, Germany
| | - Asylkhan Rakhymzhan
- Biophysical Analytics, Deutsches Rheuma-Forschungszentrum (DRFZ), a Leibniz Institute, Berlin, Germany
| | - Thomas Korte
- Molecular Biophysics, Department of Biology, Humboldt Universität zu Berlin, Berlin, Germany
| | - Barbara Koller
- Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Laboratory of Chronobiology, Berlin, Germany
- Berlin Institute of Health (BIH), Berlin, Germany
| | - Astrid Grudziecki
- Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Laboratory of Chronobiology, Berlin, Germany
- Berlin Institute of Health (BIH), Berlin, Germany
| | - Bert Maier
- Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Laboratory of Chronobiology, Berlin, Germany
- Berlin Institute of Health (BIH), Berlin, Germany
| | - Andreas Herrmann
- Molecular Biophysics, Department of Biology, Humboldt Universität zu Berlin, Berlin, Germany
| | - Raluca Niesner
- Biophysical Analytics, Deutsches Rheuma-Forschungszentrum (DRFZ), a Leibniz Institute, Berlin, Germany
- Dynamic and Functional in vivo Imaging, Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
| | - Tomasz Zemojtel
- Berlin Institute of Health (BIH) Core Genomics Facility, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Helge Ewers
- Institute for Chemistry and Biochemistry, Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Berlin, Germany
| | - Adrián E Granada
- Charité Comprehensive Cancer Center, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Hanspeter Herzel
- Institute for Theoretical Biology, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Achim Kramer
- Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Laboratory of Chronobiology, Berlin, Germany.
- Berlin Institute of Health (BIH), Berlin, Germany.
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Muñoz-Guzmán F, Caballero V, Larrondo LF. A global search for novel transcription factors impacting the Neurospora crassa circadian clock. G3 (BETHESDA, MD.) 2021; 11:jkab100. [PMID: 33792687 PMCID: PMC8495738 DOI: 10.1093/g3journal/jkab100] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 03/16/2021] [Indexed: 01/15/2023]
Abstract
Eukaryotic circadian oscillators share a common circuit architecture, a negative feedback loop in which a positive element activates the transcription of a negative one that then represses the action of the former, inhibiting its own expression. While studies in mammals and insects have revealed additional transcriptional inputs modulating the expression of core clock components, this has been less characterized in the model Neurospora crassa, where the participation of other transcriptional components impacting circadian clock dynamics remains rather unexplored. Thus, we sought to identify additional transcriptional regulators modulating the N. crassa clock, following a reverse genetic screen based on luminescent circadian reporters and a collection of transcription factors (TFs) knockouts, successfully covering close to 60% of them. Besides the canonical core clock components WC-1 and -2, none of the tested transcriptional regulators proved to be essential for rhythmicity. Nevertheless, we identified a set of 23 TFs that when absent lead to discrete, but significant, changes in circadian period. While the current level of analysis does not provide mechanistic information about how these new players modulate circadian parameters, the results of this screen reveal that an important number of light and clock-regulated TFs, involved in a plethora of processes, are capable of modulating the clockworks. This partial reverse genetic clock screen also exemplifies how the N. crassa knockout collection continues to serve as an expedite platform to address broad biological questions.
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Affiliation(s)
- Felipe Muñoz-Guzmán
- ANID—Millennium Science Initiative Program—Millennium Institute for Integrative Biology (iBio), Santiago 8331150, Chile
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
| | - Valeria Caballero
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
| | - Luis F Larrondo
- ANID—Millennium Science Initiative Program—Millennium Institute for Integrative Biology (iBio), Santiago 8331150, Chile
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
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29
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A complex of distal appendage-associated kinases linked to human disease regulates ciliary trafficking and stability. Proc Natl Acad Sci U S A 2021; 118:2018740118. [PMID: 33846249 PMCID: PMC8072220 DOI: 10.1073/pnas.2018740118] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Primary cilia (PC) are sensory organelles essential for the development and maintenance of adult tissues. Accordingly, dysfunction of PC causes human disorders called ciliopathies. Hence, a thorough understanding of the molecular regulation of PC is critical. Our findings highlight CSNK2A1 as a modulator of cilia trafficking and stability, tightly related to TTBK2 function. Enriched at the centrosome, CSNK2A1 prevents abnormal accumulation of key ciliary proteins, instability at the tip, and aberrant activation of the Sonic Hedgehog pathway. Furthermore, we establish that Csnk2a1 mutations associated with Okur-Chung neurodevelopmental disorder (OCNDS) alter cilia morphology. Thus, we report a potential linkage between CSNK2A1 ciliary function and OCNDS. Cilia biogenesis is a complex, multistep process involving the coordination of multiple cellular trafficking pathways. Despite the importance of ciliogenesis in mediating the cellular response to cues from the microenvironment, we have only a limited understanding of the regulation of cilium assembly. We previously identified Tau tubulin kinase 2 (TTBK2) as a key regulator of ciliogenesis. Here, using CRISPR kinome and biotin identification screening, we identify the CK2 catalytic subunit CSNK2A1 as an important modulator of TTBK2 function in cilia trafficking. Superresolution microscopy reveals that CSNK2A1 is a centrosomal protein concentrated at the mother centriole and associated with the distal appendages. Csnk2a1 mutant cilia are longer than those of control cells, showing instability at the tip associated with ciliary actin cytoskeleton changes. These cilia also abnormally accumulate key cilia assembly and SHH-related proteins. De novo mutations of Csnk2a1 were recently linked to the human genetic disorder Okur-Chung neurodevelopmental syndrome (OCNDS). Consistent with the role of CSNK2A1 in cilium stability, we find that expression of OCNDS-associated Csnk2a1 variants in wild-type cells causes ciliary structural defects. Our findings provide insights into mechanisms involved in ciliary length regulation, trafficking, and stability that in turn shed light on the significance of cilia instability in human disease.
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30
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Yi JS, Díaz NM, D'Souza S, Buhr ED. The molecular clockwork of mammalian cells. Semin Cell Dev Biol 2021; 126:87-96. [PMID: 33810978 DOI: 10.1016/j.semcdb.2021.03.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 03/15/2021] [Accepted: 03/17/2021] [Indexed: 12/20/2022]
Abstract
Most organisms contain self-sustained circadian clocks. These clocks can be synchronized by environmental stimuli, but can also oscillate indefinitely in isolation. In mammals this is true at the molecular level for the majority of cell types that have been examined. A core set of "clock genes" form a transcriptional/translational feedback loop (TTFL) which repeats with a period of approximately 24 h. The exact mechanism of the TTFL differs slightly in various cell types, but all involve similar family members of the core cohort of clock genes. The clock has many outputs which are unique for different tissues. Cells in diverse tissues will convert the timing signals provided by the TTFL into uniquely orchestrated transcriptional oscillations of many clock-controlled genes and cellular processes.
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Affiliation(s)
- Jonathan S Yi
- University of Washington, Dept. of Ophthalmology, 750 Republican St., Seattle, WA 98109, USA
| | - Nicolás M Díaz
- University of Washington, Dept. of Ophthalmology, 750 Republican St., Seattle, WA 98109, USA
| | - Shane D'Souza
- Center for Chronobiology, Abrahamson Pediatric Eye Institute, Division of Pediatric Ophthalmology, Cincinnati Children's Hospital, Cincinnati, OH 45229, USA
| | - Ethan D Buhr
- University of Washington, Dept. of Ophthalmology, 750 Republican St., Seattle, WA 98109, USA.
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Ribeiro RFN, Cavadas C, Silva MMC. Small-molecule modulators of the circadian clock: Pharmacological potentials in circadian-related diseases. Drug Discov Today 2021; 26:1620-1641. [PMID: 33781946 DOI: 10.1016/j.drudis.2021.03.015] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 02/20/2021] [Accepted: 03/16/2021] [Indexed: 12/29/2022]
Abstract
Disruption of circadian oscillations has a wide-ranging impact on health, with the potential to induce the development of clock-related diseases. Small-molecule modulators of the circadian clock (SMMCC) target core or noncore clock proteins, modulating physiological effects as a consequence of agonist, inverse agonist, or antagonist interference. These pharmacological modulators are usually identified using chemical screening of large libraries of active compounds. However, target-based screens, chemical optimization, and circadian crystallography have recently assisted in the identification of these compounds. In this review, we focus on established and novel SMMCCs targeting both core and noncore clock proteins, identifying their circadian targets, detailed circadian effects, and specific physiological effects. In addition, we discuss their therapeutic potential for the treatment of diverse clock-related disorders (such as metabolic-associated disorders, autoimmune diseases, mood disorders, and cancer) and as chronotherapeutics. Future perspectives are also considered, such as clinical trials, and potential safety hazards, including those in the absence of clinical trials.
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Affiliation(s)
- Rodrigo F N Ribeiro
- Centre for Neuroscience and Cell Biology (CNC), University of Coimbra, Coimbra, Portugal; Centre for Innovation in Biomedicine and Biotechnology (CIBB), University of Coimbra, Portugal; Faculty of Pharmacy, University of Coimbra, Coimbra, Portugal
| | - Cláudia Cavadas
- Centre for Neuroscience and Cell Biology (CNC), University of Coimbra, Coimbra, Portugal; Centre for Innovation in Biomedicine and Biotechnology (CIBB), University of Coimbra, Portugal; Faculty of Pharmacy, University of Coimbra, Coimbra, Portugal.
| | - Maria Manuel C Silva
- Centre for Neuroscience and Cell Biology (CNC), University of Coimbra, Coimbra, Portugal; Centre for Innovation in Biomedicine and Biotechnology (CIBB), University of Coimbra, Portugal; Faculty of Pharmacy, University of Coimbra, Coimbra, Portugal.
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32
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Astone M, Santoro MM. Time to fight: targeting the circadian clock molecular machinery in cancer therapy. Drug Discov Today 2021; 26:1164-1184. [PMID: 33549826 DOI: 10.1016/j.drudis.2021.01.023] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 11/23/2020] [Accepted: 01/22/2021] [Indexed: 02/06/2023]
Abstract
The circadian clock regulates a wide range of molecular pathways and biological processes. The expression of clock genes is often altered in cancer, fostering tumor initiation and progression. Inhibition and activation of core circadian clock genes, as well as treatments that restore circadian rhythmicity, have been successful in counteracting tumor growth in different experimental models. Here, we provide an up-to-date overview of studies that show the therapeutic effects of targeting the clock molecular machinery in cancer, both genetically and pharmacologically. We also highlight future areas for progress that offer a promising path towards innovative anticancer strategies. Substantial limitations in the current understanding of the complex interplay between the circadian clock and cancer in vivo need to be addressed in order to allow clock-targeting therapies in cancer.
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Affiliation(s)
- Matteo Astone
- Department of Biology, University of Padova, I-35131, Italy
| | - Massimo M Santoro
- Department of Biology, University of Padova, I-35131, Italy; Venetian Institute of Molecular Medicine, Via Orus 2, 35129 Padova, Italy.
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Kim SM, Vadnie CA, Philip VM, Gagnon LH, Chowdari KV, Chesler EJ, McClung CA, Logan RW. High-throughput measurement of fibroblast rhythms reveals genetic heritability of circadian phenotypes in diversity outbred mice and their founder strains. Sci Rep 2021; 11:2573. [PMID: 33510298 PMCID: PMC7843998 DOI: 10.1038/s41598-021-82069-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 01/14/2021] [Indexed: 01/21/2023] Open
Abstract
Circadian variability is driven by genetics and Diversity Outbred (DO) mice is a powerful tool for examining the genetics of complex traits because their high genetic and phenotypic diversity compared to conventional mouse crosses. The DO population combines the genetic diversity of eight founder strains including five common inbred and three wild-derived strains. In DO mice and their founders, we established a high-throughput system to measure cellular rhythms using in vitro preparations of skin fibroblasts. Among the founders, we observed strong heritability for rhythm period, robustness, phase and amplitude. We also found significant sex and strain differences for these rhythms. Extreme differences in period for molecular and behavioral rhythms were found between the inbred A/J strain and the wild-derived CAST/EiJ strain, where A/J had the longest period and CAST/EiJ had the shortest. In addition, we measured cellular rhythms in 329 DO mice, which displayed far greater phenotypic variability than the founders—80% of founders compared to only 25% of DO mice had periods of ~ 24 h. Collectively, our findings demonstrate that genetic diversity contributes to phenotypic variability in circadian rhythms, and high-throughput characterization of fibroblast rhythms in DO mice is a tractable system for examining the genetics of circadian traits.
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Affiliation(s)
- Sam-Moon Kim
- Translational Neuroscience Program, Department of Psychiatry, University of Pittsburgh School of Medicine, 450 Technology Drive, Pittsburgh, PA, 15219, USA.,Center for Systems Neurogenetics of Addiction, The Jackson Laboratory, 600 Main Street, Bar Harbor, 04609, ME, USA
| | - Chelsea A Vadnie
- Translational Neuroscience Program, Department of Psychiatry, University of Pittsburgh School of Medicine, 450 Technology Drive, Pittsburgh, PA, 15219, USA
| | - Vivek M Philip
- Center for Systems Neurogenetics of Addiction, The Jackson Laboratory, 600 Main Street, Bar Harbor, 04609, ME, USA
| | - Leona H Gagnon
- Center for Systems Neurogenetics of Addiction, The Jackson Laboratory, 600 Main Street, Bar Harbor, 04609, ME, USA
| | - Kodavali V Chowdari
- Translational Neuroscience Program, Department of Psychiatry, University of Pittsburgh School of Medicine, 450 Technology Drive, Pittsburgh, PA, 15219, USA
| | - Elissa J Chesler
- Center for Systems Neurogenetics of Addiction, The Jackson Laboratory, 600 Main Street, Bar Harbor, 04609, ME, USA
| | - Colleen A McClung
- Translational Neuroscience Program, Department of Psychiatry, University of Pittsburgh School of Medicine, 450 Technology Drive, Pittsburgh, PA, 15219, USA. .,Center for Systems Neurogenetics of Addiction, The Jackson Laboratory, 600 Main Street, Bar Harbor, 04609, ME, USA.
| | - Ryan W Logan
- Center for Systems Neurogenetics of Addiction, The Jackson Laboratory, 600 Main Street, Bar Harbor, 04609, ME, USA. .,Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine, 700 Albany Street, Boston, 02118, MA, USA.
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Maier B, Lorenzen S, Finger AM, Herzel H, Kramer A. Searching Novel Clock Genes Using RNAi-Based Screening. Methods Mol Biol 2021; 2130:103-114. [PMID: 33284439 DOI: 10.1007/978-1-0716-0381-9_8] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/15/2023]
Abstract
RNA interference (RNAi) allows for the selective downregulation of gene expression by neutralizing targeted mRNA molecules and has frequently been used in high-throughput screening endeavors. Here, we describe a protocol for the highly parallel RNAi-mediated downregulation of gene expression in order to search for components involved in circadian rhythm generation. We use lentiviral gene transfer to deliver shRNA expressing plasmids into circadian reporter cells ensuring for efficient and stable knockdown. Circadian rhythms are monitored using live-cell bioluminescence recording of synchronized reporter cells over several days. In addition, we present a new software tool (ChronoStar) for efficient, parallel time-series analysis to extract rhythm parameters such as period, phase, amplitude, and damping.
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Affiliation(s)
- Bert Maier
- Laboratory of Chronobiology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Stephan Lorenzen
- Institute for Theoretical Biology, Humboldt-Universität zu Berlin, Berlin, Germany
- Bernhard-Nocht-Institut, Hamburg, Germany
| | - Anna-Marie Finger
- Laboratory of Chronobiology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Hanspeter Herzel
- Institute for Theoretical Biology, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Achim Kramer
- Laboratory of Chronobiology, Charité-Universitätsmedizin Berlin, Berlin, Germany.
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35
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Lim ASP. Diurnal and seasonal molecular rhythms in the human brain and their relation to Alzheimer disease. HANDBOOK OF CLINICAL NEUROLOGY 2021; 179:271-284. [PMID: 34225968 DOI: 10.1016/b978-0-12-819975-6.00017-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Diurnal and seasonal rhythms influence many aspects of human physiology including brain function. Moreover, altered diurnal and seasonal behavioral and physiological rhythms have been linked to Alzheimer's disease and related dementias (ADRD). Understanding the molecular basis for these links may lead to identification of novel targets to mitigate the negative impact of normal and abnormal diurnal and seasonal rhythms on ADRD or to alleviate the adverse consequences of ADRD on normal diurnal and seasonal rhythms. Diurnally and seasonally rhythmic gene expression and epigenetic modification in the human neocortex may be a key mechanism underlying these links. This chapter will first review the observed epidemiological links between normal and abnormal diurnal and seasonal rhythmicity, cognitive impairment, and ADRD. Then it will review normal diurnal and seasonal rhythms of brain epigenetic modification and gene expression in model organisms. Finally, it will review evidence for diurnal and seasonal rhythms of epigenetic modification and gene expression the human brain in aging, Alzheimer's disease, and other brain disorders.
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Affiliation(s)
- Andrew S P Lim
- Division of Neurology, Department of Medicine, Sunnybrook Health Sciences Centre, University of Toronto, Toronto, ON, Canada.
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36
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Gopalakrishnan S, Kannan NN. Only time will tell: the interplay between circadian clock and metabolism. Chronobiol Int 2020; 38:149-167. [PMID: 33345624 DOI: 10.1080/07420528.2020.1842436] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
In most organisms ranging from cyanobacteria to humans, the endogenous timekeeping system temporally coordinates the behavioral, physiological, and metabolic processes with a periodicity close to 24 h. The timing of these daily rhythms is orchestrated by the synchronized oscillations of both the central pacemaker in the brain and the peripheral clocks located across multiple organs and tissues. A growing body of evidence suggests that the central circadian clock and peripheral clocks residing in the metabolically active tissues are incredibly well coordinated to confer coherent metabolic homeostasis. The interplay between nutrient metabolism and circadian rhythms can occur at various levels supported by the molecular clock network, multiple systemic mechanisms, and the neuroendocrine signaling pathways. While studies suggest the reciprocal regulation between circadian clock and metabolism, it is important to understand the precise mechanisms and the underlying pathways involved in the cross-talk among circadian oscillators and diverse metabolic networks. In addition to the internal synchronization of the metabolic rhythms, feeding time is considered as a potential external synchronization cue that fine tunes the timing of the circadian rhythms in metabolic peripheral clocks. A deeper understanding of how the timing of food intake and the diet composition drive the tissue-specific metabolic rhythms across the body is concomitantly important to develop novel therapeutic strategies for the metabolic disorders arising from circadian misalignment. This review summarizes the recent advancements in the circadian clock regulation of nutrient metabolism and discusses the current understanding of the metabolic feedback signals that link energy metabolism with the circadian clock.
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Affiliation(s)
- Swetha Gopalakrishnan
- Chronobiology Laboratory, School of Biology, Indian Institute of Science Education and Research (IISER) , Thiruvananthapuram, India
| | - Nisha N Kannan
- Chronobiology Laboratory, School of Biology, Indian Institute of Science Education and Research (IISER) , Thiruvananthapuram, India
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Small Molecules Targeting Biological Clock; A Novel Prospective for Anti-Cancer Drugs. Molecules 2020; 25:molecules25214937. [PMID: 33114496 PMCID: PMC7663518 DOI: 10.3390/molecules25214937] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 10/23/2020] [Accepted: 10/24/2020] [Indexed: 12/11/2022] Open
Abstract
The circadian rhythms are an intrinsic timekeeping system that regulates numerous physiological, biochemical, and behavioral processes at intervals of approximately 24 h. By regulating such processes, the circadian rhythm allows organisms to anticipate and adapt to continuously changing environmental conditions. A growing body of evidence shows that disruptions to the circadian rhythm can lead to various disorders, including cancer. Recently, crucial knowledge has arisen regarding the essential features that underlie the overt circadian rhythm and its influence on physiological outputs. This knowledge suggests that specific small molecules can be utilized to control the circadian rhythm. It has been discovered that these small molecules can regulate circadian-clock-related disorders such as metabolic, cardiovascular, inflammatory, as well as cancer. This review examines the potential use of small molecules for developing new drugs, with emphasis placed on recent progress that has been made regarding the identification of small-molecule clock modulators and their potential use in treating cancer.
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38
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Jacob H, Curtis AM, Kearney CJ. Therapeutics on the clock: Circadian medicine in the treatment of chronic inflammatory diseases. Biochem Pharmacol 2020; 182:114254. [PMID: 33010213 DOI: 10.1016/j.bcp.2020.114254] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 09/25/2020] [Accepted: 09/28/2020] [Indexed: 02/06/2023]
Abstract
The circadian clock is a collection of endogenous oscillators with a periodicity of ~ 24 h. Recently, our understanding of circadian rhythms and their regulation at genomic and physiologic scales has grown significantly. Knowledge of the circadian influence on biological processes has provided new possibilities for novel pharmacological strategies. Directly targeting the biological clock or its downstream targets, and/or using timing as a variable in drug therapy are now important pharmacological considerations. The circadian machinery mediates many aspects of the inflammatory response and, reciprocally, an inflammatory environment can disrupt circadian rhythms. Therefore, intense interest exists in leveraging circadian biology as a means to treat chronic inflammatory diseases such as sepsis, asthma, rheumatoid arthritis, osteoarthritis, and cardiovascular disease, which all display some type of circadian signature. The purpose of this review is to evaluate the crosstalk between circadian rhythms, inflammatory diseases, and their pharmacological treatment. Evidence suggests that carefully rationalized application of chronotherapy strategies - alone or in combination with small molecule modulators of circadian clock components - can improve efficacy and reduce toxicity, thus warranting further investigation and use.
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Affiliation(s)
- Haritha Jacob
- Tissue Engineering Research Group, Department of Anatomy and Regenerative Medicine, Royal College of Surgeons in Ireland (RCSI), Dublin, Ireland; Advanced Materials and Bioengineering Research Centre (AMBER), RCSI and Trinity College Dublin, Dublin, Ireland
| | - Annie M Curtis
- Tissue Engineering Research Group, Department of Anatomy and Regenerative Medicine, Royal College of Surgeons in Ireland (RCSI), Dublin, Ireland; Advanced Materials and Bioengineering Research Centre (AMBER), RCSI and Trinity College Dublin, Dublin, Ireland; School of Pharmacy and Biomolecular Sciences, RCSI, Dublin, Ireland.
| | - Cathal J Kearney
- Tissue Engineering Research Group, Department of Anatomy and Regenerative Medicine, Royal College of Surgeons in Ireland (RCSI), Dublin, Ireland; Advanced Materials and Bioengineering Research Centre (AMBER), RCSI and Trinity College Dublin, Dublin, Ireland; Department of Biomedical Engineering, University of Massachusetts Amherst, MA, USA.
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39
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Crosby P, Partch CL. New insights into non-transcriptional regulation of mammalian core clock proteins. J Cell Sci 2020; 133:133/18/jcs241174. [PMID: 32934011 DOI: 10.1242/jcs.241174] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Mammalian circadian rhythms drive ∼24 h periodicity in a wide range of cellular processes, temporally coordinating physiology and behaviour within an organism, and synchronising this with the external day-night cycle. The canonical model for this timekeeping consists of a delayed negative-feedback loop, containing transcriptional activator complex CLOCK-BMAL1 (BMAL1 is also known as ARNTL) and repressors period 1, 2 and 3 (PER1, PER2 and PER3) and cryptochrome 1 and 2 (CRY1 and CRY2), along with a number of accessory factors. Although the broad strokes of this system are defined, the exact molecular mechanisms by which these proteins generate a self-sustained rhythm with such periodicity and fidelity remains a topic of much research. Recent studies have identified prominent roles for a number of crucial post-transcriptional, translational and, particularly, post-translational events within the mammalian circadian oscillator, providing an increasingly complex understanding of the activities and interactions of the core clock proteins. In this Review, we highlight such contemporary work on non-transcriptional events and set it within our current understanding of cellular circadian timekeeping.
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Affiliation(s)
- Priya Crosby
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA
| | - Carrie L Partch
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA
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40
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van Soest I, del Olmo M, Schmal C, Herzel H. Nonlinear phenomena in models of the circadian clock. J R Soc Interface 2020; 17:20200556. [PMID: 32993432 PMCID: PMC7536064 DOI: 10.1098/rsif.2020.0556] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 08/27/2020] [Indexed: 12/14/2022] Open
Abstract
The mammalian circadian clock is well-known to be important for our sleep-wake cycles, as well as other daily rhythms such as temperature regulation, hormone release or feeding-fasting cycles. Under normal conditions, these daily cyclic events follow 24 h limit cycle oscillations, but under some circumstances, more complex nonlinear phenomena, such as the emergence of chaos, or the splitting of physiological dynamics into oscillations with two different periods, can be observed. These nonlinear events have been described at the organismic and tissue level, but whether they occur at the cellular level is still unknown. Our results show that period-doubling, chaos and splitting appear in different models of the mammalian circadian clock with interlocked feedback loops and in the absence of external forcing. We find that changes in the degradation of clock genes and proteins greatly alter the dynamics of the system and can induce complex nonlinear events. Our findings highlight the role of degradation rates in determining the oscillatory behaviour of clock components, and can contribute to the understanding of molecular mechanisms of circadian dysregulation.
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Affiliation(s)
- Inge van Soest
- Institute for Theoretical Biology, Charité and Humboldt Universität zu Berlin, 10115 Berlin, Germany
- Master Program Neuroscience and Cognition, Utrecht University, Utrecht, The Netherlands
| | - Marta del Olmo
- Institute for Theoretical Biology, Charité and Humboldt Universität zu Berlin, 10115 Berlin, Germany
| | - Christoph Schmal
- Institute for Theoretical Biology, Charité and Humboldt Universität zu Berlin, 10115 Berlin, Germany
| | - Hanspeter Herzel
- Institute for Theoretical Biology, Charité and Humboldt Universität zu Berlin, 10115 Berlin, Germany
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41
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Nikhil KL, Korge S, Kramer A. Heritable gene expression variability and stochasticity govern clonal heterogeneity in circadian period. PLoS Biol 2020; 18:e3000792. [PMID: 32745129 PMCID: PMC7425987 DOI: 10.1371/journal.pbio.3000792] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 08/13/2020] [Accepted: 07/13/2020] [Indexed: 11/18/2022] Open
Abstract
A ubiquitous feature of the circadian clock across life forms is its organization as a network of cellular oscillators, with individual cellular oscillators within the network often exhibiting considerable heterogeneity in their intrinsic periods. The interaction of coupling and heterogeneity in circadian clock networks is hypothesized to influence clock’s entrainability, but our knowledge of mechanisms governing period heterogeneity within circadian clock networks remains largely elusive. In this study, we aimed to explore the principles that underlie intercellular period variation in circadian clock networks (clonal period heterogeneity). To this end, we employed a laboratory selection approach and derived a panel of 25 clonal cell populations exhibiting circadian periods ranging from 22 to 28 h. We report that a single parent clone can produce progeny clones with a wide distribution of circadian periods, and this heterogeneity, in addition to being stochastically driven, has a heritable component. By quantifying the expression of 20 circadian clock and clock-associated genes across our clone panel, we found that inheritance of expression patterns in at least three clock genes might govern clonal period heterogeneity in circadian clock networks. Furthermore, we provide evidence suggesting that heritable epigenetic variation in gene expression regulation might underlie period heterogeneity. How do genetically identical cells exhibit a different circadian phenotype? This study reveals that a single parent clone can produce progeny with a wide distribution of circadian periods and that this heterogeneity, in addition to being stochastically driven, has a heritable component, likely via heritable epigenetic variation in gene expression regulation.
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Affiliation(s)
- K. L. Nikhil
- Charité Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität zu Berlin, Laboratory of Chronobiology, Berlin, Germany
- Berlin Institute of Health (BIH), Berlin, Germany
| | - Sandra Korge
- Charité Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität zu Berlin, Laboratory of Chronobiology, Berlin, Germany
- Berlin Institute of Health (BIH), Berlin, Germany
| | - Achim Kramer
- Charité Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität zu Berlin, Laboratory of Chronobiology, Berlin, Germany
- Berlin Institute of Health (BIH), Berlin, Germany
- * E-mail:
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Yang C, Wu J, Liu X, Wang Y, Liu B, Chen X, Wu X, Yan D, Han L, Liu S, Shan L, Shang Y. Circadian Rhythm Is Disrupted by ZNF704 in Breast Carcinogenesis. Cancer Res 2020; 80:4114-4128. [PMID: 32651256 DOI: 10.1158/0008-5472.can-20-0493] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 06/26/2020] [Accepted: 07/07/2020] [Indexed: 11/16/2022]
Abstract
Copy number gain in chromosome 8q21 is frequently detected in breast cancer, yet the oncogenic potential underlying this amplicon in breast carcinogenesis remains to be delineated. We report here that ZNF704, a gene mapped to 8q21, is recurrently amplified in various malignancies including breast cancer. ZNF704 acted as a transcriptional repressor and interacted with the transcriptional corepressor SIN3A complex. Genome-wide interrogation of transcriptional targets revealed that the ZNF704/SIN3A complex represses a panel of genes including PER2 that are critically involved in the function of the circadian clock. Overexpression of ZNF704 prolonged the period and dampened the amplitude of the circadian clock. ZNF704 promoted the proliferation and invasion of breast cancer cells in vitro and accelerated the growth and metastasis of breast cancer in vivo. Consistently, the level of ZNF704 expression inversely correlated with that of PER2 in breast carcinomas, and high level of ZNF704 correlated with advanced histologic grades, lymph node positivity, and poor prognosis of patients with breast cancer, especially those with HER2+ and basal-like subtypes. These results indicate that ZNF704 is an important regulator of the circadian clock and a potential driver for breast carcinogenesis. SIGNIFICANCE: This study indicates that ZNF704 could be a potential oncogenic factor, disrupting circadian rhythm of breast cancer cells and contributing to breast carcinogenesis.
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Affiliation(s)
- Chao Yang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Jiajing Wu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Xinhua Liu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou, China
| | - Yue Wang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing, China.,Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou, China
| | - Beibei Liu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Xing Chen
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Xiaodi Wu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Dong Yan
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Lulu Han
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Shumeng Liu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Lin Shan
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Yongfeng Shang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing, China. .,Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou, China.,Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Health Science Center, Beijing, China.,Laboratory of Cancer Epigenetics, Chinese Academy of Medical Sciences Beijing, China
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43
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Umemura Y, Yagita K. Development of the Circadian Core Machinery in Mammals. J Mol Biol 2020; 432:3611-3617. [DOI: 10.1016/j.jmb.2019.11.026] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 11/26/2019] [Accepted: 11/26/2019] [Indexed: 01/20/2023]
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44
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Miller S, Hirota T. Pharmacological Interventions to Circadian Clocks and Their Molecular Bases. J Mol Biol 2020; 432:3498-3514. [DOI: 10.1016/j.jmb.2020.01.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 12/30/2019] [Accepted: 01/02/2020] [Indexed: 12/31/2022]
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45
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Morris AR, Stanton DL, Roman D, Liu AC. Systems Level Understanding of Circadian Integration with Cell Physiology. J Mol Biol 2020; 432:3547-3564. [PMID: 32061938 DOI: 10.1016/j.jmb.2020.02.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 01/31/2020] [Accepted: 02/03/2020] [Indexed: 02/07/2023]
Abstract
The mammalian circadian clock regulates a wide variety of physiological and behavioral processes. In turn, its disruption is associated with sleep deficiency, metabolic syndrome, neurological and psychiatric disorders, and cancer. At the turn of the century, the circadian clock was determined to be regulated by a transcriptional negative feedback mechanism composed of a dozen core clock genes. More recently, large-scale genomic studies have expanded the clock into a complex network composed of thousands of gene outputs and inputs. A major task of circadian research is to utilize systems biological approaches to uncover the governing principles underlying cellular oscillatory behavior and advance understanding of biological functions at the genomic level with spatiotemporal resolution. This review focuses on the genes and pathways that provide inputs to the circadian clock. Several emerging examples include AMP-activated protein kinase AMPK, nutrient/energy sensor mTOR, NAD+-dependent deacetylase SIRT1, hypoxia-inducible factor HIF1α, oxidative stress-inducible factor NRF2, and the proinflammatory factor NF-κB. Among others that continue to be revealed, these input pathways reflect the extensive interplay between the clock and cell physiology through the regulation of core clock genes and proteins. While the scope of this crosstalk is well-recognized, precise molecular links are scarce, and the underlying regulatory mechanisms are not well understood. Future research must leverage genetic and genomic tools and technologies, network analysis, and computational modeling to characterize additional modifiers and input pathways. This systems-based framework promises to advance understanding of the circadian timekeeping system and may enable the enhancement of circadian functions through related input pathways.
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Affiliation(s)
- Andrew R Morris
- Department of Physiology and Functional Genomics, University of Florida College of Medicine, Gainesville, FL, United States of America
| | - Daniel L Stanton
- Department of Animal Sciences, University of Florida Institute of Food and Agricultural Sciences, Gainesville, FL, United States of America
| | - Destino Roman
- Department of Physiology and Functional Genomics, University of Florida College of Medicine, Gainesville, FL, United States of America
| | - Andrew C Liu
- Department of Physiology and Functional Genomics, University of Florida College of Medicine, Gainesville, FL, United States of America.
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Sinturel F, Petrenko V, Dibner C. Circadian Clocks Make Metabolism Run. J Mol Biol 2020; 432:3680-3699. [PMID: 31996313 DOI: 10.1016/j.jmb.2020.01.018] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 01/16/2020] [Accepted: 01/16/2020] [Indexed: 12/12/2022]
Abstract
Most organisms adapt to the 24-h cycle of the Earth's rotation by anticipating the time of the day through light-dark cycles. The internal time-keeping system of the circadian clocks has been developed to ensure this anticipation. The circadian system governs the rhythmicity of nearly all physiological and behavioral processes in mammals. In this review, we summarize current knowledge stemming from rodent and human studies on the tight interconnection between the circadian system and metabolism in the body. In particular, we highlight recent advances emphasizing the roles of the peripheral clocks located in the metabolic organs in regulating glucose, lipid, and protein homeostasis at the organismal and cellular levels. Experimental disruption of circadian system in rodents is associated with various metabolic disturbance phenotypes. Similarly, perturbation of the clockwork in humans is linked to the development of metabolic diseases. We discuss recent studies that reveal roles of the circadian system in the temporal coordination of metabolism under physiological conditions and in the development of human pathologies.
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Affiliation(s)
- Flore Sinturel
- Department of Medicine, Division of Endocrinology, Diabetes, Hypertension and Nutrition, Faculty of Medicine, University of Geneva, Rue Michel-Servet, 1, CH-1211, Geneva, 14, Switzerland; Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, Geneva, Switzerland; Diabetes Center, Faculty of Medicine, University of Geneva, Geneva, Switzerland; Institute of Genetics and Genomics of Geneva (iGE3), University of Geneva, Geneva, Switzerland.
| | - Volodymyr Petrenko
- Department of Medicine, Division of Endocrinology, Diabetes, Hypertension and Nutrition, Faculty of Medicine, University of Geneva, Rue Michel-Servet, 1, CH-1211, Geneva, 14, Switzerland; Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, Geneva, Switzerland; Diabetes Center, Faculty of Medicine, University of Geneva, Geneva, Switzerland; Institute of Genetics and Genomics of Geneva (iGE3), University of Geneva, Geneva, Switzerland
| | - Charna Dibner
- Department of Medicine, Division of Endocrinology, Diabetes, Hypertension and Nutrition, Faculty of Medicine, University of Geneva, Rue Michel-Servet, 1, CH-1211, Geneva, 14, Switzerland; Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, Geneva, Switzerland; Diabetes Center, Faculty of Medicine, University of Geneva, Geneva, Switzerland; Institute of Genetics and Genomics of Geneva (iGE3), University of Geneva, Geneva, Switzerland.
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Okamoto-Uchida Y, Izawa J, Nishimura A, Hattori A, Suzuki N, Hirayama J. Post-translational Modifications are Required for Circadian Clock Regulation in Vertebrates. Curr Genomics 2019; 20:332-339. [PMID: 32476990 PMCID: PMC7235395 DOI: 10.2174/1389202919666191014094349] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 09/05/2019] [Accepted: 09/06/2019] [Indexed: 01/01/2023] Open
Abstract
Circadian clocks are intrinsic, time-tracking systems that bestow upon organisms a survival advantage. Under natural conditions, organisms are trained to follow a 24-h cycle under environmental time cues such as light to maximize their physiological efficiency. The exact timing of this rhythm is established via cell-autonomous oscillators called cellular clocks, which are controlled by transcription/translation-based negative feedback loops. Studies using cell-based systems and genetic techniques have identified the molecular mechanisms that establish and maintain cellular clocks. One such mechanism, known as post-translational modification, regulates several aspects of these cellular clock components, including their stability, subcellular localization, transcriptional activity, and interaction with other proteins and signaling pathways. In addition, these mechanisms contribute to the integration of external signals into the cellular clock machinery. Here, we describe the post-translational modifications of cellular clock regulators that regulate circadian clocks in vertebrates.
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Affiliation(s)
- Yoshimi Okamoto-Uchida
- Division of Medicinal Safety Science, National Institute of Health Sciences, Tokyo, Japan
| | - Junko Izawa
- Department of Clinical Engineering, Faculty of Health Sciences, Komatsu University, 10-10 Doihara-machi, Komatsu, Ishikawa, 923-0921, Japan
| | - Akari Nishimura
- Department of Clinical Engineering, Faculty of Health Sciences, Komatsu University, 10-10 Doihara-machi, Komatsu, Ishikawa, 923-0921, Japan
| | - Atsuhiko Hattori
- College of Liberal Arts and Sciences, Tokyo Medical and Dental University, Ichikawa, Chiba, Japan
| | - Nobuo Suzuki
- Noto Marine Laboratory, Division of Marine Environmental Studies, Institute of Nature and Environmental Technology, Kanazawa University, Noto-cho, Ishikawa 927-0553, Japan
| | - Jun Hirayama
- Department of Clinical Engineering, Faculty of Health Sciences, Komatsu University, 10-10 Doihara-machi, Komatsu, Ishikawa, 923-0921, Japan
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Molecular mechanisms and physiological importance of circadian rhythms. Nat Rev Mol Cell Biol 2019; 21:67-84. [PMID: 31768006 DOI: 10.1038/s41580-019-0179-2] [Citation(s) in RCA: 543] [Impact Index Per Article: 108.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/19/2019] [Indexed: 12/12/2022]
Abstract
To accommodate daily recurring environmental changes, animals show cyclic variations in behaviour and physiology, which include prominent behavioural states such as sleep-wake cycles but also a host of less conspicuous oscillations in neurological, metabolic, endocrine, cardiovascular and immune functions. Circadian rhythmicity is created endogenously by genetically encoded molecular clocks, whose components cooperate to generate cyclic changes in their own abundance and activity, with a periodicity of about a day. Throughout the body, such molecular clocks convey temporal control to the function of organs and tissues by regulating pertinent downstream programmes. Synchrony between the different circadian oscillators and resonance with the solar day is largely enabled by a neural pacemaker, which is directly responsive to certain environmental cues and able to transmit internal time-of-day representations to the entire body. In this Review, we discuss aspects of the circadian clock in Drosophila melanogaster and mammals, including the components of these molecular oscillators, the function and mechanisms of action of central and peripheral clocks, their synchronization and their relevance to human health.
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Droin C, Paquet ER, Naef F. Low-dimensional Dynamics of Two Coupled Biological Oscillators. NATURE PHYSICS 2019; 15:1086-1094. [PMID: 32528550 PMCID: PMC7289635 DOI: 10.1038/s41567-019-0598-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 06/18/2019] [Indexed: 06/11/2023]
Abstract
The circadian clock and the cell cycle are two biological oscillatory processes that coexist within individual cells. These two oscillators were found to interact, which can lead to their synchronization. Here, we develop a method to identify a low-dimensional stochastic model of the coupled system directly from time-lapse imaging in single cells. In particular, we infer the coupling and non-linear dynamics of the two oscillators from thousands of mouse and human single-cell fluorescence microscopy traces. This coupling predicts multiple phase-locked states showing different degrees of robustness against molecular fluctuations inherent to cellular-scale biological oscillators. For the 1:1 state, the predicted phase-shifts upon period perturbations were validated experimentally. Moreover, the phase-locked states are temperature-independent and evolutionarily conserved from mouse to human, hinting at a common underlying dynamical mechanism. Finally, we detect a signature of the coupled dynamics in a physiological context, explaining why tissues with different proliferation states exhibited shifted circadian clock phases.
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Okamoto-Uchida Y, Nishimura A, Izawa J, Hattori A, Suzuki N, Hirayama J. The Use of Chemical Compounds to Identify the Regulatory Mechanisms of Vertebrate Circadian Clocks. Curr Drug Targets 2019; 21:425-432. [PMID: 31556855 DOI: 10.2174/1389450120666190926143120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 09/04/2019] [Accepted: 09/11/2019] [Indexed: 11/22/2022]
Abstract
Circadian clocks are intrinsic, time-tracking processes that confer a survival advantage on an organism. Under natural conditions, they follow approximately a 24-h day, modulated by environmental time cues, such as light, to maximize an organism's physiological efficiency. The exact timing of this rhythm is established by cell-autonomous oscillators called cellular clocks, which are controlled by transcription-translation negative feedback loops. Studies of cell-based systems and wholeanimal models have utilized a pharmacological approach in which chemical compounds are used to identify molecular mechanisms capable of establishing and maintaining cellular clocks, such as posttranslational modifications of cellular clock regulators, chromatin remodeling of cellular clock target genes' promoters, and stability control of cellular clock components. In addition, studies with chemical compounds have contributed to the characterization of light-signaling pathways and their impact on the cellular clock. Here, the use of chemical compounds to study the molecular, cellular, and behavioral aspects of the vertebrate circadian clock system is described.
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Affiliation(s)
- Yoshimi Okamoto-Uchida
- Division of Medicinal Safety Science, National Institute of Health Sciences, Tokyo, Japan
| | - Akari Nishimura
- Department of Clinical Engineering, Faculty of Health Sciences, Komatsu University, Komatsu, Ishikawa, Japan
| | - Junko Izawa
- Department of Clinical Engineering, Faculty of Health Sciences, Komatsu University, Komatsu, Ishikawa, Japan
| | - Atsuhiko Hattori
- College of Liberal Arts and Sciences, Tokyo Medical and Dental University, Ichikawa, Chiba, Japan
| | - Nobuo Suzuki
- Noto Marine Laboratory, Division of Marine Environmental Studies, Institute of Nature and Environmental Technology, Kanazawa University, Noto-cho, Ishikawa 927-0553, Japan
| | - Jun Hirayama
- Department of Clinical Engineering, Faculty of Health Sciences, Komatsu University, Komatsu, Ishikawa, Japan
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