101
|
De Nobrega AK, Lyons LC. Aging and the clock: Perspective from flies to humans. Eur J Neurosci 2020; 51:454-481. [PMID: 30269400 PMCID: PMC6441388 DOI: 10.1111/ejn.14176] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2018] [Revised: 09/10/2018] [Accepted: 09/17/2018] [Indexed: 12/15/2022]
Abstract
Endogenous circadian oscillators regulate molecular, cellular and physiological rhythms, synchronizing tissues and organ function to coordinate activity and metabolism with environmental cycles. The technological nature of modern society with round-the-clock work schedules and heavy reliance on personal electronics has precipitated a striking increase in the incidence of circadian and sleep disorders. Circadian dysfunction contributes to an increased risk for many diseases and appears to have adverse effects on aging and longevity in animal models. From invertebrate organisms to humans, the function and synchronization of the circadian system weakens with age aggravating the age-related disorders and pathologies. In this review, we highlight the impacts of circadian dysfunction on aging and longevity and the reciprocal effects of aging on circadian function with examples from Drosophila to humans underscoring the highly conserved nature of these interactions. Additionally, we review the potential for using reinforcement of the circadian system to promote healthy aging and mitigate age-related pathologies. Advancements in medicine and public health have significantly increased human life span in the past century. With the demographics of countries worldwide shifting to an older population, there is a critical need to understand the factors that shape healthy aging. Drosophila melanogaster, as a model for aging and circadian interactions, has the capacity to facilitate the rapid advancement of research in this area and provide mechanistic insights for targeted investigations in mammals.
Collapse
Affiliation(s)
- Aliza K De Nobrega
- Program in Neuroscience, Department of Biological Science, Florida State University, Tallahassee, Florida
| | - Lisa C Lyons
- Program in Neuroscience, Department of Biological Science, Florida State University, Tallahassee, Florida
| |
Collapse
|
102
|
Puyskens A, Stinn A, van der Vaart M, Kreuchwig A, Protze J, Pei G, Klemm M, Guhlich-Bornhof U, Hurwitz R, Krishnamoorthy G, Schaaf M, Krause G, Meijer AH, Kaufmann SHE, Moura-Alves P. Aryl Hydrocarbon Receptor Modulation by Tuberculosis Drugs Impairs Host Defense and Treatment Outcomes. Cell Host Microbe 2019; 27:238-248.e7. [PMID: 31901518 DOI: 10.1016/j.chom.2019.12.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 10/30/2019] [Accepted: 12/06/2019] [Indexed: 12/20/2022]
Abstract
Antimicrobial resistance in tuberculosis (TB) is a public health threat of global dimension, worsened by increasing drug resistance. Host-directed therapy (HDT) is an emerging concept currently explored as an adjunct therapeutic strategy for TB. One potential host target is the ligand-activated transcription factor aryl hydrocarbon receptor (AhR), which binds TB virulence factors and controls antibacterial responses. Here, we demonstrate that in the context of therapy, the AhR binds several TB drugs, including front line drugs rifampicin (RIF) and rifabutin (RFB), resulting in altered host defense and drug metabolism. AhR sensing of TB drugs modulates host defense mechanisms, notably impairs phagocytosis, and increases TB drug metabolism. Targeting AhR in vivo with a small-molecule inhibitor increases RFB-treatment efficacy. Thus, the AhR markedly impacts TB outcome by affecting both host defense and drug metabolism. As a corollary, we propose the AhR as a potential target for HDT in TB in adjunct to canonical chemotherapy.
Collapse
Affiliation(s)
- Andreas Puyskens
- Department of Immunology, Max Planck Institute for Infection Biology, Charitéplatz 1, Berlin 10117, Germany
| | - Anne Stinn
- Department of Immunology, Max Planck Institute for Infection Biology, Charitéplatz 1, Berlin 10117, Germany; Department for Structural Infection Biology, Center for Structural Systems Biology, Notkestraße 85, Hamburg 22607, Germany
| | - Michiel van der Vaart
- Institute of Biology, Leiden University, Sylviusweg 72, Leiden 2333, the Netherlands
| | - Annika Kreuchwig
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Strasse 10, Berlin 13125, Germany
| | - Jonas Protze
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Strasse 10, Berlin 13125, Germany
| | - Gang Pei
- Institute of Immunology, Friedrich Loeffler Institute, Südufer 10, Greifswald-Insel Riems 17493, Germany
| | - Marion Klemm
- Department of Immunology, Max Planck Institute for Infection Biology, Charitéplatz 1, Berlin 10117, Germany
| | - Ute Guhlich-Bornhof
- Department of Immunology, Max Planck Institute for Infection Biology, Charitéplatz 1, Berlin 10117, Germany
| | - Robert Hurwitz
- Protein Purification Core Facility, Max Planck Institute for Infection Biology, Charitéplatz 1, Berlin 10117, Germany
| | - Gopinath Krishnamoorthy
- Department of Immunology, Max Planck Institute for Infection Biology, Charitéplatz 1, Berlin 10117, Germany
| | - Marcel Schaaf
- Institute of Biology, Leiden University, Sylviusweg 72, Leiden 2333, the Netherlands
| | - Gerd Krause
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Strasse 10, Berlin 13125, Germany
| | - Annemarie H Meijer
- Institute of Biology, Leiden University, Sylviusweg 72, Leiden 2333, the Netherlands
| | - Stefan H E Kaufmann
- Department of Immunology, Max Planck Institute for Infection Biology, Charitéplatz 1, Berlin 10117, Germany; Hagler Institute for Advanced Study at Texas A&M University, College Station, TX 77843, USA.
| | - Pedro Moura-Alves
- Department of Immunology, Max Planck Institute for Infection Biology, Charitéplatz 1, Berlin 10117, Germany; Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7DQ, UK.
| |
Collapse
|
103
|
Keshvari M, Nejadtaghi M, Hosseini-Beheshti F, Rastqar A, Patel N. Exploring the role of circadian clock gene and association with cancer pathophysiology. Chronobiol Int 2019; 37:151-175. [PMID: 31791146 DOI: 10.1080/07420528.2019.1681440] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Most of the processes that occur in the mind and body follow natural rhythms. Those with a cycle length of about one day are called circadian rhythms. These rhythms are driven by a system of self-sustained clocks and are entrained by environmental cues such as light-dark cycles as well as food intake. In mammals, the circadian clock system is hierarchically organized such that the master clock in the suprachiasmatic nuclei of the hypothalamus integrates environmental information and synchronizes the phase of oscillators in peripheral tissues.The circadian system is responsible for regulating a variety of physiological and behavioral processes, including feeding behavior and energy metabolism. Studies revealed that the circadian clock system consists primarily of a set of clock genes. Several genes control the biological clock, including BMAL1, CLOCK (positive regulators), CRY1, CRY2, PER1, PER2, and PER3 (negative regulators) as indicators of the peripheral clock.Circadian has increasingly become an important area of medical research, with hundreds of studies pointing to the body's internal clocks as a factor in both health and disease. Thousands of biochemical processes from sleep and wakefulness to DNA repair are scheduled and dictated by these internal clocks. Cancer is an example of health problems where chronotherapy can be used to improve outcomes and deliver a higher quality of care to patients.In this article, we will discuss knowledge about molecular mechanisms of the circadian clock and the role of clocks in physiology and pathophysiology of concerns.
Collapse
Affiliation(s)
- Mahtab Keshvari
- Department of Pharmacology and Physiology, Faculty of Medicine and Health Sciences, University of Sherbrooke, Sherbrooke, Canada
| | - Mahdieh Nejadtaghi
- Department of Medical Genetics, faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | | | - Ali Rastqar
- Department of Psychiatry and Neuroscience, Université Laval, Quebec, Canada
| | - Niraj Patel
- Centre de Recherche CERVO, Université Laval, Québec, Canada
| |
Collapse
|
104
|
|
105
|
Diurnal oscillations of endogenous H 2O 2 sustained by p66 Shc regulate circadian clocks. Nat Cell Biol 2019; 21:1553-1564. [PMID: 31768048 DOI: 10.1038/s41556-019-0420-4] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 10/01/2019] [Indexed: 02/04/2023]
Abstract
Redox balance, an essential feature of healthy physiological steady states, is regulated by circadian clocks, but whether or how endogenous redox signalling conversely regulates clockworks in mammals remains unknown. Here, we report circadian rhythms in the levels of endogenous H2O2 in mammalian cells and mouse livers. Using an unbiased method to screen for H2O2-sensitive transcription factors, we discovered that rhythmic redox control of CLOCK directly by endogenous H2O2 oscillations is required for proper intracellular clock function. Importantly, perturbations in the rhythm of H2O2 levels induced by the loss of p66Shc, which oscillates rhythmically in the liver and suprachiasmatic nucleus (SCN) of mice, disturb the rhythmic redox control of CLOCK function, reprogram hepatic transcriptome oscillations, lengthen the circadian period in mice and modulate light-induced clock resetting. Our findings suggest that redox signalling rhythms are intrinsically coupled to the circadian system through reversible oxidative modification of CLOCK and constitute essential mechanistic timekeeping components in mammals.
Collapse
|
106
|
Barik S. Molecular Interactions between Pathogens and the Circadian Clock. Int J Mol Sci 2019; 20:ijms20235824. [PMID: 31756974 PMCID: PMC6928883 DOI: 10.3390/ijms20235824] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Revised: 11/17/2019] [Accepted: 11/17/2019] [Indexed: 12/12/2022] Open
Abstract
The daily periodicity of the Earth's rotation around the Sun, referred to as circadian (Latin "circa" = about, and "diem" = day), is also mirrored in the behavior and metabolism of living beings. The discovery that dedicated cellular genes control various aspects of this periodicity has led to studies of the molecular mechanism of the circadian response at the cellular level. It is now established that the circadian genes impact on a large network of hormonal, metabolic, and immunological pathways, affecting multiple aspects of biology. Recent studies have extended the role of the circadian system to the regulation of infection, host-pathogen interaction, and the resultant disease outcome. This critical review summarizes our current knowledge of circadian-pathogen interaction at both systemic and cellular levels, but with emphasis on the molecular aspects of the regulation. Wherever applicable, the potential of a direct interaction between circadian factors and pathogenic macromolecules is also explored. Finally, this review offers new directions and guidelines for future research in this area, which should facilitate progress.
Collapse
|
107
|
Freeman SL, Kwon H, Portolano N, Parkin G, Venkatraman Girija U, Basran J, Fielding AJ, Fairall L, Svistunenko DA, Moody PCE, Schwabe JWR, Kyriacou CP, Raven EL. Heme binding to human CLOCK affects interactions with the E-box. Proc Natl Acad Sci U S A 2019; 116:19911-19916. [PMID: 31527239 PMCID: PMC6778266 DOI: 10.1073/pnas.1905216116] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The circadian clock is an endogenous time-keeping system that is ubiquitous in animals and plants as well as some bacteria. In mammals, the clock regulates the sleep-wake cycle via 2 basic helix-loop-helix PER-ARNT-SIM (bHLH-PAS) domain proteins-CLOCK and BMAL1. There is emerging evidence to suggest that heme affects circadian control, through binding of heme to various circadian proteins, but the mechanisms of regulation are largely unknown. In this work we examine the interaction of heme with human CLOCK (hCLOCK). We present a crystal structure for the PAS-A domain of hCLOCK, and we examine heme binding to the PAS-A and PAS-B domains. UV-visible and electron paramagnetic resonance spectroscopies are consistent with a bis-histidine ligated heme species in solution in the oxidized (ferric) PAS-A protein, and by mutagenesis we identify His144 as a ligand to the heme. There is evidence for flexibility in the heme pocket, which may give rise to an additional Cys axial ligand at 20K (His/Cys coordination). Using DNA binding assays, we demonstrate that heme disrupts binding of CLOCK to its E-box DNA target. Evidence is presented for a conformationally mobile protein framework, which is linked to changes in heme ligation and which has the capacity to affect binding to the E-box. Within the hCLOCK structural framework, this would provide a mechanism for heme-dependent transcriptional regulation.
Collapse
Affiliation(s)
- Samuel L Freeman
- School of Chemistry, University of Bristol, BS8 1TS Bristol, United Kingdom
| | - Hanna Kwon
- School of Chemistry, University of Bristol, BS8 1TS Bristol, United Kingdom
| | - Nicola Portolano
- Department of Chemistry, University of Leicester, LE1 7RH Leicester, United Kingdom
- Leicester Institute of Structural and Chemical Biology, University of Leicester, LE1 7RH Leicester, United Kingdom
| | - Gary Parkin
- Department of Chemistry, University of Leicester, LE1 7RH Leicester, United Kingdom
- Leicester Institute of Structural and Chemical Biology, University of Leicester, LE1 7RH Leicester, United Kingdom
| | - Umakhanth Venkatraman Girija
- Department of Chemistry, University of Leicester, LE1 7RH Leicester, United Kingdom
- Leicester Institute of Structural and Chemical Biology, University of Leicester, LE1 7RH Leicester, United Kingdom
| | - Jaswir Basran
- Department of Chemistry, University of Leicester, LE1 7RH Leicester, United Kingdom
- Leicester Institute of Structural and Chemical Biology, University of Leicester, LE1 7RH Leicester, United Kingdom
| | - Alistair J Fielding
- School of Pharmacy and Biomolecular Science, Liverpool John Moores University, Liverpool L3 3AF, United Kingdom
| | - Louise Fairall
- Leicester Institute of Structural and Chemical Biology, University of Leicester, LE1 7RH Leicester, United Kingdom
- Department of Molecular and Cell Biology, University of Leicester, LE1 7RH Leicester, United Kingdom
| | - Dimitri A Svistunenko
- School of Biological Sciences, University of Essex, Colchester, Essex CO4 3SQ, United Kingdom
| | - Peter C E Moody
- Leicester Institute of Structural and Chemical Biology, University of Leicester, LE1 7RH Leicester, United Kingdom
- Department of Molecular and Cell Biology, University of Leicester, LE1 7RH Leicester, United Kingdom
| | - John W R Schwabe
- Leicester Institute of Structural and Chemical Biology, University of Leicester, LE1 7RH Leicester, United Kingdom
- Department of Molecular and Cell Biology, University of Leicester, LE1 7RH Leicester, United Kingdom
| | - Charalambos P Kyriacou
- Department of Genetics and Genome Biology, University of Leicester, LE1 7RH Leicester, United Kingdom
| | - Emma L Raven
- School of Chemistry, University of Bristol, BS8 1TS Bristol, United Kingdom;
| |
Collapse
|
108
|
Lu M, Lan Y, Xiao J, Song M, Chen C, Liang C, Huang Q, Cao Y, Ho CT. Capsaicin Ameliorates the Redox Imbalance and Glucose Metabolism Disorder in an Insulin-Resistance Model via Circadian Clock-Related Mechanisms. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:10089-10096. [PMID: 31423784 DOI: 10.1021/acs.jafc.9b04016] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Circadian rhythms are closely associated with metabolic homeostasis. Metabolic disorders can be alleviated by many bioactive components through controlling of clock gene expressions. Capsaicin has been demonstrated with many beneficial effects including anti-obesity and anti-insulin resistance activities, yet whether the rhythmic expression of circadian clock genes are involved in the regulation of redox imbalance and glucose metabolism disorder by capsaicin remains unclear. In this work, the insulin resistance was induced in HepG2 cells by treatment of glucosamine. Glucose uptake levels, reactive oxygen species, H2O2 production, and mitochondrial membrane potential (MMP) were measured with/without capsaicin cotreatment. The mRNA and protein expressions of core circadian clock genes were evaluated by RT-qPCR and western blot analysis. Our study revealed that circadian misalignment could be ameliorated by capsaicin. The glucosamine-induced cellular redox imbalance and glucose metabolism disorder were ameliorated by capsaicin in a Bmal1-dependent manner.
Collapse
Affiliation(s)
| | | | | | | | | | | | - Qingrong Huang
- Department of Food Science , Rutgers University , New Brunswick , New Jersey 08901 , United States
| | | | - Chi-Tang Ho
- Department of Food Science , Rutgers University , New Brunswick , New Jersey 08901 , United States
| |
Collapse
|
109
|
Stenzinger M, Karpova D, Unterrainer C, Harenkamp S, Wiercinska E, Hoerster K, Pfeffer M, Maronde E, Bonig H. Hematopoietic-Extrinsic Cues Dictate Circadian Redistribution of Mature and Immature Hematopoietic Cells in Blood and Spleen. Cells 2019; 8:E1033. [PMID: 31491915 PMCID: PMC6769956 DOI: 10.3390/cells8091033] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 08/29/2019] [Accepted: 09/02/2019] [Indexed: 12/27/2022] Open
Abstract
Circadian oscillations in circulating leukocyte subsets including immature hematopoietic cells have been appreciated; the origin and nature of these alterations remain elusive. Our analysis of wild-type C57BL/6 mice under constant darkness confirmed circadian fluctuations of circulating leukocytes and clonogenic cells in blood and spleen but not bone marrow. Clock gene deficient Bmal1-/- mice lacked this regulation. Cell cycle analyses in the different hematopoietic compartments excluded circadian changes in total cell numbers, rather favoring shifting hematopoietic cell redistribution as the underlying mechanism. Transplant chimeras demonstrate that circadian rhythms within the stroma mediate the oscillations independently of hematopoietic-intrinsic cues. We provide evidence of circadian CXCL12 regulation via clock genes in vitro and were able to confirm CXCL12 oscillation in bone marrow and blood in vivo. Our studies further implicate cortisol as the conveyor of circadian input to bone marrow stroma and mediator of the circadian leukocyte oscillation. In summary, we establish hematopoietic-extrinsic cues as causal for circadian redistribution of circulating mature/immature blood cells.
Collapse
Affiliation(s)
- Miriam Stenzinger
- Institute for Immunology, University Hospital Heidelberg and Institute for Clinical Transfusion Medicine and Cell Therapy, 69120 Heidelberg, Germany
- Institute for Transfusion Medicine and Immunohematology, Goethe University and German Red Cross Blood Service Baden-Württemberg-Hessen, Institute Frankfurt a. M.; 60528 Frankfurt a. M., Germany
| | - Darja Karpova
- Institute for Transfusion Medicine and Immunohematology, Goethe University and German Red Cross Blood Service Baden-Württemberg-Hessen, Institute Frankfurt a. M.; 60528 Frankfurt a. M., Germany
- Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Christian Unterrainer
- Institute for Immunology, University Hospital Heidelberg and Institute for Clinical Transfusion Medicine and Cell Therapy, 69120 Heidelberg, Germany
| | - Sabine Harenkamp
- Institute for Transfusion Medicine and Immunohematology, Goethe University and German Red Cross Blood Service Baden-Württemberg-Hessen, Institute Frankfurt a. M.; 60528 Frankfurt a. M., Germany
| | - Eliza Wiercinska
- Institute for Transfusion Medicine and Immunohematology, Goethe University and German Red Cross Blood Service Baden-Württemberg-Hessen, Institute Frankfurt a. M.; 60528 Frankfurt a. M., Germany
| | - Keven Hoerster
- Institute for Transfusion Medicine and Immunohematology, Goethe University and German Red Cross Blood Service Baden-Württemberg-Hessen, Institute Frankfurt a. M.; 60528 Frankfurt a. M., Germany
| | - Martina Pfeffer
- Institute for Anatomy II, Division of Medicine, Heinrich Heine University, 40225 Düsseldorf, Germany
| | - Erik Maronde
- Institute for Anatomy III, Goethe University, 60596 Frankfurt a. M., Germany
| | - Halvard Bonig
- Institute for Transfusion Medicine and Immunohematology, Goethe University and German Red Cross Blood Service Baden-Württemberg-Hessen, Institute Frankfurt a. M.; 60528 Frankfurt a. M., Germany.
| |
Collapse
|
110
|
Kolonko M, Greb-Markiewicz B. bHLH-PAS Proteins: Their Structure and Intrinsic Disorder. Int J Mol Sci 2019; 20:ijms20153653. [PMID: 31357385 PMCID: PMC6695611 DOI: 10.3390/ijms20153653] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 07/15/2019] [Accepted: 07/16/2019] [Indexed: 12/21/2022] Open
Abstract
The basic helix–loop–helix/Per-ARNT-SIM (bHLH–PAS) proteins are a class of transcriptional regulators, commonly occurring in living organisms and highly conserved among vertebrates and invertebrates. These proteins exhibit a relatively well-conserved domain structure: the bHLH domain located at the N-terminus, followed by PAS-A and PAS-B domains. In contrast, their C-terminal fragments present significant variability in their primary structure and are unique for individual proteins. C-termini were shown to be responsible for the specific modulation of protein action. In this review, we present the current state of knowledge, based on NMR and X-ray analysis, concerning the structural properties of bHLH–PAS proteins. It is worth noting that all determined structures comprise only selected domains (bHLH and/or PAS). At the same time, substantial parts of proteins, comprising their long C-termini, have not been structurally characterized to date. Interestingly, these regions appear to be intrinsically disordered (IDRs) and are still a challenge to research. We aim to emphasize the significance of IDRs for the flexibility and function of bHLH–PAS proteins. Finally, we propose modern NMR methods for the structural characterization of the IDRs of bHLH–PAS proteins.
Collapse
Affiliation(s)
- Marta Kolonko
- Department of Biochemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wroclaw, Poland
| | - Beata Greb-Markiewicz
- Department of Biochemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wroclaw, Poland.
| |
Collapse
|
111
|
Verlande A, Masri S. Circadian Clocks and Cancer: Timekeeping Governs Cellular Metabolism. Trends Endocrinol Metab 2019; 30:445-458. [PMID: 31155396 PMCID: PMC6679985 DOI: 10.1016/j.tem.2019.05.001] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 04/26/2019] [Accepted: 05/02/2019] [Indexed: 12/30/2022]
Abstract
The circadian clock is a biological mechanism that dictates an array of rhythmic physiological processes. Virtually all cells contain a functional clock whose disruption results in altered timekeeping and detrimental systemic effects, including cancer. Recent advances have connected genetic disruption of the clock with multiple transcriptional and signaling networks controlling tumor initiation and progression. An additional feature of this circadian control relies on cellular metabolism, both within the tumor microenvironment and the organism systemically. A discussion of major advances related to cancer metabolism and the circadian clock will be outlined, including new efforts related to metabolic flux of transformed cells, metabolic heterogeneity of tumors, and the implications of circadian control of these pathways.
Collapse
Affiliation(s)
- Amandine Verlande
- Department of Biological Chemistry, University of California, Irvine, CA 92697, USA; Chao Family Comprehensive Cancer Center, University of California, Irvine, CA 92867, USA; Center for Epigenetics and Metabolism, University of California, Irvine, CA 92697, USA
| | - Selma Masri
- Department of Biological Chemistry, University of California, Irvine, CA 92697, USA; Chao Family Comprehensive Cancer Center, University of California, Irvine, CA 92867, USA; Center for Epigenetics and Metabolism, University of California, Irvine, CA 92697, USA.
| |
Collapse
|
112
|
Castelo-Szekely V, De Matos M, Tusup M, Pascolo S, Ule J, Gatfield D. Charting DENR-dependent translation reinitiation uncovers predictive uORF features and links to circadian timekeeping via Clock. Nucleic Acids Res 2019; 47:5193-5209. [PMID: 30982898 PMCID: PMC6547434 DOI: 10.1093/nar/gkz261] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 03/25/2019] [Accepted: 04/08/2019] [Indexed: 02/05/2023] Open
Abstract
The non-canonical initiation factor DENR promotes translation reinitiation on mRNAs harbouring upstream open reading frames (uORFs). Moreover, DENR depletion shortens circadian period in mouse fibroblasts, suggesting involvement of uORF usage and reinitiation in clock regulation. To identify DENR-regulated translation events transcriptome-wide and, in particular, specific core clock transcripts affected by this mechanism, we have used ribosome profiling in DENR-deficient NIH3T3 cells. We uncovered 240 transcripts with altered translation rate, and used linear regression analysis to extract 5' UTR features predictive of DENR dependence. Among core clock genes, we identified Clock as a DENR target. Using Clock 5' UTR mutants, we mapped the specific uORF through which DENR acts to regulate CLOCK protein biosynthesis. Notably, these experiments revealed an alternative downstream start codon, likely representing the bona fide CLOCK N-terminus. Our findings provide insights into uORF-mediated translational regulation that can regulate the mammalian circadian clock and gene expression at large.
Collapse
Affiliation(s)
- Violeta Castelo-Szekely
- Center for Integrative Genomics, University of Lausanne, Genopode, 1015 Lausanne, Switzerland
| | - Mara De Matos
- Center for Integrative Genomics, University of Lausanne, Genopode, 1015 Lausanne, Switzerland
| | - Marina Tusup
- Department of Dermatology, University Hospital of Zurich, Gloriastrasse 31, 8091 Zurich, Switzerland
- Faculty of Medicine, University of Zurich, 8091 Zurich, Switzerland
| | - Steve Pascolo
- Department of Dermatology, University Hospital of Zurich, Gloriastrasse 31, 8091 Zurich, Switzerland
- Faculty of Medicine, University of Zurich, 8091 Zurich, Switzerland
| | - Jernej Ule
- Department of Neuromuscular Diseases, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - David Gatfield
- Center for Integrative Genomics, University of Lausanne, Genopode, 1015 Lausanne, Switzerland
| |
Collapse
|
113
|
Chen H, Gao L, Yang D, Xiao Y, Zhang M, Li C, Wang A, Jin Y. Coordination between the circadian clock and androgen signaling is required to sustain rhythmic expression of Elovl3 in mouse liver. J Biol Chem 2019; 294:7046-7056. [PMID: 30862677 PMCID: PMC6497949 DOI: 10.1074/jbc.ra118.005950] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Revised: 02/19/2019] [Indexed: 12/18/2022] Open
Abstract
ELOVL3 is a very long-chain fatty acid elongase, and its mRNA levels display diurnal rhythmic changes exclusively in adult male mouse livers. This cyclical expression of hepatic Elovl3 is potentially controlled by the circadian clock, related hormones, and transcriptional factors. It remains unknown, however, whether the circadian clock, in conjunction with androgen signaling, functions in maintaining the rhythmic expression of Elovl3 in a sexually dimorphic manner. Under either zeitgeber or circadian time, WT mouse livers exhibited a robust circadian rhythmicity in the expression of circadian clock genes and Elovl3 In contrast, male Bmal1-/- mice displayed severely weakened expression of hepatic circadian clock genes, resulting in relatively high, but nonrhythmic, Elovl3 expression levels. ChIP assays revealed that NR1D1 binds to the Elovl3 promoter upon circadian change in WT mouse livers in vivo, and a diminished binding was observed in male Bmal1-/- mouse livers. Additionally, female mouse livers exhibited constant low levels of Elovl3 expression. Castration markedly reduced Elovl3 expression levels in male mouse livers but did not disrupt circadian variation of Elovl3 Injection of female mice with 5α-dihydrotestosterone induced Elovl3 rhythmicity in the liver. In AML12 cells, 5α-dihydrotestosterone also elevated Elovl3 expression in a time-dependent manner. In contrast, flutamide efficiently attenuated this induction effect. In conclusion, a lack of either the circadian clock or androgen signaling impairs hepatic Elovl3 expression, highlighting the observation that coordination between the circadian clock and androgen signaling is required to sustain the rhythmic expression of Elovl3 in mouse liver.
Collapse
Affiliation(s)
- Huatao Chen
- From the Departments of Clinical Veterinary Medicine and
- the Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Northwest A&F University, Yangling, 712100 Shaanxi, China
| | - Lei Gao
- From the Departments of Clinical Veterinary Medicine and
- the Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Northwest A&F University, Yangling, 712100 Shaanxi, China
| | - Dan Yang
- From the Departments of Clinical Veterinary Medicine and
- the Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Northwest A&F University, Yangling, 712100 Shaanxi, China
| | - Yaoyao Xiao
- From the Departments of Clinical Veterinary Medicine and
- the Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Northwest A&F University, Yangling, 712100 Shaanxi, China
| | - Manhui Zhang
- From the Departments of Clinical Veterinary Medicine and
- the Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Northwest A&F University, Yangling, 712100 Shaanxi, China
| | - Cuimei Li
- From the Departments of Clinical Veterinary Medicine and
- the Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Northwest A&F University, Yangling, 712100 Shaanxi, China
| | - Aihua Wang
- the Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Northwest A&F University, Yangling, 712100 Shaanxi, China
- Preventive Veterinary Medicine, College of Veterinary Medicine, and
| | - Yaping Jin
- From the Departments of Clinical Veterinary Medicine and
- the Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Northwest A&F University, Yangling, 712100 Shaanxi, China
| |
Collapse
|
114
|
Chang WH, Lai AG. Timing gone awry: distinct tumour suppressive and oncogenic roles of the circadian clock and crosstalk with hypoxia signalling in diverse malignancies. J Transl Med 2019; 17:132. [PMID: 31014368 PMCID: PMC6480786 DOI: 10.1186/s12967-019-1880-9] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 04/09/2019] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND The circadian clock governs a large variety of fundamentally important physiological processes in all three domains of life. Consequently, asynchrony in timekeeping mechanisms could give rise to cellular dysfunction underpinning many disease pathologies including human neoplasms. Yet, detailed pan-cancer evidence supporting this notion has been limited. METHODS In an integrated approach uniting genomic, transcriptomic and clinical data of 21 cancer types (n = 18,484), we interrogated copy number and transcript profiles of 32 circadian clock genes to identify putative loss-of-function (ClockLoss) and gain-of-function (ClockGain) players. Kaplan-Meier, Cox regression and receiver operating characteristic analyses were employed to evaluate the prognostic significance of both gene sets. RESULTS ClockLoss and ClockGain were associated with tumour-suppressing and tumour-promoting roles respectively. Downregulation of ClockLoss genes resulted in significantly higher mortality rates in five cancer cohorts (n = 2914): bladder (P = 0.027), glioma (P < 0.0001), pan-kidney (P = 0.011), clear cell renal cell (P < 0.0001) and stomach (P = 0.0007). In contrast, patients with high expression of oncogenic ClockGain genes had poorer survival outcomes (n = 2784): glioma (P < 0.0001), pan-kidney (P = 0.0034), clear cell renal cell (P = 0.014), lung (P = 0.046) and pancreas (P = 0.0059). Both gene sets were independent of other clinicopathological features to permit further delineation of tumours within the same stage. Circadian reprogramming of tumour genomes resulted in activation of numerous oncogenic pathways including those associated with cancer stem cells, suggesting that the circadian clock may influence self-renewal mechanisms. Within the hypoxic tumour microenvironment, circadian dysregulation is exacerbated by tumour hypoxia in glioma, renal, lung and pancreatic cancers, resulting in additional death risks. Tumour suppressive ClockLoss genes were negatively correlated with hypoxia inducible factor-1A targets in glioma patients, providing a novel framework for investigating the hypoxia-clock signalling axis. CONCLUSIONS Loss of timekeeping fidelity promotes tumour progression and influences clinical outcomes. ClockLoss and ClockGain may offer novel druggable targets for improving patient prognosis. Both gene sets can be used for patient stratification in adjuvant chronotherapy treatment. Emerging interactions between the circadian clock and hypoxia may be harnessed to achieve therapeutic advantage using hypoxia-modifying compounds in combination with first-line treatments.
Collapse
Affiliation(s)
- Wai Hoong Chang
- Nuffield Department of Medicine, University of Oxford, Old Road Campus, Oxford, OX3 7FZ UK
| | - Alvina G. Lai
- Nuffield Department of Medicine, University of Oxford, Old Road Campus, Oxford, OX3 7FZ UK
| |
Collapse
|
115
|
Abstract
Circadian oscillators are networks of biochemical feedback loops that generate 24-hour rhythms in organisms from bacteria to animals. These periodic rhythms result from a complex interplay among clock components that are specific to the organism, but share molecular mechanisms across kingdoms. A full understanding of these processes requires detailed knowledge, not only of the biochemical properties of clock proteins and their interactions, but also of the three-dimensional structure of clockwork components. Posttranslational modifications and protein–protein interactions have become a recent focus, in particular the complex interactions mediated by the phosphorylation of clock proteins and the formation of multimeric protein complexes that regulate clock genes at transcriptional and translational levels. This review covers the structural aspects of circadian oscillators, and serves as a primer for this exciting realm of structural biology.
Collapse
Affiliation(s)
- Reena Saini
- Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland.,Max-Planck-Institut für Pflanzenzüchtungsforschung, Cologne, Germany
| | - Mariusz Jaskolski
- Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland.,Department of Crystallography, Faculty of Chemistry, A. Mickiewicz University, Poznan, Poland
| | - Seth J Davis
- Max-Planck-Institut für Pflanzenzüchtungsforschung, Cologne, Germany. .,Department of Biology, University of York, York, UK.
| |
Collapse
|
116
|
ER stress activation impairs the expression of circadian clock and clock-controlled genes in NIH3T3 cells via an ATF4-dependent mechanism. Cell Signal 2019; 57:89-101. [PMID: 30703445 DOI: 10.1016/j.cellsig.2019.01.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 01/25/2019] [Accepted: 01/25/2019] [Indexed: 02/06/2023]
Abstract
Endoplasmic reticulum (ER) stress and circadian clockwork signaling pathways mutually regulate various cellular functions, but the details regarding the cross-talk between these pathways in mammalian cells are unclear. In this study, whether perturbation of ER stress signaling affects the cellular circadian clockwork and transcription of clock-controlled genes was investigated in NIH3T3 mouse fibroblasts. An NIH3T3 cell model stably expressing luciferase (Luc) under the control of the Bmal1 clock gene promoter was established using a lentiviral system. Then, Luc activity was monitored in real-time to detect Bmal1-Luc oscillations. The ER stress activators thapsigargin (Tg) and tunicamycin (Tm) markedly reduced Bmal1-Luc oscillation amplitudes and induced phase delay shifts in NIH3T3 cells. Treatment with Tg/Tm activated ER stress signaling by upregulating GRP78, CHOP, ATF6, and ATF4 and simultaneously significantly decreased BMAL1 protein levels and inhibited the transcription of circadian clock (Bmal1, Per2, Nr1d1, and Dbp) and clock-controlled (Scad1, Fgf7, and Arnt) genes. 4-Phenylbutyric acid, an ER stress inhibitor, alleviated the transcriptional repression of the circadian clock genes and partially restored Bmal1-Luc oscillation amplitudes in Tg- or Tm-treated NIH3T3 cells. More importantly, knock-down of ATF4, but not ATF6, in Tg-treated NIH3T3 cells partially rescued Bmal1-Luc oscillation amplitudes and mRNA expression of the four circadian clock genes. Taken together, our study demonstrates that ER stress activation inhibits the transcription of circadian clock and clock-controlled genes via an ATF4-dependent mechanism.
Collapse
|
117
|
Streamlined procedure for gene knockouts using all-in-one adenoviral CRISPR-Cas9. Sci Rep 2019; 9:277. [PMID: 30670765 PMCID: PMC6342919 DOI: 10.1038/s41598-018-36736-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Accepted: 11/26/2018] [Indexed: 12/21/2022] Open
Abstract
CRISPR-Cas9 is a powerful gene editing technique that can induce mutations in a target gene of interest in almost any mammalian cell line. However, its practicality can be limited if target cell lines are difficult to transfect and do not proliferate. In the current study, we have developed a streamlined approach for CRISPR-based gene knockouts with three key advantages, which allows phenotypic assay of gene knockouts without clonal selection and expansion. First, it integrates into a single, all-in-one vector transgenes for Cas9, sgRNA, and a fluorescence marker. Second, we used the Gateway system to rapidly clone specific sgRNAs into the all-in-one vector through PCR and in vitro recombination, without conventional enzyme digestion and ligation. Third, it uses adenovirus for the capacity to package the all-in-one vector, and for its high efficiency of transduction. We tested the all-in-one adenoviral CRISPR-Cas9 in a circadian clock model cell line U2OS, and demonstrated that essential clock genes such as Bmal1 and Per1 were knocked out so efficiently that functional assays could be performed from the heterogenic population without any clonal selection and expansion. This streamlined approach may prove invaluable for rapid functional assays of candidate genes in diverse biological pathways, including the circadian clock.
Collapse
|
118
|
Abstract
In this review from Murre, the evolution of HLH genes, the structures of HLH domains, and the elaborate activities of HLH proteins in multicellular life are discussed. Helix–loop–helix (HLH) proteins are dimeric transcription factors that control lineage- and developmental-specific gene programs. Genes encoding for HLH proteins arose in unicellular organisms >600 million years ago and then duplicated and diversified from ancestral genes across the metazoan and plant kingdoms to establish multicellularity. Hundreds of HLH proteins have been identified with diverse functions in a wide variety of cell types. HLH proteins orchestrate lineage specification, commitment, self-renewal, proliferation, differentiation, and homing. HLH proteins also regulate circadian clocks, protect against hypoxic stress, promote antigen receptor locus assembly, and program transdifferentiation. HLH proteins deposit or erase epigenetic marks, activate noncoding transcription, and sequester chromatin remodelers across the chromatin landscape to dictate enhancer–promoter communication and somatic recombination. Here the evolution of HLH genes, the structures of HLH domains, and the elaborate activities of HLH proteins in multicellular life are discussed.
Collapse
Affiliation(s)
- Cornelis Murre
- Division of Biological Sciences, University of California at San Diego, La Jolla, California 92903, USA
| |
Collapse
|
119
|
Rosensweig C, Green CB. Periodicity, repression, and the molecular architecture of the mammalian circadian clock. Eur J Neurosci 2018; 51:139-165. [PMID: 30402960 DOI: 10.1111/ejn.14254] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 10/03/2018] [Accepted: 10/22/2018] [Indexed: 12/12/2022]
Abstract
Large molecular machines regulate daily cycles of transcriptional activity and help generate rhythmic behavior. In recent years, structural and biochemical analyses have elucidated a number of principles guiding the interactions of proteins that form the basis of circadian timing. In its simplest form, the circadian clock is composed of a transcription/translation feedback loop. However, this description elides a complicated process of activator recruitment, chromatin decompaction, recruitment of coactivators, expression of repressors, formation of a repressive complex, repression of the activators, and ultimately degradation of the repressors and reinitiation of the cycle. Understanding the core principles underlying the clock requires careful examination of molecular and even atomic level details of these processes. Here, we review major structural and biochemical findings in circadian biology and make the argument that shared protein interfaces within the clockwork are critical for both the generation of rhythmicity and timing of the clock.
Collapse
Affiliation(s)
- Clark Rosensweig
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Carla B Green
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, Texas
| |
Collapse
|
120
|
Emerging role of circadian rhythm in bone remodeling. J Mol Med (Berl) 2018; 97:19-24. [PMID: 30446776 DOI: 10.1007/s00109-018-1723-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 11/07/2018] [Accepted: 11/09/2018] [Indexed: 12/31/2022]
Abstract
The 24-h rhythm of behavioral and physiological processes is a typical biological phenomenon regulated by a group of circadian rhythm genes. Dysfunction of the circadian rhythm can cause a wide range of problems, such as cancer and metabolic diseases. In recent decades, increased understanding of the roles of circadian rhythm genes in the bone remodeling process have been documented, including osteoblastic bone formation, osteoclastic bone resorption, and osteoblast/osteoclast communication. A timely review of the current findings may help to facilitate the new field of circadian rhythmic bone remodeling research. Targeted pharmacological modulation of circadian rhythm genes is a possible therapeutic approach through which to overcome bone remodeling problems in the future.
Collapse
|
121
|
Opposite Carcinogenic Effects of Circadian Clock Gene BMAL1. Sci Rep 2018; 8:16023. [PMID: 30375470 PMCID: PMC6207783 DOI: 10.1038/s41598-018-34433-4] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 10/17/2018] [Indexed: 12/19/2022] Open
Abstract
The circadian clock confers daily rhythmicity on many biochemical and physiological functions and its disruption is associated with increased risks of developing obesity, diabetes, heart disease and cancer. Although, there are studies on the role of Bmal1 in carcinogenesis using germline, conditional or tissue-specific knockouts, it is still not well understood how BMAL1 gene affects cancer-related biological events at the molecular level. We, therefore, took an in vitro approach to understand the contribution of BMAL1 in this molecular mechanism using human breast epithelial cell lines by knocking out BMAL1 gene with CRISPR technology. We preferred epithelial cells over fibroblasts as the most of cancers originate from epithelial cells. After obtaining BMAL1 knockouts by targeting the gene at two different sites from non-tumorigenic MCF10A and invasive tumorigenic MDA-MB-231 cells, we analysed apoptosis and invasion properties of the cell lines as representative events in tumor development. BMAL1 disruption sensitized both cell lines to a bulky-DNA adduct forming agent (cisplatin) and a double-strand break-inducing agent (doxorubicin), while it enhanced the invasive properties of MDA-MB-231 cells. These results show that the disruption of clock genes may have opposing carcinogenic effects.
Collapse
|
122
|
Chiesa JJ, Baidanoff FM, Golombek DA. Don't just say no: Differential pathways and pharmacological responses to diverse nitric oxide donors. Biochem Pharmacol 2018; 156:1-9. [PMID: 30080991 DOI: 10.1016/j.bcp.2018.08.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 08/02/2018] [Indexed: 12/18/2022]
Abstract
Nitric oxide (NO) is a gaseous free radical molecule with a short half-life (∼1 s), which can gain or lose an electron into three interchangeable redox-dependent forms, the radical (NO), the nitrosonium cation (NO+), and nitroxyl anion (HNO). NO acts as an intra and extracellular signaling molecule regulating a wide range of functions in the cardiovascular, immune, and nervous system. NO donors are collectively known by their ability to release NOin vitro and in vivo, being proposed as therapeutic pharmacological tools for the treatment of several pathologies, such as cardiovascular disease. The highly reactive NO molecule is easily oxidized under physiological conditions to N-oxides, nitrate/nitrite and nitrogen dioxide. Different cellular responses are triggered depending on: 1) NO concentration [e.g., nanomolar for heme coordination in the allosteric site of guanylate cyclase (sGC) enzyme]; 2) the type of chemical bound to the nitrosated group (i.e., bound to nitrogen, N-nitro, or bound to sulphur atom, S-nitro) determining post-translational cysteine nitrosation; 3) the time-dependent availability of molecular targets. Classic NO donors are: organic nitrates (e.g., nitroglycerin, or glyceryl trinitrate, GTN; isosorbide mononitrate, ISMN), diazeniumdiolates having a diolate group [or NONOates, e.g., 2-(N,N-diethylamino)-diazenolate-2-oxide], S-nitrosothiols (e.g., S-nitroso glutathione, GSNO; S-nitroso-N-acetylpenicillamine, SNAP) or the organic salt sodium nitroprusside (SNP). In addition, nitroxyl (HNO) donors such as Piloty's acid and Angeli's salt can also be considered. The specific NO form released, as well as its differential reactivity to thiols, could act on different molecular targets and should be discussed in the context of: a) the type and amount of NO species determining the sensitivity of molecular targets (e.g., heme coordination, or S-nitrosation); b) the cellular redox state that could gate different effects. Experimental designs should take special care when choosing which NO donors to use, since different outcomes are to be expected. This article will comment recent findings regarding physiological responses involving NO species and their pharmacological modulation with donor drugs, especially in the context of the photic transduction pathways at the hypothalamic circadian clock.
Collapse
Affiliation(s)
- Juan J Chiesa
- Laboratorio de Cronobiología, Universidad Nacional de Quilmes/CONICET, Argentina
| | - Fernando M Baidanoff
- Laboratorio de Cronobiología, Universidad Nacional de Quilmes/CONICET, Argentina
| | - Diego A Golombek
- Laboratorio de Cronobiología, Universidad Nacional de Quilmes/CONICET, Argentina.
| |
Collapse
|
123
|
Dyar KA, Hubert MJ, Mir AA, Ciciliot S, Lutter D, Greulich F, Quagliarini F, Kleinert M, Fischer K, Eichmann TO, Wright LE, Peña Paz MI, Casarin A, Pertegato V, Romanello V, Albiero M, Mazzucco S, Rizzuto R, Salviati L, Biolo G, Blaauw B, Schiaffino S, Uhlenhaut NH. Transcriptional programming of lipid and amino acid metabolism by the skeletal muscle circadian clock. PLoS Biol 2018; 16:e2005886. [PMID: 30096135 PMCID: PMC6105032 DOI: 10.1371/journal.pbio.2005886] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 08/22/2018] [Accepted: 07/27/2018] [Indexed: 12/30/2022] Open
Abstract
Circadian clocks are fundamental physiological regulators of energy homeostasis, but direct transcriptional targets of the muscle clock machinery are unknown. To understand how the muscle clock directs rhythmic metabolism, we determined genome-wide binding of the master clock regulators brain and muscle ARNT-like protein 1 (BMAL1) and REV-ERBα in murine muscles. Integrating occupancy with 24-hr gene expression and metabolomics after muscle-specific loss of BMAL1 and REV-ERBα, here we unravel novel molecular mechanisms connecting muscle clock function to daily cycles of lipid and protein metabolism. Validating BMAL1 and REV-ERBα targets using luciferase assays and in vivo rescue, we demonstrate how a major role of the muscle clock is to promote diurnal cycles of neutral lipid storage while coordinately inhibiting lipid and protein catabolism prior to awakening. This occurs by BMAL1-dependent activation of Dgat2 and REV-ERBα-dependent repression of major targets involved in lipid metabolism and protein turnover (MuRF-1, Atrogin-1). Accordingly, muscle-specific loss of BMAL1 is associated with metabolic inefficiency, impaired muscle triglyceride biosynthesis, and accumulation of bioactive lipids and amino acids. Taken together, our data provide a comprehensive overview of how genomic binding of BMAL1 and REV-ERBα is related to temporal changes in gene expression and metabolite fluctuations.
Collapse
Affiliation(s)
- Kenneth Allen Dyar
- Helmholtz Diabetes Center (HMGU) and German Center for Diabetes Research (DZD), Institute for Diabetes and Obesity (IDO), Munich, Germany
- Venetian Institute of Molecular Medicine (VIMM), Padova, Italy
| | - Michaël Jean Hubert
- Helmholtz Diabetes Center (HMGU) and German Center for Diabetes Research (DZD), Institute for Diabetes and Obesity (IDO), Munich, Germany
| | - Ashfaq Ali Mir
- Helmholtz Diabetes Center (HMGU) and German Center for Diabetes Research (DZD), Institute for Diabetes and Obesity (IDO), Munich, Germany
| | | | - Dominik Lutter
- Helmholtz Diabetes Center (HMGU) and German Center for Diabetes Research (DZD), Institute for Diabetes and Obesity (IDO), Munich, Germany
| | - Franziska Greulich
- Helmholtz Diabetes Center (HMGU) and German Center for Diabetes Research (DZD), Institute for Diabetes and Obesity (IDO), Munich, Germany
| | - Fabiana Quagliarini
- Helmholtz Diabetes Center (HMGU) and German Center for Diabetes Research (DZD), Institute for Diabetes and Obesity (IDO), Munich, Germany
| | - Maximilian Kleinert
- Helmholtz Diabetes Center (HMGU) and German Center for Diabetes Research (DZD), Institute for Diabetes and Obesity (IDO), Munich, Germany
| | - Katrin Fischer
- Helmholtz Diabetes Center (HMGU) and German Center for Diabetes Research (DZD), Institute for Diabetes and Obesity (IDO), Munich, Germany
| | | | | | | | - Alberto Casarin
- Clinical Genetics Unit, Department of Woman and Child Health, University of Padova, and IRP Città della Speranza, Padova, Italy
| | - Vanessa Pertegato
- Clinical Genetics Unit, Department of Woman and Child Health, University of Padova, and IRP Città della Speranza, Padova, Italy
| | | | - Mattia Albiero
- Venetian Institute of Molecular Medicine (VIMM), Padova, Italy
| | - Sara Mazzucco
- Clinica Medica, Department of Medical Sciences, University of Trieste, Trieste, Italy
| | - Rosario Rizzuto
- Department of Biomedical Sciences, University of Padova, Padova, Italy
| | - Leonardo Salviati
- Clinical Genetics Unit, Department of Woman and Child Health, University of Padova, and IRP Città della Speranza, Padova, Italy
| | - Gianni Biolo
- Clinica Medica, Department of Medical Sciences, University of Trieste, Trieste, Italy
| | - Bert Blaauw
- Venetian Institute of Molecular Medicine (VIMM), Padova, Italy
- Department of Biomedical Sciences, University of Padova, Padova, Italy
| | | | - N. Henriette Uhlenhaut
- Helmholtz Diabetes Center (HMGU) and German Center for Diabetes Research (DZD), Institute for Diabetes and Obesity (IDO), Munich, Germany
- Gene Center, Ludwig-Maximilians-Universitaet (LMU), Munich, Germany
| |
Collapse
|
124
|
Deng W, Zhu S, Zeng L, Liu J, Kang R, Yang M, Cao L, Wang H, Billiar TR, Jiang J, Xie M, Tang D. The Circadian Clock Controls Immune Checkpoint Pathway in Sepsis. Cell Rep 2018; 24:366-378. [PMID: 29996098 PMCID: PMC6094382 DOI: 10.1016/j.celrep.2018.06.026] [Citation(s) in RCA: 104] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 02/28/2018] [Accepted: 06/05/2018] [Indexed: 12/21/2022] Open
Abstract
Sepsis and septic shock are associated with life-threatening organ dysfunction caused by an impaired host response to infections. Although circadian clock disturbance impairs the early inflammatory response, its impact on post-septic immunosuppression remains poorly elucidated. Here, we show that Bmal1, a core circadian clock gene, plays a role in the regulation of host immune responses in experimental sepsis. Mechanistically, Bmal1 deficiency in macrophages increases PKM2 expression and lactate production, which is required for expression of the immune checkpoint protein PD-L1 in a STAT1-dependent manner. Consequently, targeted ablation of Pkm2 in myeloid cells or administration of anti-PD-L1-neutralizing antibody or supplementation with recombinant interleukin-7 (IL-7) facilitates microbial clearance, inhibits T cell apoptosis, reduces multiple organ dysfunction, and reduces septic death in Bmal1-deficient mice. Collectively, these findings suggest that the circadian clock controls the immune checkpoint pathway in macrophages and therefore represents a potential therapeutic target for lethal infection.
Collapse
Affiliation(s)
- Wenjun Deng
- The Third Affiliated Hospital, Center for DAMP Biology, Key Laboratory for Major Obstetric Diseases of Guangdong Province, Key Laboratory of Protein Modification and Degradation of Guangdong Higher Education Institutes, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, Guangdong 510510, China; Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Shan Zhu
- The Third Affiliated Hospital, Center for DAMP Biology, Key Laboratory for Major Obstetric Diseases of Guangdong Province, Key Laboratory of Protein Modification and Degradation of Guangdong Higher Education Institutes, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, Guangdong 510510, China
| | - Ling Zeng
- State Key Laboratory of Trauma, Burns and Combined Injury, Research Institute of Surgery, Research Institute for Traffic Medicine of People's Liberation Army, Daping Hospital, Third Military Medical University, Chongqing 400042, China
| | - Jiao Liu
- The Third Affiliated Hospital, Center for DAMP Biology, Key Laboratory for Major Obstetric Diseases of Guangdong Province, Key Laboratory of Protein Modification and Degradation of Guangdong Higher Education Institutes, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, Guangdong 510510, China
| | - Rui Kang
- Department of Surgery, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Minghua Yang
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Lizhi Cao
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Haichao Wang
- Laboratory of Emergency Medicine, North Shore University Hospital and The Feinstein Institute for Medical Research, Manhasset, NY 11030, USA
| | - Timothy R Billiar
- Department of Surgery, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Jianxin Jiang
- State Key Laboratory of Trauma, Burns and Combined Injury, Research Institute of Surgery, Research Institute for Traffic Medicine of People's Liberation Army, Daping Hospital, Third Military Medical University, Chongqing 400042, China
| | - Min Xie
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China.
| | - Daolin Tang
- The Third Affiliated Hospital, Center for DAMP Biology, Key Laboratory for Major Obstetric Diseases of Guangdong Province, Key Laboratory of Protein Modification and Degradation of Guangdong Higher Education Institutes, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, Guangdong 510510, China; Department of Surgery, University of Pittsburgh, Pittsburgh, PA 15213, USA.
| |
Collapse
|
125
|
Martínez-García EA, Zavala-Cerna MG, Lujano-Benítez AV, Sánchez-Hernández PE, Martín-Márquez BT, Sandoval-García F, Vázquez-Del Mercado M. Potential Chronotherapeutic Optimization of Antimalarials in Systemic Lupus Erythematosus: Is Toll-Like Receptor 9 Expression Dependent on the Circadian Cycle in Humans? Front Immunol 2018; 9:1497. [PMID: 30034390 PMCID: PMC6043638 DOI: 10.3389/fimmu.2018.01497] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 06/15/2018] [Indexed: 12/13/2022] Open
Abstract
Toll-like receptor 9 (TLR9) belongs to the group of endosomal receptors of the innate immune system with the ability to recognize hypomethylated CpG sequences from DNA. There is scarce information about TLR9 expression and its association with the circadian cycle (CC). Different patterns of TLR9 expression are regulated by the CC in mice, with an elevated expression at Zeitgeber time 19 (1:00 a.m.); nevertheless, we still need to corroborate this in humans. In systemic lupus erythematosus (SLE), the inhibitory effect of chloroquine (CQ) on TLR9 is limited. TLR9 activation has been associated with the presence of some autoantibodies: anti-Sm/RNP, anti-histone, anti-Ro, anti-La, and anti-double-stranded DNA. Treatment with CQ for SLE has been proven to be useful, in part by interfering with HLA-antigen coupling and with TLR9 ligand recognition. Studies have shown that TLR9 inhibitors such as antimalarial drugs are able to mask TLR9-binding sites on nucleic acids. The data presented here provide the basic information that could be useful for other clinical researchers to design studies that will have an impact in achieving a chronotherapeutic effect by defining the ideal time for CQ administration in SLE patients, consequently reducing the pathological effects that follow the activation of TLR9.
Collapse
Affiliation(s)
- Erika Aurora Martínez-García
- Instituto de Investigación en Reumatología y del Sistema Músculo Esquelético, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Mexico
- Departamento de Fisiología, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Mexico
- UDG-CA-703, Inmunología y Reumatología, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Mexico
| | - Maria Guadalupe Zavala-Cerna
- Immunology Research Laboratory, Programa Internacional de Medicina, Universidad Autonoma de Guadalajara, Guadalajara, Mexico
| | - Andrea Verónica Lujano-Benítez
- Instituto de Investigación en Reumatología y del Sistema Músculo Esquelético, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Mexico
| | - Pedro Ernesto Sánchez-Hernández
- Departamento de Fisiología, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Mexico
- Laboratorio de Inmunología, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Mexico
| | - Beatriz Teresita Martín-Márquez
- Instituto de Investigación en Reumatología y del Sistema Músculo Esquelético, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Mexico
- UDG-CA-703, Inmunología y Reumatología, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Mexico
| | - Flavio Sandoval-García
- Instituto de Investigación en Reumatología y del Sistema Músculo Esquelético, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Mexico
- Departamento de Clínicas Médicas, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Mexico
- UDG CA-701, Inmunometabolismo en Enfermedades Emergentes (GIIEE), Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Mexico
| | - Mónica Vázquez-Del Mercado
- Instituto de Investigación en Reumatología y del Sistema Músculo Esquelético, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Mexico
- UDG-CA-703, Inmunología y Reumatología, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Mexico
- Hospital Civil de Guadalajara “Juan I. Menchaca”, Servicio de Reumatología, Programa Nacional de Posgrados de Calidad (PNPC), Consejo Nacional de Ciencia y Tecnología (CONACYT), Guadalajara, Mexico
| |
Collapse
|
126
|
Baker JR, Gilbert J, Paula S, Zhu X, Sakoff JA, McCluskey A. Dichlorophenylacrylonitriles as AhR Ligands That Display Selective Breast Cancer Cytotoxicity in vitro. ChemMedChem 2018; 13:1447-1458. [PMID: 29771007 DOI: 10.1002/cmdc.201800256] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Indexed: 12/21/2022]
Abstract
Knoevenagel condensation of 3,4-dichloro- and 2,6-dichlorophenylacetonitriles gave a library of dichlorophenylacrylonitriles. Our leads (Z)-2-(3,4-dichlorophenyl)-3-(1H-pyrrol-2-yl)acrylonitrile (5) and (Z)-2-(3,4-dichlorophenyl)-3-(4-nitrophenyl)acrylonitrile (6) displayed 0.56±0.03 and 0.127±0.04 μm growth inhibition (GI50 ) and 260-fold selectivity for the MCF-7 breast cancer cell line. A 2,6-dichlorophenyl moiety saw a 10-fold decrease in potency; additional nitrogen moieties (-NO2 ) enhanced activity (Z)-2-(2,6-dichloro-3-nitrophenyl)-3-(2-nitrophenyl)acrylonitrile (26) and (Z)-2-(2,6-dichloro-3-nitrophenyl)-3-(3-nitrophenyl)acrylonitrile (27), with the corresponding -NH2 analogues (Z)-2-(3-amino-2,6-dichlorophenyl)-3-(2-aminophenyl)acrylonitrile (29) and (Z)-2-(3-amino-2,6-dichlorophenyl)-3-(3-aminophenyl)acrylonitrile (30) being more potent. Despite this, both 29 (2.8±0.03 μm) and 30 (2.8±0.03 μm) were found to be 10-fold less cytotoxic than 6. A bromine moiety effected a 3-fold enhancement in solubility with (Z)-3-(5-bromo-1H-pyrrol-2-yl)-2-(3,4-dichlorophenyl)acrylonitrile 18 relative to 5 at 211 μg mL-1 . Modeling-guided synthesis saw the introduction of 4-aminophenyl substituents (Z)-3-(4-aminophenyl)-2-(3,4-dichlorophenyl)acrylonitrile (35) and (Z)-N-(4-(2-cyano-2-(3,4-dichlorophenyl)vinyl)phenyl)acetamide (38), with respective GI50 values of 0.030±0.014 and 0.034±0.01 μm. Other analogues such as 35 and 36 were found to have sub-micromolar potency against our panel of cancer cell lines (HT29, colon; U87 and SJ-G2, glioblastoma; A2780, ovarian; H460, lung; A431, skin; Du145, prostate; BE2-C, neuroblastoma; MIA, pancreas; and SMA, murine glioblastoma), except compound 38 against the U87 cell line. A more extensive evaluation of 38 ((Z)-N-(4-(2-cyano-2-(3,4-dichlorophenyl)vinyl)phenyl)acetamide) in a panel of drug-resistant breast carcinoma cell lines showed 10-206 nm potency against MDAMB468, T47D, ZR-75-1, SKBR3, and BT474. Molecular Operating Environment docking scores showed a good correlation between predicted binding efficiencies and observed MCF-7 cytotoxicity. This supports the use of this model in the development of breast-cancer-specific drugs.
Collapse
Affiliation(s)
- Jennifer R Baker
- Chemistry, School of Environmental & Life Sciences, The University of Newcastle, University Drive, Callaghan, NSW, 2308, Australia
| | - Jayne Gilbert
- Experimental Therapeutics Group, Department of Medical Oncology, Calvary Mater Hospital, Edith Street, Waratah, NSW, 2298, Australia
| | - Stefan Paula
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN, USA
| | - Xiao Zhu
- Research Computing, Information Technology at Purdue (ITaP), Purdue University, 155 South Grant Street, West Lafayette, IN, USA
| | - Jennette A Sakoff
- Experimental Therapeutics Group, Department of Medical Oncology, Calvary Mater Hospital, Edith Street, Waratah, NSW, 2298, Australia
| | - Adam McCluskey
- Chemistry, School of Environmental & Life Sciences, The University of Newcastle, University Drive, Callaghan, NSW, 2308, Australia
| |
Collapse
|
127
|
Crnko S, Cour M, Van Laake LW, Lecour S. Vasculature on the clock: Circadian rhythm and vascular dysfunction. Vascul Pharmacol 2018; 108:1-7. [PMID: 29778521 DOI: 10.1016/j.vph.2018.05.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2017] [Revised: 04/23/2018] [Accepted: 05/10/2018] [Indexed: 01/08/2023]
Abstract
The master mammalian circadian clock (i.e. central clock), located in the suprachiasmatic nucleus of the hypothalamus, orchestrates the synchronization of the daily behavioural and physiological rhythms to better adapt the organism to the external environment in an anticipatory manner. This central clock is entrained by a variety of signals, the best established being light and food. However, circadian cycles are not simply the consequences of these two cues but are generated by endogenous circadian clocks. Indeed, clock machinery is found in mainly all tissues and cell types, including cells of the vascular system such as endothelial cells, fibroblasts, smooth muscle cells and stem cells. This machinery physiologically contributes to modulate the daily vascular function, and its disturbance therefore plays a major role in the pathophysiology of vascular dysfunction. Therapies targeting the circadian rhythm may therefore be of benefit against vascular disease.
Collapse
Affiliation(s)
- Sandra Crnko
- Division Heart and Lungs and Regenerative Medicine Center, University Medical Center Utrecht, The Netherlands
| | - Martin Cour
- Hatter Institute for Cardiovascular research in Africa and Lionel Opie Preclinical Imaging Core Facility, Faculty of Health Sciences, University of Cape Town, South Africa
| | - Linda W Van Laake
- Division Heart and Lungs and Regenerative Medicine Center, University Medical Center Utrecht, The Netherlands
| | - Sandrine Lecour
- Hatter Institute for Cardiovascular research in Africa and Lionel Opie Preclinical Imaging Core Facility, Faculty of Health Sciences, University of Cape Town, South Africa.
| |
Collapse
|
128
|
Sun H, Zhang Y, Shi Y, Li Y, Li W, Wang Z. Evolution of the CLOCK and BMAL1 genes in a subterranean rodent species (Lasiopodomys mandarinus). Int J Biol Macromol 2018; 109:932-940. [DOI: 10.1016/j.ijbiomac.2017.11.076] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Revised: 11/10/2017] [Accepted: 11/12/2017] [Indexed: 12/01/2022]
|
129
|
|
130
|
Luciano AK, Zhou W, Santana JM, Kyriakides C, Velazquez H, Sessa WC. CLOCK phosphorylation by AKT regulates its nuclear accumulation and circadian gene expression in peripheral tissues. J Biol Chem 2018; 293:9126-9136. [PMID: 29588368 DOI: 10.1074/jbc.ra117.000773] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 03/09/2018] [Indexed: 12/16/2022] Open
Abstract
Circadian locomotor output cycles kaput (CLOCK) is a transcription factor that activates transcription of clock-controlled genes by heterodimerizing with BMAL1 and binding to E-box elements on DNA. Although several phosphorylation sites on CLOCK have already been identified, this study characterizes a novel phosphorylation site at serine 845 (Ser-836 in humans). Here, we show that CLOCK is a novel AKT substrate in vitro and in cells, and this phosphorylation site is a negative regulator of CLOCK nuclear localization by acting as a binding site for 14-3-3 proteins. To examine the role of CLOCK phosphorylation in vivo, ClockS845A knockin mice were generated using CRISPR/Cas9 technology. ClockS845A mice are essentially normal with normal central circadian rhythms and hemodynamics. However, examination of core circadian gene expression from peripheral tissues demonstrated that ClockS845A mice have diminished expression of Per2, Reverba, Dbp, and Npas2 in skeletal muscle and Per2, Reverba, Dbp, Per1, Rora, and Npas2 in the liver during the circadian cycle. The reduction in Dbp levels is associated with reduced H3K9ac at E-boxes where CLOCK binds despite no change in total CLOCK levels. Thus, CLOCK phosphorylation by AKT on Ser-845 regulates its nuclear translocation and the expression levels of certain core circadian genes in insulin-sensitive tissues.
Collapse
Affiliation(s)
- Amelia K Luciano
- From the Departments of Pharmacology and.,the Vascular Biology and Therapeutics Program (VBT), Yale University School of Medicine, New Haven, Connecticut 06520 and
| | - Wenping Zhou
- Cell Biology and.,the Vascular Biology and Therapeutics Program (VBT), Yale University School of Medicine, New Haven, Connecticut 06520 and
| | - Jeans M Santana
- From the Departments of Pharmacology and.,the Vascular Biology and Therapeutics Program (VBT), Yale University School of Medicine, New Haven, Connecticut 06520 and
| | - Cleo Kyriakides
- From the Departments of Pharmacology and.,the Vascular Biology and Therapeutics Program (VBT), Yale University School of Medicine, New Haven, Connecticut 06520 and
| | - Heino Velazquez
- the Department of Internal Medicine, Veterans Affairs Connecticut Healthcare System, West Haven, Connecticut 06516
| | - William C Sessa
- From the Departments of Pharmacology and .,the Vascular Biology and Therapeutics Program (VBT), Yale University School of Medicine, New Haven, Connecticut 06520 and
| |
Collapse
|
131
|
Rosensweig C, Reynolds KA, Gao P, Laothamatas I, Shan Y, Ranganathan R, Takahashi JS, Green CB. An evolutionary hotspot defines functional differences between CRYPTOCHROMES. Nat Commun 2018; 9:1138. [PMID: 29556064 PMCID: PMC5859286 DOI: 10.1038/s41467-018-03503-6] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 02/19/2018] [Indexed: 12/30/2022] Open
Abstract
Mammalian circadian clocks are driven by a transcription/translation feedback loop composed of positive regulators (CLOCK/BMAL1) and repressors (CRYPTOCHROME 1/2 (CRY1/2) and PER1/2). To understand the structural principles of regulation, we used evolutionary sequence analysis to identify co-evolving residues within the CRY/PHL protein family. Here we report the identification of an ancestral secondary cofactor-binding pocket as an interface in repressive CRYs, mediating regulation through direct interaction with CLOCK and BMAL1. Mutations weakening binding between CLOCK/BMAL1 and CRY1 lead to acceleration of the clock, suggesting that subtle sequence divergences at this site can modulate clock function. Divergence between CRY1 and CRY2 at this site results in distinct periodic output. Weaker interactions between CRY2 and CLOCK/BMAL1 at this pocket are strengthened by co-expression of PER2, suggesting that PER expression limits the length of the repressive phase in CRY2-driven rhythms. Overall, this work provides a model for the mechanism and evolutionary variation of clock regulatory mechanisms. The molecular mechanisms that define the periodicity or rate of the circadian clock are not well understood. Here the authors use a multidisciplinary approach and identify a mechanism for period regulation that depends on the affinity of the core clock proteins for one another.
Collapse
Affiliation(s)
- Clark Rosensweig
- Department of Neuroscience, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX, 75390, USA.,Department of Neurobiology, Northwestern University, 2205 Tech Drive, Pancoe 2230, Evanston, IL, 60208, USA
| | - Kimberly A Reynolds
- Department of Biophysics, University of Texas Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX, 75390, USA.,The Green Center for Systems Biology, University of Texas Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX, 75390, USA
| | - Peng Gao
- Department of Neuroscience, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX, 75390, USA
| | - Isara Laothamatas
- Department of Neuroscience, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX, 75390, USA
| | - Yongli Shan
- Department of Neuroscience, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX, 75390, USA
| | - Rama Ranganathan
- Department of Biophysics, University of Texas Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX, 75390, USA.,The Green Center for Systems Biology, University of Texas Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX, 75390, USA.,Department of Pharmacology, University of Texas Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX, 75390, USA.,The Center for the Physics of Evolving Systems, Biochemistry and Molecular Biology, The Institute for Molecular Engineering, University of Chicago, 929 East 57th Street, Chicago, IL, 60637, USA
| | - Joseph S Takahashi
- Department of Neuroscience, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX, 75390, USA.,Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Carla B Green
- Department of Neuroscience, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX, 75390, USA.
| |
Collapse
|
132
|
Davis BT, Voigt RM, Shaikh M, Forsyth CB, Keshavarzian A. Circadian Mechanisms in Alcohol Use Disorder and Tissue Injury. Alcohol Clin Exp Res 2018; 42:668-677. [PMID: 29450896 DOI: 10.1111/acer.13612] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2017] [Accepted: 02/06/2018] [Indexed: 12/12/2022]
Abstract
Heavy use of alcohol can lead to addictive behaviors and to eventual alcohol-related tissue damage. While increased consumption of alcohol has been attributed to various factors including level of alcohol exposure and environmental factors such as stress, data from behavioral scientists and physiological researchers are revealing roles for the circadian rhythm in mediating the development of behaviors associated with alcohol use disorder as well as the tissue damage that drives physiological disease. In this work, we compile recent work on the complex mutually influential relationship that exists between the core circadian rhythm and the pharmacodynamics of alcohol. As we do so, we highlight implications of the relationship between alcohol and common circadian mechanisms of effected organs on alcohol consumption, metabolism, toxicity, and pathology.
Collapse
Affiliation(s)
| | | | | | | | - Ali Keshavarzian
- Division of Digestive Disease and Nutrition, Section of Gastroenterology, Department of Internal Medicine, Rush University Medical Center, Chicago, Illinois
| |
Collapse
|
133
|
Suyama K, Silagi ES, Choi H, Sakabe K, Mochida J, Shapiro IM, Risbud MV. Circadian factors BMAL1 and RORα control HIF-1α transcriptional activity in nucleus pulposus cells: implications in maintenance of intervertebral disc health. Oncotarget 2018; 7:23056-71. [PMID: 27049729 PMCID: PMC5029610 DOI: 10.18632/oncotarget.8521] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 03/21/2016] [Indexed: 12/31/2022] Open
Abstract
BMAL1 and RORα are major regulators of the circadian molecular oscillator. Since previous work in other cell types has shown cross talk between circadian rhythm genes and hypoxic signaling, we investigated the role of BMAL1 and RORα in controlling HIF-1-dependent transcriptional responses in NP cells that exist in the physiologically hypoxic intervertebral disc. HIF-1-dependent HRE reporter activity was further promoted by co-transfection with either BMAL1 or RORα. In addition, stable silencing of BMAL1 or inhibition of RORα activity resulted in decreased HRE activation. Inhibition of RORα also modulated HIF1α-TAD activity. Interestingly, immunoprecipitation studies showed no evidence of BMAL1, CLOCK or RORα binding to HIF-1α in NP cells. Noteworthy, stable silencing of BMAL1 as well as inhibition of RORα decreased expression of select HIF-1 target genes including VEGF, PFKFB3 and Eno1. To delineate if BMAL1 plays a role in maintenance of disc health, we studied the spinal phenotype of BMAL1-null mice. The lumbar discs of null mice evidenced decreased height, and several parameters associated with vertebral trabecular bone quality were also affected in nulls. In addition, null animals showed a higher ratio of cells to matrix in NP tissue and hyperplasia of the annulus fibrosus. Taken together, our results indicate that BMAL1 and RORα form a regulatory loop in the NP and control HIF-1 activity without direct interaction. Importantly, activities of these circadian rhythm molecules may play a role in the adaptation of NP cells to their unique niche.
Collapse
Affiliation(s)
- Kaori Suyama
- Department of Orthopaedic Surgery, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, USA.,Department of Orthopaedic Surgery, Surgical Science, Tokai University School of Medicine, Isehara, Kanagawa, Japan.,Department of Anatomy and Cellular Biology, Basic Medical Science, Tokai University School of Medicine, Isehara, Kanagawa, Japan
| | - Elizabeth S Silagi
- Department of Orthopaedic Surgery, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, USA.,Program in Cell and Developmental Biology, Jefferson College of Biomedical Sciences, Thomas Jefferson University, Philadelphia, USA
| | - Hyowon Choi
- Department of Orthopaedic Surgery, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, USA.,Program in Cell and Developmental Biology, Jefferson College of Biomedical Sciences, Thomas Jefferson University, Philadelphia, USA
| | - Kou Sakabe
- Department of Anatomy and Cellular Biology, Basic Medical Science, Tokai University School of Medicine, Isehara, Kanagawa, Japan
| | - Joji Mochida
- Department of Orthopaedic Surgery, Surgical Science, Tokai University School of Medicine, Isehara, Kanagawa, Japan
| | - Irving M Shapiro
- Department of Orthopaedic Surgery, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, USA.,Program in Cell and Developmental Biology, Jefferson College of Biomedical Sciences, Thomas Jefferson University, Philadelphia, USA
| | - Makarand V Risbud
- Department of Orthopaedic Surgery, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, USA.,Program in Cell and Developmental Biology, Jefferson College of Biomedical Sciences, Thomas Jefferson University, Philadelphia, USA
| |
Collapse
|
134
|
Nakatani Y, Hisatomi O. Quantitative analyses of the equilibria among DNA complexes of a blue-light-regulated bZIP module, Photozipper. Biophys Physicobiol 2018; 15:8-17. [PMID: 29450110 PMCID: PMC5812316 DOI: 10.2142/biophysico.15.0_8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 11/21/2017] [Indexed: 01/28/2023] Open
Abstract
Aureochrome1 is a blue-light-receptor protein identified in a stramenopile alga, Vaucheria frigida. Photozipper (PZ) is an N-terminally truncated, monomeric, V. frigida aureochrome1 fragment containing a basic leucine zipper (bZIP) domain and a light–oxygen–voltage (LOV)-sensing domain. PZ dimerizes upon photoexcitation and consequently increases its affinity for the target sequence. In the present study, to understand the equilibria among DNA complexes of PZ, DNA binding by PZ and mutational variants was quantitatively investigated by electrophoretic-mobility-shift assay and fluorescence-correlation spectroscopy in the dark and light states. DNA binding by PZ was sequence-specific and light-dependent. The half-maximal effective concentration of PZ for binding to the target DNA sequence was ~40 nM in the light, which was >10-fold less than the value in the dark. By contrast, the dimeric PZ-S2C variant (with intermolecular disulfide bonds) had higher affinity for the target sequence, with dissociation constants of ~4 nM, irrespective of the light conditions. Substitutions of Glu159 and Lys164 in the leucine zipper region decreased the affinity of PZ for the target sequence, especially in the light, suggesting that these residues form inter-helical salt bridges between leucine zipper regions, stabilizing the dimer–DNA complex. Our quantitative analyses of the equilibria in PZ–DNA-complex formation suggest that the blue-light-induced dimerization of LOV domains and coiled-coil formation by leucine zipper regions are the primary determinants of the affinity of PZ for the target sequence.
Collapse
Affiliation(s)
- Yoichi Nakatani
- Department of Earth and Space Science, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
| | - Osamu Hisatomi
- Department of Earth and Space Science, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
| |
Collapse
|
135
|
Zhao J, Zhou X, Tang Q, Yu R, Yu S, Long Y, Cao C, Han J, Shi A, Mao JJ, Chen X, Chen L. BMAL1 Deficiency Contributes to Mandibular Dysplasia by Upregulating MMP3. Stem Cell Reports 2018; 10:180-195. [PMID: 29276151 PMCID: PMC5768965 DOI: 10.1016/j.stemcr.2017.11.017] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2017] [Revised: 11/23/2017] [Accepted: 11/24/2017] [Indexed: 02/06/2023] Open
Abstract
Skeletal mandibular hypoplasia (SMH), one of the common types of craniofacial deformities, seriously affects appearance, chewing, pronunciation, and breathing. Moreover, SMH is prone to inducing obstructive sleep apnea syndrome. We found that brain and muscle ARNT-like 1 (BMAL1), the core component of the molecular circadian oscillator, was significantly decreased in mandibles of juvenile SMH patients. Accordingly, SMH was observed in circadian-rhythm-disrupted or BMAL1-deficient mice. RNA sequencing and protein chip analyses suggested that matrix metallopeptidase 3 (MMP3) is the potential target of BMAL1. Interestingly, in juvenile SMH patients, we observed that MMP3 was obviously increased. Consistently, MMP3 was upregulated during the whole growth period of 3-10 weeks in Bmal1-/- mice. Given these findings, we set out to characterize the underlying mechanism and found BMAL1 deficiency enhanced Mmp3 transcription through activating p65 phosphorylation. Together, our results provide insight into the mechanism by which BMAL1 is implicated in the pathogenesis of SMH.
Collapse
Affiliation(s)
- Jiajia Zhao
- Department of Stomatology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Xin Zhou
- Department of Stomatology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Qingming Tang
- Department of Stomatology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Ran Yu
- Department of Stomatology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Shaoling Yu
- Department of Stomatology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Yanlin Long
- Department of Stomatology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Cen Cao
- Department of Stomatology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Jun Han
- Department of Stomatology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Anbing Shi
- Department of Biochemistry and Molecular Biology, School of Basic Medicine and the Collaborative Innovation Center for Brain Science, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Jeremy J Mao
- Center for Craniofacial Regeneration, College of Dental Medicine, Columbia University Medical Center, New York, NY 10032, USA
| | - Xiong Chen
- Department of Otolaryngology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Lili Chen
- Department of Stomatology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China.
| |
Collapse
|
136
|
Circadian modification network of a core clock driver BMAL1 to harmonize physiology from brain to peripheral tissues. Neurochem Int 2018; 119:11-16. [PMID: 29305918 DOI: 10.1016/j.neuint.2017.12.013] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 12/20/2018] [Accepted: 12/31/2018] [Indexed: 12/20/2022]
Abstract
Circadian clocks dictate various physiological functions by brain SCN (a central clock) -orchestrating the temporal harmony of peripheral clocks of tissues/organs in the whole body, with adaptability to environments by resetting their timings. Dysfunction of this circadian adaptation system (CAS) occasionally causes/exacerbates diseases. CAS is based on cell-autonomous molecular clocks, which oscillate via a core transcriptional/translational feedback loop with clock genes/proteins, e.g., BMAL1: CLOCK circadian transcription driver and CRY1/2 and PER1/2 suppressors, and is modulated by various regulatory loops including clock protein modifications. Among mutants with a single clock gene, BMAL1-deficient mice exhibit the most drastic loss of circadian functions. Here, we highlight on numerous circadian protein modifications of mammalian BMAL1, e.g., multiple phosphorylations, SUMOylation, ubiquitination, acetylation, O-GlcNAcylation and S-nitrosylation, which mutually interplay to control molecular clocks and coordinate physiological functions from the brain to peripheral tissues through the input and output of the clocks.
Collapse
|
137
|
De Nobrega AK, Lyons LC. Drosophila: An Emergent Model for Delineating Interactions between the Circadian Clock and Drugs of Abuse. Neural Plast 2017; 2017:4723836. [PMID: 29391952 PMCID: PMC5748135 DOI: 10.1155/2017/4723836] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Accepted: 08/13/2017] [Indexed: 01/12/2023] Open
Abstract
Endogenous circadian oscillators orchestrate rhythms at the cellular, physiological, and behavioral levels across species to coordinate activity, for example, sleep/wake cycles, metabolism, and learning and memory, with predictable environmental cycles. The 21st century has seen a dramatic rise in the incidence of circadian and sleep disorders with globalization, technological advances, and the use of personal electronics. The circadian clock modulates alcohol- and drug-induced behaviors with circadian misalignment contributing to increased substance use and abuse. Invertebrate models, such as Drosophila melanogaster, have proven invaluable for the identification of genetic and molecular mechanisms underlying highly conserved processes including the circadian clock, drug tolerance, and reward systems. In this review, we highlight the contributions of Drosophila as a model system for understanding the bidirectional interactions between the circadian system and the drugs of abuse, alcohol and cocaine, and illustrate the highly conserved nature of these interactions between Drosophila and mammalian systems. Research in Drosophila provides mechanistic insights into the corresponding behaviors in higher organisms and can be used as a guide for targeted inquiries in mammals.
Collapse
Affiliation(s)
- Aliza K. De Nobrega
- Department of Biological Science, Program in Neuroscience, Florida State University, Tallahassee, FL 32306, USA
| | - Lisa C. Lyons
- Department of Biological Science, Program in Neuroscience, Florida State University, Tallahassee, FL 32306, USA
| |
Collapse
|
138
|
Lin R, Mo Y, Zha H, Qu Z, Xie P, Zhu ZJ, Xu Y, Xiong Y, Guan KL. CLOCK Acetylates ASS1 to Drive Circadian Rhythm of Ureagenesis. Mol Cell 2017; 68:198-209.e6. [PMID: 28985504 DOI: 10.1016/j.molcel.2017.09.008] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Revised: 07/24/2017] [Accepted: 09/06/2017] [Indexed: 11/23/2022]
Abstract
In addition to responding to environmental entrainment with diurnal variation, metabolism is also tightly controlled by cell-autonomous circadian clock. Extensive studies have revealed key roles of transcription in circadian control. Post-transcriptional regulation for the rhythmic gating of metabolic enzymes remains elusive. Here, we show that arginine biosynthesis and subsequent ureagenesis are collectively regulated by CLOCK (circadian locomotor output cycles kaput) in circadian rhythms. Facilitated by BMAL1 (brain and muscle Arnt-like protein), CLOCK directly acetylates K165 and K176 of argininosuccinate synthase (ASS1) to inactivate ASS1, which catalyzes the rate-limiting step of arginine biosynthesis. ASS1 acetylation by CLOCK exhibits circadian oscillation in human cells and mouse liver, possibly caused by rhythmic interaction between CLOCK and ASS1, leading to the circadian regulation of ASS1 and ureagenesis. Furthermore, we also identified NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9 (NDUFA9) and inosine-5'-monophosphate dehydrogenase 2 (IMPDH2) as acetylation substrates of CLOCK. Taken together, CLOCK modulates metabolic rhythmicity by acting as a rhythmic acetyl-transferase for metabolic enzymes.
Collapse
Affiliation(s)
- Ran Lin
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Molecular and Cell Biology Laboratory, Institute of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai 200032, China.
| | - Yan Mo
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Molecular and Cell Biology Laboratory, Institute of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Haihong Zha
- Interdisciplinary Research Center on Biology and Chemistry and Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China
| | - Zhipeng Qu
- Cam-Su Genomic Resource Center, Soochow University, Suzhou 215123, China
| | - Pancheng Xie
- Cam-Su Genomic Resource Center, Soochow University, Suzhou 215123, China
| | - Zheng-Jiang Zhu
- Interdisciplinary Research Center on Biology and Chemistry and Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China
| | - Ying Xu
- Cam-Su Genomic Resource Center, Soochow University, Suzhou 215123, China
| | - Yue Xiong
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Molecular and Cell Biology Laboratory, Institute of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai 200032, China; Department of Biochemistry and Biophysics, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
| | - Kun-Liang Guan
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Molecular and Cell Biology Laboratory, Institute of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai 200032, China; Department of Pharmacology and Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093, USA.
| |
Collapse
|
139
|
Chen Z, Yoo SH, Takahashi JS. Development and Therapeutic Potential of Small-Molecule Modulators of Circadian Systems. Annu Rev Pharmacol Toxicol 2017; 58:231-252. [PMID: 28968186 DOI: 10.1146/annurev-pharmtox-010617-052645] [Citation(s) in RCA: 103] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Circadian timekeeping systems drive oscillatory gene expression to regulate essential cellular and physiological processes. When the systems are perturbed, pathological consequences ensue and disease risks rise. A growing number of small-molecule modulators have been reported to target circadian systems. Such small molecules, identified via high-throughput screening or derivatized from known scaffolds, have shown promise as drug candidates to improve biological timing and physiological outputs in disease models. In this review, we first briefly describe the circadian system, including the core oscillator and the cellular networks. Research progress on clock-modulating small molecules is presented, focusing on development strategies and biological efficacies. We highlight the therapeutic potential of small molecules in clock-related pathologies, including jet lag and shiftwork; various chronic diseases, particularly metabolic disease; and aging. Emerging opportunities to identify and exploit clock modulators as novel therapeutic agents are discussed.
Collapse
Affiliation(s)
- Zheng Chen
- Department of Biochemistry and Molecular Biology, University of Texas Health Science Center at Houston, Houston, Texas 77030, USA;
| | - Seung-Hee Yoo
- Department of Biochemistry and Molecular Biology, University of Texas Health Science Center at Houston, Houston, Texas 77030, USA;
| | - Joseph S Takahashi
- Department of Neuroscience and Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| |
Collapse
|
140
|
Aryal RP, Kwak PB, Tamayo AG, Gebert M, Chiu PL, Walz T, Weitz CJ. Macromolecular Assemblies of the Mammalian Circadian Clock. Mol Cell 2017; 67:770-782.e6. [PMID: 28886335 PMCID: PMC5679067 DOI: 10.1016/j.molcel.2017.07.017] [Citation(s) in RCA: 162] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Revised: 06/14/2017] [Accepted: 07/13/2017] [Indexed: 10/18/2022]
Abstract
The mammalian circadian clock is built on a feedback loop in which PER and CRY proteins repress their own transcription. We found that in mouse liver nuclei all three PERs, both CRYs, and Casein Kinase-1δ (CK1δ) are present together in an ∼1.9-MDa repressor assembly that quantitatively incorporates its CLOCK-BMAL1 transcription factor target. Prior to incorporation, CLOCK-BMAL1 exists in an ∼750-kDa complex. Single-particle electron microscopy (EM) revealed nuclear PER complexes purified from mouse liver to be quasi-spherical ∼40-nm structures. In the cytoplasm, PERs, CRYs, and CK1δ were distributed into several complexes of ∼0.9-1.1 MDa that appear to constitute an assembly pathway regulated by GAPVD1, a cytoplasmic trafficking factor. Single-particle EM of two purified cytoplasmic PER complexes revealed ∼20-nm and ∼25-nm structures, respectively, characterized by flexibly tethered globular domains. Our results define the macromolecular assemblies comprising the circadian feedback loop and provide an initial structural view of endogenous eukaryotic clock machinery.
Collapse
Affiliation(s)
- Rajindra P Aryal
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Pieter Bas Kwak
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Alfred G Tamayo
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Michael Gebert
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Po-Lin Chiu
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Thomas Walz
- Laboratory of Molecular Electron Microscopy, Rockefeller University, New York, NY 10065, USA
| | - Charles J Weitz
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA.
| |
Collapse
|
141
|
Zhang Y, Markert MJ, Groves SC, Hardin PE, Merlin C. Vertebrate-like CRYPTOCHROME 2 from monarch regulates circadian transcription via independent repression of CLOCK and BMAL1 activity. Proc Natl Acad Sci U S A 2017; 114:E7516-E7525. [PMID: 28831003 PMCID: PMC5594645 DOI: 10.1073/pnas.1702014114] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Circadian repression of CLOCK-BMAL1 by PERIOD and CRYPTOCHROME (CRY) in mammals lies at the core of the circadian timekeeping mechanism. CRY repression of CLOCK-BMAL1 and regulation of circadian period are proposed to rely primarily on competition for binding with coactivators on an α-helix located within the transactivation domain (TAD) of the BMAL1 C terminus. This model has, however, not been tested in vivo. Here, we applied CRISPR/Cas9-mediated mutagenesis in the monarch butterfly (Danaus plexippus), which possesses a vertebrate-like CRY (dpCRY2) and an ortholog of BMAL1, to show that insect CRY2 regulates circadian repression through TAD α-helix-dependent and -independent mechanisms. Monarch mutants lacking the BMAL1 C terminus including the TAD exhibited arrhythmic eclosion behavior. In contrast, mutants lacking the TAD α-helix but retaining the most distal C-terminal residues exhibited robust rhythms during the first day of constant darkness (DD1), albeit with a delayed peak of eclosion. Phase delay in this mutant on DD1 was exacerbated in the presence of a single functional allele of dpCry2, and rhythmicity was abolished in the absence of dpCRY2. Reporter assays in Drosophila S2 cells further revealed that dpCRY2 represses through two distinct mechanisms: a TAD-dependent mechanism that involves the dpBMAL1 TAD α-helix and dpCLK W328 and a TAD-independent mechanism involving dpCLK E333. Together, our results provide evidence for independent mechanisms of vertebrate-like CRY circadian regulation on the BMAL1 C terminus and the CLK PAS-B domain and demonstrate the importance of a BMAL1 TAD-independent mechanism for generating circadian rhythms in vivo.
Collapse
Affiliation(s)
- Ying Zhang
- Department of Biology, Texas A&M University, College Station, TX 77843
- Center for Biological Clocks Research, Texas A&M University, College Station, TX 77843
| | - Matthew J Markert
- Department of Biology, Texas A&M University, College Station, TX 77843
- Center for Biological Clocks Research, Texas A&M University, College Station, TX 77843
| | - Shayna C Groves
- Department of Biology, Texas A&M University, College Station, TX 77843
- Center for Biological Clocks Research, Texas A&M University, College Station, TX 77843
| | - Paul E Hardin
- Department of Biology, Texas A&M University, College Station, TX 77843
- Center for Biological Clocks Research, Texas A&M University, College Station, TX 77843
| | - Christine Merlin
- Department of Biology, Texas A&M University, College Station, TX 77843;
- Center for Biological Clocks Research, Texas A&M University, College Station, TX 77843
| |
Collapse
|
142
|
Yang SL, Ren QG, Wen L, Hu JL, Wang HY. Research progress on circadian clock genes in common abdominal malignant tumors. Oncol Lett 2017; 14:5091-5098. [PMID: 29113149 PMCID: PMC5661368 DOI: 10.3892/ol.2017.6856] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2016] [Accepted: 07/03/2017] [Indexed: 02/01/2023] Open
Abstract
The circadian clock refers to the inherent biological rhythm of an organism, which, is accurately regulated by numerous clock genes. Studies in recent years have reported that the abnormal expression of clock genes is ubiquitous in common abdominal malignant tumors, including liver, colorectal, gastric and pancreatic cancer. In addition, the abnormal expression of certain clock genes is closely associated with clinical tumor parameters or patient prognosis. Studies in clock genes may expand the knowledge about the mechanism of occurrence and development of tumors, and may provide a new approach for tumor therapy. The present study summarizes the research progress in this field.
Collapse
Affiliation(s)
- Sheng-Li Yang
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, P.R. China
| | - Quan-Guang Ren
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, P.R. China
| | - Lu Wen
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, P.R. China
| | - Jian-Li Hu
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, P.R. China
| | - Heng-Yi Wang
- Department of Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, P.R. China
| |
Collapse
|
143
|
Gillessen M, Kwak PB, Tamayo A. A simple method to measure CLOCK-BMAL1 DNA binding activity in tissue and cell extracts. F1000Res 2017; 6:1316. [DOI: 10.12688/f1000research.11685.1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/24/2017] [Indexed: 01/05/2023] Open
Abstract
The proteins CLOCK and BMAL1 form a heterodimeric transcription factor essential to circadian rhythms in mammals. Daily rhythms of CLOCK-BMAL1 DNA binding activity are known to oscillate with target gene expression in vivo. Here we present a highly sensitive assay that recapitulates native CLOCK-BMAL1 DNA binding rhythms from crude tissue extracts, which we call the Clock Protein-DNA Binding Assay (CPDBA). This method can detect less than 2-fold differences in DNA binding activity, and can deliver results in two hours or less using 10 microliters or less of crude extract, while requiring neither specialized equipment nor expensive probes. To demonstrate the sensitivity and versatility of this assay, we show that enzymatic removal of phosphate groups from proteins in tissue extracts or pharmacological inhibition of casein kinase I in cell culture increased CLOCK-BMAL1 DNA binding activity by ~1.5 to ~2 fold, as measured by the CPDBA. In addition, we show that the CPDBA can measure CLOCK-BMAL1 binding to reconstituted chromatin. The CPDBA is a sensitive, fast, efficient and versatile probe of clock function.
Collapse
|
144
|
Gillessen M, Kwak PB, Tamayo A. A simple method to measure CLOCK-BMAL1 DNA binding activity in tissue and cell extracts. F1000Res 2017; 6:1316. [PMID: 28928952 PMCID: PMC5580408 DOI: 10.12688/f1000research.11685.2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/20/2017] [Indexed: 12/14/2022] Open
Abstract
The proteins CLOCK and BMAL1 form a heterodimeric transcription factor essential to circadian rhythms in mammals. Daily rhythms of CLOCK-BMAL1 DNA binding activity are known to oscillate with target gene expression in vivo. Here we present a highly sensitive assay that recapitulates native CLOCK-BMAL1 DNA binding rhythms from crude tissue extracts, which we call the Clock Protein-DNA Binding Assay (CPDBA). This method can detect less than 2-fold differences in DNA binding activity, and can deliver results in two hours or less using 10 microliters (~10 micrograms) or less of crude extract, while requiring neither specialized equipment nor expensive probes. To demonstrate the sensitivity and versatility of this assay, we show that enzymatic removal of phosphate groups from proteins in tissue extracts or pharmacological inhibition of casein kinase I in cell culture increased CLOCK-BMAL1 DNA binding activity by ~1.5 to ~2 fold, as measured by the CPDBA. In addition, we show that the CPDBA can measure CLOCK-BMAL1 binding to reconstituted chromatin. The CPDBA is a sensitive, fast, efficient and versatile probe of clock function.
Collapse
Affiliation(s)
- Maud Gillessen
- Department of Neurobiology, Harvard Medical School, Boston, MA, 02115, USA.,Department of Biology, University of Namur, 5000 Namur, Belgium
| | - Pieter Bas Kwak
- Department of Neurobiology, Harvard Medical School, Boston, MA, 02115, USA
| | - Alfred Tamayo
- Department of Neurobiology, Harvard Medical School, Boston, MA, 02115, USA
| |
Collapse
|
145
|
Hou Z, Su L, Pei J, Grishin NV, Zhang H. Crystal Structure of the CLOCK Transactivation Domain Exon19 in Complex with a Repressor. Structure 2017; 25:1187-1194.e3. [PMID: 28669630 DOI: 10.1016/j.str.2017.05.023] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Revised: 05/04/2017] [Accepted: 05/25/2017] [Indexed: 11/24/2022]
Abstract
In the canonical clock model, CLOCK:BMAL1-mediated transcriptional activation is feedback regulated by its repressors CRY and PER and, in association with other coregulators, ultimately generates oscillatory gene expression patterns. How CLOCK:BMAL1 interacts with coregulator(s) is not well understood. Here we report the crystal structures of the mouse CLOCK transactivating domain Exon19 in complex with CIPC, a potent circadian repressor that functions independently of CRY and PER. The Exon19:CIPC complex adopts a three-helical coiled-coil bundle conformation containing two Exon19 helices and one CIPC. Unique to Exon19:CIPC, three highly conserved polar residues, Asn341 of CIPC and Gln544 of the two Exon19 helices, are located at the mid-section of the coiled-coil bundle interior and form hydrogen bonds with each other. Combining results from protein database search, sequence analysis, and mutagenesis studies, we discovered for the first time that CLOCK Exon19:CIPC interaction is a conserved transcription regulatory mechanism among mammals, fish, flies, and other invertebrates.
Collapse
Affiliation(s)
- Zhiqiang Hou
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Lijing Su
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jimin Pei
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Nick V Grishin
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Hong Zhang
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
| |
Collapse
|
146
|
Schulte KW, Green E, Wilz A, Platten M, Daumke O. Structural Basis for Aryl Hydrocarbon Receptor-Mediated Gene Activation. Structure 2017; 25:1025-1033.e3. [PMID: 28602820 DOI: 10.1016/j.str.2017.05.008] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Revised: 04/28/2017] [Accepted: 05/10/2017] [Indexed: 12/15/2022]
Abstract
The aryl hydrocarbon receptor (AHR) and the AHR nuclear translocator (ARNT) constitute a heterodimeric basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain containing transcription factor with central functions in development and cellular homeostasis. AHR is activated by xenobiotics, notably dioxin, as well as by exogenous and endogenous metabolites. Modulation of AHR activity holds promise for the treatment of diseases featuring altered cellular homeostasis, such as cancer or autoimmune disorders. Here, we present the crystal structure of a heterodimeric AHR:ARNT complex containing the PAS A and bHLH domain bound to its target DNA. The structure provides insights into the DNA binding mode of AHR and elucidates how stable dimerization of AHR:ARNT is achieved through sophisticated domain interplay via three specific interfaces. Using mutational analyses, we prove the relevance of the observed interfaces for AHR-mediated gene activation. Thus, our work establishes the structural basis of AHR assembly and DNA interaction and provides a template for targeted drug design.
Collapse
Affiliation(s)
- Kathrin Wiebke Schulte
- Crystallography Department, Max-Delbrück-Center for Molecular Medicine, Robert-Rössle-Strasse 10, 13125 Berlin, Germany; Institute of Chemistry and Biochemistry, Freie Universität Berlin, Takustrasse 6, 14195 Berlin, Germany
| | - Edward Green
- Department of Neurology, University Hospital Heidelberg and National Center for Tumor Diseases, 69120 Heidelberg, Germany; Clinical Cooperation Unit Neuroimmunology and Brain Tumor Immunology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Annabel Wilz
- Clinical Cooperation Unit Neuroimmunology and Brain Tumor Immunology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Michael Platten
- Department of Neurology, University Hospital Heidelberg and National Center for Tumor Diseases, 69120 Heidelberg, Germany; Clinical Cooperation Unit Neuroimmunology and Brain Tumor Immunology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; Department of Neurology, Universitätsmedizin Mannheim, Medical Faculty Mannheim, Heidelberg University, 68167 Mannheim, Germany.
| | - Oliver Daumke
- Crystallography Department, Max-Delbrück-Center for Molecular Medicine, Robert-Rössle-Strasse 10, 13125 Berlin, Germany; Institute of Chemistry and Biochemistry, Freie Universität Berlin, Takustrasse 6, 14195 Berlin, Germany.
| |
Collapse
|
147
|
|
148
|
Corrada D, Denison MS, Bonati L. Structural modeling of the AhR:ARNT complex in the bHLH-PASA-PASB region elucidates the key determinants of dimerization. MOLECULAR BIOSYSTEMS 2017; 13:981-990. [PMID: 28393157 PMCID: PMC5576476 DOI: 10.1039/c7mb00005g] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Elucidation of the dimerization process of the aryl hydrocarbon receptor (AhR) with the AhR nuclear translocator (ARNT) is crucial for understanding the mechanisms underlying the functional activity of AhR, including mediation of the toxicity of environmental contaminants. In this work, for the first time a structural model of the AhR:ARNT dimer encompassing the entire bHLH-PASA-PASB domain region is proposed. It is developed by using a template-based modeling approach, relying on the recently available crystallographic structures of two dimers of homologous systems in the bHLH-PAS family of proteins: the CLOCK:BMAL1 and the HIF2α:ARNT heterodimers. The structural and energetic characteristics of the modeled AhR:ARNT protein-protein interface are determined by evaluating the variations in solvent accessible surface area, the total binding free energy and the per-residue free energy contributions obtained by the MM-GBSA method and the Energy Decomposition Analysis. The analyses of the intricate network of inter-domain interactions at the dimerization interfaces provide insights into the key determinants of dimerization. These are confirmed by comparison of the computational findings with the available experimental mutagenesis and functional analysis data. The results presented here on the AhR:ARNT dimer structure and interactions provide a framework to start analyzing the mechanism of AhR transformation into its functional DNA binding form.
Collapse
Affiliation(s)
- Dario Corrada
- Department of Earth and Environmental Sciences, University of Milano-Bicocca, Piazza della Scienza, 1 - 20126, Milan, Italy.
| | | | | |
Collapse
|
149
|
Structural hierarchy controlling dimerization and target DNA recognition in the AHR transcriptional complex. Proc Natl Acad Sci U S A 2017; 114:5431-5436. [PMID: 28396409 DOI: 10.1073/pnas.1617035114] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The aryl hydrocarbon receptor (AHR) belongs to the PAS (PER-ARNT-SIM) family transcription factors and mediates broad responses to numerous environmental pollutants and cellular metabolites, modulating diverse biological processes from adaptive metabolism, acute toxicity, to normal physiology of vascular and immune systems. The AHR forms a transcriptionally active heterodimer with ARNT (AHR nuclear translocator), which recognizes the dioxin response element (DRE) in the promoter of downstream genes. We determined the crystal structure of the mammalian AHR-ARNT heterodimer in complex with the DRE, in which ARNT curls around AHR into a highly intertwined asymmetric architecture, with extensive heterodimerization interfaces and AHR interdomain interactions. Specific recognition of the DRE is determined locally by the DNA-binding residues, which discriminates it from the closely related hypoxia response element (HRE), and is globally affected by the dimerization interfaces and interdomain interactions. Changes at the interdomain interactions caused either AHR constitutive nuclear localization or failure to translocate to nucleus, underlying an allosteric structural pathway for mediating ligand-induced exposure of nuclear localization signal. These observations, together with the global higher flexibility of the AHR PAS-A and its loosely packed structural elements, suggest a dynamic structural hierarchy for complex scenarios of AHR activation induced by its diverse ligands.
Collapse
|
150
|
Sobel JA, Krier I, Andersin T, Raghav S, Canella D, Gilardi F, Kalantzi AS, Rey G, Weger B, Gachon F, Dal Peraro M, Hernandez N, Schibler U, Deplancke B, Naef F. Transcriptional regulatory logic of the diurnal cycle in the mouse liver. PLoS Biol 2017; 15:e2001069. [PMID: 28414715 PMCID: PMC5393560 DOI: 10.1371/journal.pbio.2001069] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Accepted: 03/10/2017] [Indexed: 12/11/2022] Open
Abstract
Many organisms exhibit temporal rhythms in gene expression that propel diurnal cycles in physiology. In the liver of mammals, these rhythms are controlled by transcription-translation feedback loops of the core circadian clock and by feeding-fasting cycles. To better understand the regulatory interplay between the circadian clock and feeding rhythms, we mapped DNase I hypersensitive sites (DHSs) in the mouse liver during a diurnal cycle. The intensity of DNase I cleavages cycled at a substantial fraction of all DHSs, suggesting that DHSs harbor regulatory elements that control rhythmic transcription. Using chromatin immunoprecipitation followed by DNA sequencing (ChIP-seq), we found that hypersensitivity cycled in phase with RNA polymerase II (Pol II) loading and H3K27ac histone marks. We then combined the DHSs with temporal Pol II profiles in wild-type (WT) and Bmal1-/- livers to computationally identify transcription factors through which the core clock and feeding-fasting cycles control diurnal rhythms in transcription. While a similar number of mRNAs accumulated rhythmically in Bmal1-/- compared to WT livers, the amplitudes in Bmal1-/- were generally lower. The residual rhythms in Bmal1-/- reflected transcriptional regulators mediating feeding-fasting responses as well as responses to rhythmic systemic signals. Finally, the analysis of DNase I cuts at nucleotide resolution showed dynamically changing footprints consistent with dynamic binding of CLOCK:BMAL1 complexes. Structural modeling suggested that these footprints are driven by a transient heterotetramer binding configuration at peak activity. Together, our temporal DNase I mappings allowed us to decipher the global regulation of diurnal transcription rhythms in the mouse liver.
Collapse
Affiliation(s)
- Jonathan Aryeh Sobel
- The Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Irina Krier
- The Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Teemu Andersin
- Department of Molecular Biology, University of Geneva, Geneva, Switzerland
| | - Sunil Raghav
- The Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Donatella Canella
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Federica Gilardi
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Alexandra Styliani Kalantzi
- The Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Guillaume Rey
- The Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Benjamin Weger
- Department of Diabetes and Circadian Rhythms, Nestlé Institute of Health Sciences, Lausanne, Switzerland
| | - Frédéric Gachon
- Department of Diabetes and Circadian Rhythms, Nestlé Institute of Health Sciences, Lausanne, Switzerland
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Matteo Dal Peraro
- The Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Nouria Hernandez
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Ueli Schibler
- Department of Molecular Biology, University of Geneva, Geneva, Switzerland
| | - Bart Deplancke
- The Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Felix Naef
- The Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | | |
Collapse
|