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Epigenetics of Circadian Rhythms in Imprinted Neurodevelopmental Disorders. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2018; 157:67-92. [PMID: 29933957 DOI: 10.1016/bs.pmbts.2017.11.023] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
DNA sequence information alone cannot account for the immense variability between chromosomal alleles within diverse cell types in the brain, whether these differences are observed across time, cell type, or parental origin. The complex control and maintenance of gene expression and modulation are regulated by a multitude of molecular and cellular mechanisms that layer on top of the genetic code. The integration of genetic and environmental signals required for regulating brain development and function is achieved in part by a dynamic epigenetic landscape that includes DNA methylation, histone modifications, and noncoding RNAs. These epigenetic mechanisms establish and maintain core biological processes, including genomic imprinting and entrainment of circadian rhythms. This chapter will focus on how the epigenetic layers of DNA methylation and long, noncoding RNAs interact with circadian rhythms at specific imprinted chromosomal loci associated with the human neurodevelopmental disorders Prader-Willi, Angelman, Kagami-Ogata, and Temple syndromes.
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102
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Mendoza-Viveros L, Obrietan K, Cheng HYM. Commentary: miR-132/212 Modulates Seasonal Adaptation and Dendritic Morphology of the Central Circadian Clock. JOURNAL OF NEUROLOGY & NEUROMEDICINE 2018; 3:21-25. [PMID: 29682634 PMCID: PMC5906796 DOI: 10.29245/2572.942x/2017/1.1169] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Daily rhythms in behavior and physiology are coordinated by an endogenous clock located in the suprachiasmatic nucleus (SCN) of the hypothalamus. This central pacemaker also relays day length information to allow for seasonal adaptation, a process for which melatonin signaling is essential. How the SCN encodes day length is not fully understood. MicroRNAs (miRNAs) are small, non-coding RNAs that regulate gene expression by directing target mRNAs for degradation or translational repression. The miR-132/212 cluster plays a key role in facilitating neuronal plasticity, and miR-132 has been shown previously to modulate resetting of the central clock. A recent study from our group showed that miR-132/212 in mice is required for optimal adaptation to seasons and non-24-hour light/dark cycles through regulation of its target gene, methyl CpG-binding protein (MeCP2), in the SCN and dendritic spine density of SCN neurons. Furthermore, in the seasonal rodent Mesocricetus auratus (Syrian hamster), adaptation to short photoperiods is accompanied by structural plasticity in the SCN independently of melatonin signaling, thus further supporting a key role for SCN structural and, in turn, functional plasticity in the coding of day length. In this commentary, we discuss our recent findings in context of what is known about day length encoding by the SCN, and propose future directions.
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Affiliation(s)
- Lucia Mendoza-Viveros
- Department of Biology, University of Toronto Mississauga, Mississauga, ON, L5L 1C6, Canada
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, M5S 3G3, Canada
| | - Karl Obrietan
- Department of Neuroscience, Ohio State University, Columbus, OH, 43210, USA
| | - Hai-Ying M. Cheng
- Department of Biology, University of Toronto Mississauga, Mississauga, ON, L5L 1C6, Canada
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, M5S 3G3, Canada
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103
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Cytosine modifications exhibit circadian oscillations that are involved in epigenetic diversity and aging. Nat Commun 2018; 9:644. [PMID: 29440637 PMCID: PMC5811577 DOI: 10.1038/s41467-018-03073-7] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Accepted: 12/20/2017] [Indexed: 01/12/2023] Open
Abstract
Circadian rhythmicity governs a remarkable array of fundamental biological functions and is mediated by cyclical transcriptomic and proteomic activities. Epigenetic factors are also involved in this circadian machinery; however, despite extensive efforts, detection and characterization of circadian cytosine modifications at the nucleotide level have remained elusive. In this study, we report that a large proportion of epigenetically variable cytosines show a circadian pattern in their modification status in mice. Importantly, the cytosines with circadian epigenetic oscillations significantly overlap with the cytosines exhibiting age-related changes in their modification status. Our findings suggest that evolutionary advantageous processes such as circadian rhythmicity can also contribute to an organism’s deterioration. While epigenetic factors have been implicated in the circadian rhythm, the detection of circadian cytosine modifications has remained elusive. Here the authors identify a large number of epigenetically variable cytosines that show circadian oscillations in their modification status in mice.
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104
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Rittschof CC, Hughes KA. Advancing behavioural genomics by considering timescale. Nat Commun 2018; 9:489. [PMID: 29434301 PMCID: PMC5809431 DOI: 10.1038/s41467-018-02971-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 01/10/2018] [Indexed: 12/31/2022] Open
Abstract
Animal behavioural traits often covary with gene expression, pointing towards a genomic constraint on organismal responses to environmental cues. This pattern highlights a gap in our understanding of the time course of environmentally responsive gene expression, and moreover, how these dynamics are regulated. Advances in behavioural genomics explore how gene expression dynamics are correlated with behavioural traits that range from stable to highly labile. We consider the idea that certain genomic regulatory mechanisms may predict the timescale of an environmental effect on behaviour. This temporally minded approach could inform both organismal and evolutionary questions ranging from the remediation of early life social trauma to understanding the evolution of trait plasticity.
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Affiliation(s)
- Clare C Rittschof
- Department of Entomology, University of Kentucky, Lexington, KY, 40546, USA.
| | - Kimberly A Hughes
- Department of Biological Sciences, Florida State University, Tallahassee, FL, 32306, USA
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105
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Ding CJ, Liang LX, Diao S, Su XH, Zhang BY. Genome-wide analysis of day/night DNA methylation differences in Populus nigra. PLoS One 2018; 13:e0190299. [PMID: 29293569 PMCID: PMC5749751 DOI: 10.1371/journal.pone.0190299] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Accepted: 12/12/2017] [Indexed: 12/19/2022] Open
Abstract
DNA methylation is an important mechanism of epigenetic modification. Methylation changes during stress responses and developmental processes have been well studied; however, their role in plant adaptation to the day/night cycle is poorly understood. In this study, we detected global methylation patterns in leaves of the black poplar Populus nigra ‘N46’ at 8:00 and 24:00 by methylated DNA immunoprecipitation sequencing (MeDIP-seq). We found 10,027 and 10,242 genes to be methylated in the 8:00 and 24:00 samples, respectively. The methylated genes appeared to be involved in multiple biological processes, molecular functions, and cellular components, suggesting important roles for DNA methylation in poplar cells. Comparing the 8:00 and 24:00 samples, only 440 differentially methylated regions (DMRs) overlapped with genic regions, including 193 hyper- and 247 hypo-methylated DMRs, and may influence the expression of 137 downstream genes. Most hyper-methylated genes were associated with transferase activity, kinase activity, and phosphotransferase activity, whereas most hypo-methylated genes were associated with protein binding, ATP binding, and adenyl ribonucleotide binding, suggesting that different biological processes were activated during the day and night. Our results indicated that methylated genes were prevalent in the poplar genome, but that only a few of these participated in diurnal gene expression regulation.
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Affiliation(s)
- Chang-Jun Ding
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Li-Xiong Liang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Shu Diao
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Xiao-Hua Su
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Bing-Yu Zhang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- * E-mail:
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106
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Abstract
Self-sustained and synchronized to environmental stimuli, circadian clocks are under genetic and epigenetic regulation. Recent findings have greatly increased our understanding of epigenetic plasticity governed by circadian clock. Thus, the link between circadian clock and epigenetic machinery is reciprocal. Circadian clock can affect epigenetic features including genomic DNA methylation, noncoding RNA, mainly miRNA expression, and histone modifications resulted in their 24-h rhythms. Concomitantly, these epigenetic events can directly modulate cyclic system of transcription and translation of core circadian genes and indirectly clock output genes. Significant findings interlocking circadian clock, epigenetics, and cancer have been revealed, particularly in breast, colorectal, and blood cancers. Aberrant methylation of circadian gene promoter regions and miRNA expression affected circadian gene expression, together with 24-h expression oscillation pace have been frequently observed.
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107
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O'Callaghan EK, Green EW, Franken P, Mongrain V. Omics Approaches in Sleep-Wake Regulation. Handb Exp Pharmacol 2018; 253:59-81. [PMID: 29796779 DOI: 10.1007/164_2018_125] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Although sleep seems an obvious and simple behaviour, it is extremely complex involving numerous interactions both at the neuronal and the molecular levels. While we have gained detailed insight into the molecules and neuronal networks responsible for the circadian organization of sleep and wakefulness, the molecular underpinnings of the homeostatic aspect of sleep regulation are still unknown and the focus of a considerable research effort. In the last 20 years, the development of techniques allowing the simultaneous measurement of hundreds to thousands of molecular targets (i.e. 'omics' approaches) has enabled the unbiased study of the molecular pathways regulated by and regulating sleep. In this chapter, we will review how the different omics approaches, including transcriptomics, epigenomics, proteomics, and metabolomics, have advanced sleep research. We present relevant data in the framework of the two-process model in which circadian and homeostatic processes interact to regulate sleep. The integration of the different omics levels, known as 'systems genetics', will eventually lead to a better understanding of how information flows from the genome, to molecules, to networks, and finally to sleep both in health and disease.
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Affiliation(s)
- Emma K O'Callaghan
- Center for Advanced Research in Sleep Medicine and Research Center, Hôpital du Sacré-Coeur de Montréal, Montreal, QC, Canada.,Department of Neuroscience, Université de Montréal, Montreal, QC, Canada
| | - Edward W Green
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Paul Franken
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Valérie Mongrain
- Center for Advanced Research in Sleep Medicine and Research Center, Hôpital du Sacré-Coeur de Montréal, Montreal, QC, Canada. .,Department of Neuroscience, Université de Montréal, Montreal, QC, Canada.
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108
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Ecker S, Pancaldi V, Valencia A, Beck S, Paul DS. Epigenetic and Transcriptional Variability Shape Phenotypic Plasticity. Bioessays 2017; 40. [PMID: 29251357 DOI: 10.1002/bies.201700148] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Revised: 10/31/2017] [Indexed: 12/15/2022]
Abstract
Epigenetic and transcriptional variability contribute to the vast diversity of cellular and organismal phenotypes and are key in human health and disease. In this review, we describe different types, sources, and determinants of epigenetic and transcriptional variability, enabling cells and organisms to adapt and evolve to a changing environment. We highlight the latest research and hypotheses on how chromatin structure and the epigenome influence gene expression variability. Further, we provide an overview of challenges in the analysis of biological variability. An improved understanding of the molecular mechanisms underlying epigenetic and transcriptional variability, at both the intra- and inter-individual level, provides great opportunity for disease prevention, better therapeutic approaches, and personalized medicine.
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Affiliation(s)
- Simone Ecker
- UCL Cancer Institute, University College London, 72 Huntley Street, London, WC1E 6BT, UK
| | - Vera Pancaldi
- Barcelona Supercomputing Center (BSC), C/ Jordi Girona 39-31, 08034, Barcelona, Spain
| | - Alfonso Valencia
- Barcelona Supercomputing Center (BSC), C/ Jordi Girona 39-31, 08034, Barcelona, Spain.,ICREA, Pg. Lluís Companys 23, 08010, Barcelona, Spain
| | - Stephan Beck
- UCL Cancer Institute, University College London, 72 Huntley Street, London, WC1E 6BT, UK
| | - Dirk S Paul
- MRC/BHF Cardiovascular Epidemiology Unit Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK.,Department of Human Genetics Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1HH, UK
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109
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Salavaty A, Mohammadi N, Shahmoradi M, Naderi Soorki M. Bioinformatic Analysis of Circadian Expression of Oncogenes and Tumor Suppressor Genes. Bioinform Biol Insights 2017; 11:1177932217746991. [PMID: 29276378 PMCID: PMC5734456 DOI: 10.1177/1177932217746991] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 11/11/2017] [Indexed: 01/09/2023] Open
Abstract
Background Circadian rhythms are physiological and behavioral cycles with a period of approximately 24 hours that control various functions including gene expression. Circadian disruption is associated with a variety of diseases, especially cancer. Although some of the oncogenes and tumor suppressor genes (TSGs) are known as clock-controlled genes (CCGs), the analysis and annotation of circadian expression of most human oncogenes and TSGs are still lacking. This study aims to investigate the circadian expression of a list of human oncogenes and TSGs. Methods A bioinformatic analysis was conducted on a gene library comprising 120 genes to investigate the circadian expression of human oncogenes and TSGs. To achieve this purpose, the genotranscriptomic data were retrieved from COSMIC and analyzed by R statistical software. Furthermore, the acquired data were analyzed at the transcriptomic and proteomic levels using several publicly available databases. Also, the significance of all analyses was confirmed statistically. Results Altogether, our results indicated that 7 human oncogenes/TSGs may be expressed and function in a circadian manner. These oncogenes/TSGs showed a circadian expression pattern at CircaDB database and associated with at least one of the circadian genes/CCGs based on both genotranscriptomic and correlation analyses. Conclusions Although 4 of 7 finally outputted genes have been previously reported to be clock controlled, heretofore there is no report about the circadian expression of 3 other genes. Considering the importance of oncogenes/TSGs in the initiation and progression of cancer, further studies are suggested for the identification of exact circadian expression patterns of these 3 human oncogenes/TSGs.
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Affiliation(s)
- Adrian Salavaty
- Division of Biotechnology, Department of Cell and Molecular Biology, Faculty of Chemistry, University of Kashan, Kashan, Iran
| | - Niloufar Mohammadi
- Department of Biology, Friedrich Alexander University of Erlangen-Nürnberg, Erlangen, Germany
| | - Mozhdeh Shahmoradi
- Division of Biotechnology, Department of Cell and Molecular Biology, Faculty of Chemistry, University of Kashan, Kashan, Iran
| | - Maryam Naderi Soorki
- Department of Genetics, Faculty of Science, Shahid Chamran University of Ahvaz, Ahvaz, Iran
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110
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Gavery MR, Roberts SB. Epigenetic considerations in aquaculture. PeerJ 2017; 5:e4147. [PMID: 29230373 PMCID: PMC5723431 DOI: 10.7717/peerj.4147] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 11/17/2017] [Indexed: 12/14/2022] Open
Abstract
Epigenetics has attracted considerable attention with respect to its potential value in many areas of agricultural production, particularly under conditions where the environment can be manipulated or natural variation exists. Here we introduce key concepts and definitions of epigenetic mechanisms, including DNA methylation, histone modifications and non-coding RNA, review the current understanding of epigenetics in both fish and shellfish, and propose key areas of aquaculture where epigenetics could be applied. The first key area is environmental manipulation, where the intention is to induce an ‘epigenetic memory’ either within or between generations to produce a desired phenotype. The second key area is epigenetic selection, which, alone or combined with genetic selection, may increase the reliability of producing animals with desired phenotypes. Based on aspects of life history and husbandry practices in aquaculture species, the application of epigenetic knowledge could significantly affect the productivity and sustainability of aquaculture practices. Conversely, clarifying the role of epigenetic mechanisms in aquaculture species may upend traditional assumptions about selection practices. Ultimately, there are still many unanswered questions regarding how epigenetic mechanisms might be leveraged in aquaculture.
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Affiliation(s)
- Mackenzie R Gavery
- School of Aquatic & Fishery Sciences, University of Washington, Seattle, WA, USA
| | - Steven B Roberts
- School of Aquatic & Fishery Sciences, University of Washington, Seattle, WA, USA
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111
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Stevenson TJ. Epigenetic Regulation of Biological Rhythms: An Evolutionary Ancient Molecular Timer. Trends Genet 2017; 34:90-100. [PMID: 29221677 DOI: 10.1016/j.tig.2017.11.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2017] [Revised: 11/09/2017] [Accepted: 11/15/2017] [Indexed: 01/12/2023]
Abstract
Biological rhythms are pervasive in nature, yet our understanding of the molecular mechanisms that govern timing is far from complete. The rapidly emerging research focus on epigenetic plasticity has revealed a system that is highly dynamic and reversible. In this Opinion, I propose an epigenetic clock model that outlines how molecular modifications, such as DNA methylation, are integral components for timing endogenous biological rhythms. The hypothesis proposed is that an epigenetic clock serves to maintain the period of molecular rhythms via control over the phase of gene transcription and this timing mechanism resides in all cells, from unicellular to complex organisms. The model also provides a novel framework for the timing of epigenetic modifications during the lifespan and transgenerational inheritance of an organism.
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Affiliation(s)
- Tyler J Stevenson
- Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, AB24 2TZ, UK.
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112
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Schmitz J, Metz GA, Güntürkün O, Ocklenburg S. Beyond the genome—Towards an epigenetic understanding of handedness ontogenesis. Prog Neurobiol 2017; 159:69-89. [DOI: 10.1016/j.pneurobio.2017.10.005] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 09/18/2017] [Accepted: 10/26/2017] [Indexed: 12/13/2022]
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113
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Helm B, Visser ME, Schwartz W, Kronfeld-Schor N, Gerkema M, Piersma T, Bloch G. Two sides of a coin: ecological and chronobiological perspectives of timing in the wild. Philos Trans R Soc Lond B Biol Sci 2017; 372:20160246. [PMID: 28993490 PMCID: PMC5647273 DOI: 10.1098/rstb.2016.0246] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/20/2017] [Indexed: 12/19/2022] Open
Abstract
Most processes within organisms, and most interactions between organisms and their environment, have distinct time profiles. The temporal coordination of such processes is crucial across levels of biological organization, but disciplines differ widely in their approaches to study timing. Such differences are accentuated between ecologists, who are centrally concerned with a holistic view of an organism in relation to its external environment, and chronobiologists, who emphasize internal timekeeping within an organism and the mechanisms of its adjustment to the environment. We argue that ecological and chronobiological perspectives are complementary, and that studies at the intersection will enable both fields to jointly overcome obstacles that currently hinder progress. However, to achieve this integration, we first have to cross some conceptual barriers, clarifying prohibitively inaccessible terminologies. We critically assess main assumptions and concepts in either field, as well as their common interests. Both approaches intersect in their need to understand the extent and regulation of temporal plasticity, and in the concept of 'chronotype', i.e. the characteristic temporal properties of individuals which are the targets of natural and sexual selection. We then highlight promising developments, point out open questions, acknowledge difficulties and propose directions for further integration of ecological and chronobiological perspectives through Wild Clock research.This article is part of the themed issue 'Wild Clocks: integrating chronobiology and ecology to understand timekeeping in free-living animals'.
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Affiliation(s)
- Barbara Helm
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Graham Kerr Building, Glasgow G128QQ, UK
| | - Marcel E Visser
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), PO 50, 6700 AB Wageningen, The Netherlands
| | - William Schwartz
- Department of Neurology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA, USA
| | | | - Menno Gerkema
- Chronobiology, Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, Groningen, The Netherlands
| | - Theunis Piersma
- NIOZ Royal Netherlands Institute for Sea Research, Department of Coastal Systems and Utrecht University, 1790 AB Den Burg, Texel, The Netherlands
- Conservation Ecology Group, Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, Groningen, The Netherlands
| | - Guy Bloch
- Department of Ecology, Evolution, and Behavior, The A. Silberman Institute of Life Sciences, Hebrew University, Jerusalem 91904, Israel
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114
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Brown LA, Williams J, Taylor L, Thomson RJ, Nolan PM, Foster RG, Peirson SN. Meta-analysis of transcriptomic datasets identifies genes enriched in the mammalian circadian pacemaker. Nucleic Acids Res 2017; 45:9860-9873. [PMID: 28973476 PMCID: PMC5737434 DOI: 10.1093/nar/gkx714] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 08/04/2017] [Indexed: 12/14/2022] Open
Abstract
The master circadian pacemaker in mammals is located in the suprachiasmatic nuclei (SCN) which regulate physiology and behaviour, as well as coordinating peripheral clocks throughout the body. Investigating the function of the SCN has often focused on the identification of rhythmically expressed genes. However, not all genes critical for SCN function are rhythmically expressed. An alternative strategy is to characterize those genes that are selectively enriched in the SCN. Here, we examined the transcriptome of the SCN and whole brain (WB) of mice using meta-analysis of publicly deposited data across a range of microarray platforms and RNA-Seq data. A total of 79 microarrays were used (24 SCN and 55 WB samples, 4 different microarray platforms), alongside 17 RNA-Seq data files (7 SCN and 10 WB). 31 684 MGI gene symbols had data for at least one platform. Meta-analysis using a random effects model for weighting individual effect sizes (derived from differential expression between relevant SCN and WB samples) reliably detected known SCN markers. SCN-enriched transcripts identified in this study provide novel insights into SCN function, including identifying genes which may play key roles in SCN physiology or provide SCN-specific drivers.
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Affiliation(s)
- Laurence A Brown
- Sleep and Circadian Neuroscience Institute (SCNi), Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, OX1 3RE, UK
| | - John Williams
- MRC Harwell Institute, Harwell Campus, Oxfordshire OX11 0RD, UK
| | - Lewis Taylor
- Sleep and Circadian Neuroscience Institute (SCNi), Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, OX1 3RE, UK
| | - Ross J Thomson
- Sleep and Circadian Neuroscience Institute (SCNi), Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, OX1 3RE, UK
| | - Patrick M Nolan
- MRC Harwell Institute, Harwell Campus, Oxfordshire OX11 0RD, UK
| | - Russell G Foster
- Sleep and Circadian Neuroscience Institute (SCNi), Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, OX1 3RE, UK
| | - Stuart N Peirson
- Sleep and Circadian Neuroscience Institute (SCNi), Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, OX1 3RE, UK
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115
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Myung J, Pauls SD. Encoding seasonal information in a two-oscillator model of the multi-oscillator circadian clock. Eur J Neurosci 2017; 48:2718-2727. [PMID: 28921823 DOI: 10.1111/ejn.13697] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 09/01/2017] [Accepted: 09/11/2017] [Indexed: 02/01/2023]
Abstract
The suprachiasmatic nucleus (SCN) is a collection of about 10 000 neurons, each of which functions as a circadian clock with slightly different periods and phases, that work in concert with form and maintain the master circadian clock for the organism. The diversity among neurons confers on the SCN the ability to robustly encode both the 24-h light pattern as well as the seasonal time. Cluster synchronization brings the different neurons into line and reduces the large population to essentially two oscillators, coordinated by a macroscopic network motif of asymmetric repulsive-attractive coupling. We recount the steps leading to this simplification and rigorously examine the two-oscillator case by seeking an analytical solution. Through these steps, we identify physiologically relevant parameters that shape the behaviour of the SCN network and delineate its ability to store past details of seasonal variation in photoperiod.
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Affiliation(s)
- Jihwan Myung
- Computational Neuroscience Unit, Okinawa Institute of Science and Technology, Lab 2 Level B, 1919-1 Tancha Onna-son, Kunigami, Okinawa 904-0495, Japan.,Graduate Institute of Humanities in Medicine, Taipei Medical University, Taipei, Taiwan.,TMU-Research Center of Brain and Consciousness, Shuang Ho Hospital, New Taipei City, Taiwan
| | - Scott D Pauls
- Department of Mathematics, Dartmouth College, 6188 Kemeny Hall, Hanover, NH 03755, USA
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116
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West AC, Smith L, Ray DW, Loudon ASI, Brown TM, Bechtold DA. Misalignment with the external light environment drives metabolic and cardiac dysfunction. Nat Commun 2017; 8:417. [PMID: 28900189 PMCID: PMC5595905 DOI: 10.1038/s41467-017-00462-2] [Citation(s) in RCA: 97] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 06/30/2017] [Indexed: 12/20/2022] Open
Abstract
Most organisms use internal biological clocks to match behavioural and physiological processes to specific phases of the day-night cycle. Central to this is the synchronisation of internal processes across multiple organ systems. Environmental desynchrony (e.g. shift work) profoundly impacts human health, increasing cardiovascular disease and diabetes risk, yet the underlying mechanisms remain unclear. Here, we characterise the impact of desynchrony between the internal clock and the external light-dark (LD) cycle on mammalian physiology. We reveal that even under stable LD environments, phase misalignment has a profound effect, with decreased metabolic efficiency and disrupted cardiac function including prolonged QT interval duration. Importantly, physiological dysfunction is not driven by disrupted core clock function, nor by an internal desynchrony between organs, but rather the altered phase relationship between the internal clockwork and the external environment. We suggest phase misalignment as a major driver of pathologies associated with shift work, chronotype and social jetlag.The misalignment between internal circadian rhythm and the day-night cycle can be caused by genetic, behavioural and environmental factors, and may have a profound impact on human physiology. Here West et al. show that desynchrony between the internal clock and the external environment alter metabolic parameters and cardiac function in mice.
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Affiliation(s)
- Alexander C West
- Division of Diabetes, Endocrinology and Gastroenterology, School of Medicine, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, M13 9PL, UK
| | - Laura Smith
- Division of Diabetes, Endocrinology and Gastroenterology, School of Medicine, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, M13 9PL, UK
| | - David W Ray
- Division of Diabetes, Endocrinology and Gastroenterology, School of Medicine, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, M13 9PL, UK
| | - Andrew S I Loudon
- Division of Diabetes, Endocrinology and Gastroenterology, School of Medicine, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, M13 9PL, UK
| | - Timothy M Brown
- Division of Diabetes, Endocrinology and Gastroenterology, School of Medicine, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, M13 9PL, UK
| | - David A Bechtold
- Division of Diabetes, Endocrinology and Gastroenterology, School of Medicine, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, M13 9PL, UK.
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Yoshinaka K, Yamaguchi A, Matsumura R, Node K, Tokuda I, Akashi M. Effect of different light-dark schedules on estrous cycle in mice, and implications for mitigating the adverse impact of night work. Genes Cells 2017; 22:876-884. [PMID: 28884885 DOI: 10.1111/gtc.12522] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Accepted: 08/03/2017] [Indexed: 12/29/2022]
Abstract
Approximately 20% of workers in developed countries are involved in night work. Nevertheless, many studies have strongly suggested that night-work-induced chronic circadian misalignment increases the risk of a diverse range of health problems. Although a relation between night work and irregular menstrual cycles has been indicated epidemiologically, a direct causal link remains elusive. Here, we report that repetitive reversal of light-dark (LD) cycles triggers irregular estrous cycles in mice. The findings showed that the estrous cycle remained irregular for more than four weeks after the mice were returned to regular LD cycles. Importantly, the magnitude of the negative impact of reversed LD cycles on the estrous cycle, or more specifically the decreased number of normal estrous cycles during the observation period, was dependent on the difference in the frequency of LD reversal. Presently, no clear solution to prevent night-work-mediated menstrual abnormalities is available, and reducing night work in modern society is difficult. Our findings indicate that optimizing work schedules could significantly prevent menstrual problems without reducing total night-work time.
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Affiliation(s)
- Kiichi Yoshinaka
- The Research Institute for Time Studies, Yamaguchi University, 1677-1 Yoshida, Yamaguchi, 753-8511, Japan
| | - Ai Yamaguchi
- The Research Institute for Time Studies, Yamaguchi University, 1677-1 Yoshida, Yamaguchi, 753-8511, Japan
| | - Ritsuko Matsumura
- The Research Institute for Time Studies, Yamaguchi University, 1677-1 Yoshida, Yamaguchi, 753-8511, Japan
| | - Koichi Node
- Department of Cardiovascular Medicine, Saga University, 5-1-1 Nabeshima, Saga, 849-8501, Japan
| | - Isao Tokuda
- Department of Mechanical Engineering, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, 525-8577, Japan
| | - Makoto Akashi
- The Research Institute for Time Studies, Yamaguchi University, 1677-1 Yoshida, Yamaguchi, 753-8511, Japan
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Delayed Cryptochrome Degradation Asymmetrically Alters the Daily Rhythm in Suprachiasmatic Clock Neuron Excitability. J Neurosci 2017; 37:7824-7836. [PMID: 28698388 PMCID: PMC5559760 DOI: 10.1523/jneurosci.0691-17.2017] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Revised: 06/01/2017] [Accepted: 06/08/2017] [Indexed: 11/30/2022] Open
Abstract
Suprachiasmatic nuclei (SCN) neurons contain an intracellular molecular circadian clock and the Cryptochromes (CRY1/2), key transcriptional repressors of this molecular apparatus, are subject to post-translational modification through ubiquitination and targeting for proteosomal degradation by the ubiquitin E3 ligase complex. Loss-of-function point mutations in a component of this ligase complex, Fbxl3, delay CRY1/2 degradation, reduce circadian rhythm strength, and lengthen the circadian period by ∼2.5 h. The molecular clock drives circadian changes in the membrane properties of SCN neurons, but it is unclear how alterations in CRY1/2 stability affect SCN neurophysiology. Here we use male and female Afterhours mice which carry the circadian period lengthening loss-of-function Fbxl3Afh mutation and perform patch-clamp recordings from SCN brain slices across the projected day/night cycle. We find that the daily rhythm in membrane excitability in the ventral SCN (vSCN) was enhanced in amplitude and delayed in timing in Fbxl3Afh/Afh mice. At night, vSCN cells from Fbxl3Afh/Afh mice were more hyperpolarized, receiving more GABAergic input than their Fbxl3+/+ counterparts. Unexpectedly, the progression to daytime hyperexcited states was slowed by Afh mutation, whereas the decline to hypoexcited states was accelerated. In long-term bioluminescence recordings, GABAA receptor blockade desynchronized the Fbxl3+/+ but not the Fbxl3Afh/Afh vSCN neuronal network. Further, a neurochemical mimic of the light input pathway evoked larger shifts in molecular clock rhythms in Fbxl3Afh/Afh compared with Fbxl3+/+ SCN slices. These results reveal unanticipated consequences of delaying CRY degradation, indicating that the Afh mutation prolongs nighttime hyperpolarized states of vSCN cells through increased GABAergic synaptic transmission. SIGNIFICANCE STATEMENT The intracellular molecular clock drives changes in SCN neuronal excitability, but it is unclear how mutations affecting post-translational modification of molecular clock proteins influence the temporal expression of SCN neuronal state or intercellular communication within the SCN network. Here we show for the first time, that a mutation that prolongs the stability of key components of the intracellular clock, the cryptochrome proteins, unexpectedly increases in the expression of hypoexcited neuronal state in the ventral SCN at night and enhances hyperpolarization of ventral SCN neurons at this time. This is accompanied by increased GABAergic signaling and by enhanced responsiveness to a neurochemical mimic of the light input pathway to the SCN. Therefore, post-translational modification shapes SCN neuronal state and network properties.
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119
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Tomita T, Kurita R, Onishi Y. Epigenetic regulation of the circadian clock: role of 5-aza-2'-deoxycytidine. Biosci Rep 2017; 37:BSR20170053. [PMID: 28487473 PMCID: PMC5437938 DOI: 10.1042/bsr20170053] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Revised: 04/30/2017] [Accepted: 05/08/2017] [Indexed: 12/18/2022] Open
Abstract
We have been investigating transcriptional regulation of the BMAL1 gene, a critical component of the mammalian clock system including DNA methylation. Here, a more detailed analysis of the regulation of DNA methylation of BMAL1 proceeded in RPMI8402 lymphoma cells. We found that CpG islands in the BMAL1 and the PER2 promoters were hyper- and hypomethylated, respectively and that 5-aza-2'-deoxycytidine (aza-dC) not only enhanced PER2 gene expression but also PER2 oscillation within 24 h in RPMI8402 cells. That is, such hypermethylation of CpG islands in the BMAL1 promoter restricted PER2 expression which was recovered by aza-dC within 1 day in these cells. These results suggest that the circadian clock system can be recovered through BMAL1 expression induced by aza-dC within a day. The RPIB9 promoter of RPMI8402 cells, which is a methylation hotspot in lymphoblastic leukemia, was also hypermethylated and aza-dC gradually recovered RPIB9 expression in 3 days. In addition, methylation-specific PCR revealed a different degree of aza-dC-induced methylation release between BMAL1 and RPIB9 These results suggest that the aza-dC-induced recovery of gene expression from DNA methylation is dependent on a gene, for example the rapid response to demethylation by the circadian system, and thus, is of importance to clinical strategies for treating cancer.
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Affiliation(s)
- Tatsunosuke Tomita
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), DBT-AIST International Laboratory for Advanced Biomedicine (DAILAB), Higashi 1-1-1, Tsukuba 305-8566, Japan
| | - Ryoji Kurita
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), DBT-AIST International Laboratory for Advanced Biomedicine (DAILAB), Higashi 1-1-1, Tsukuba 305-8566, Japan
| | - Yoshiaki Onishi
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), DBT-AIST International Laboratory for Advanced Biomedicine (DAILAB), Higashi 1-1-1, Tsukuba 305-8566, Japan
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120
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Patke A, Murphy PJ, Onat OE, Krieger AC, Özçelik T, Campbell SS, Young MW. Mutation of the Human Circadian Clock Gene CRY1 in Familial Delayed Sleep Phase Disorder. Cell 2017; 169:203-215.e13. [PMID: 28388406 DOI: 10.1016/j.cell.2017.03.027] [Citation(s) in RCA: 231] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2017] [Revised: 02/18/2017] [Accepted: 03/20/2017] [Indexed: 12/12/2022]
Abstract
Patterns of daily human activity are controlled by an intrinsic circadian clock that promotes ∼24 hr rhythms in many behavioral and physiological processes. This system is altered in delayed sleep phase disorder (DSPD), a common form of insomnia in which sleep episodes are shifted to later times misaligned with the societal norm. Here, we report a hereditary form of DSPD associated with a dominant coding variation in the core circadian clock gene CRY1, which creates a transcriptional inhibitor with enhanced affinity for circadian activator proteins Clock and Bmal1. This gain-of-function CRY1 variant causes reduced expression of key transcriptional targets and lengthens the period of circadian molecular rhythms, providing a mechanistic link to DSPD symptoms. The allele has a frequency of up to 0.6%, and reverse phenotyping of unrelated families corroborates late and/or fragmented sleep patterns in carriers, suggesting that it affects sleep behavior in a sizeable portion of the human population.
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Affiliation(s)
- Alina Patke
- Laboratory of Genetics, The Rockefeller University, New York, NY 10065, USA.
| | - Patricia J Murphy
- Laboratory of Human Chronobiology, Weill Cornell Medical College, White Plains, NY 10605, USA
| | - Onur Emre Onat
- Department of Molecular Biology and Genetics, Faculty of Science, Bilkent University, Ankara 06800, Turkey
| | - Ana C Krieger
- Department of Medicine, Center for Sleep Medicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - Tayfun Özçelik
- Department of Molecular Biology and Genetics, Faculty of Science, Bilkent University, Ankara 06800, Turkey
| | - Scott S Campbell
- Laboratory of Human Chronobiology, Weill Cornell Medical College, White Plains, NY 10605, USA
| | - Michael W Young
- Laboratory of Genetics, The Rockefeller University, New York, NY 10065, USA.
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Cronin P, McCarthy MJ, Lim ASP, Salmon DP, Galasko D, Masliah E, De Jager PL, Bennett DA, Desplats P. Circadian alterations during early stages of Alzheimer's disease are associated with aberrant cycles of DNA methylation in BMAL1. Alzheimers Dement 2017; 13:689-700. [PMID: 27883893 PMCID: PMC5785929 DOI: 10.1016/j.jalz.2016.10.003] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Revised: 09/16/2016] [Accepted: 10/10/2016] [Indexed: 10/20/2022]
Abstract
INTRODUCTION Circadian alterations are prevalent in Alzheimer's disease (AD) and may contribute to cognitive impairment, behavioral symptoms, and neurodegeneration. Epigenetic mechanisms regulate the circadian clock, and changes in DNA methylation have been reported in AD brains, but the pathways that mediate circadian deregulation in AD are incompletely understood. We hypothesized that aberrant DNA methylation may affect circadian rhythms in AD. METHODS We investigated DNA methylation, transcription, and expression of BMAL1, a positive regulator of the circadian clock, in cultured fibroblasts and brain samples from two independent cohorts of aging and AD. RESULTS DNA methylation modulated rhythmic expression of clock genes in cultured fibroblasts. Moreover, rhythmic methylation of BMAL1 was altered in AD brains and fibroblasts and correlated with transcription cycles. DISCUSSION Our results indicate that cycles of DNA methylation contribute to the regulation of BMAL1 rhythms in the brain. Hence, aberrant epigenetic patterns may be linked to circadian alterations in AD.
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Affiliation(s)
- Peter Cronin
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
| | - Michael J McCarthy
- Psychiatry Service, Veterans Affairs San Diego Health Care System, San Diego, CA, USA; Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
| | - Andrew S P Lim
- Division of Neurology, Department of Medicine, Sunnybrook Health Sciences Centre, University of Toronto, Toronto, ON, Canada
| | - David P Salmon
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
| | - Douglas Galasko
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
| | - Eliezer Masliah
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA; Department of Pathology, University of California San Diego, La Jolla, CA, USA
| | - Philip L De Jager
- Departments of Neurology, Brigham and Women's Hospital, Boston, MA, USA; Department of Psychiatry, Brigham and Women's Hospital, Boston, MA, USA
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Paula Desplats
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA; Department of Pathology, University of California San Diego, La Jolla, CA, USA.
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Abstract
PURPOSE OF THE REVIEW A wide array of sleep and circadian deficits have been observed in patients with Alzheimer's Disease (AD). However, the vast majority of these studies have focused on later-stage AD, and do not shed light on the possibility that circadian dysfunction contributes to AD pathogenesis. The goal of this review it to examine the evidence supporting or refuting the hypothesis that circadian dysfunction plays an important role in early AD pathogenesis or AD risk in humans. RECENT FINDINGS Few studies have addressed the role of the circadian system in very early AD, or prior to AD diagnosis. AD appears to have a long presymtomatic phase during which pathology is present but cognition remains normal. Studies evaluating circadian function in cognitively-normal elderly or early-stage AD have thus far not incorporated AD biomarkers. Thus, the cause-and-effect relationship between circadian dysfunction and early-stage AD remains unclear. SUMMARY Circadian dysfunction becomes apparent in AD as dementia progresses, but it is unknown at which point in the pathogenic process rhythms begin to deteriorate. Further, it is unknown if exposure to circadian disruption in middle age increases AD risk later in life. This review address gaps in current knowledge on this topic, and proposes several critical directions for future research which might help to clarify the potential pathogenic role of circadian clock dysfunction in AD.
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Affiliation(s)
- Erik S. Musiek
- Dept. of Neurology, Knight Alzheimer Disease Research Center, Washington University School of Medicine, St. Louis MO, USA
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123
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Abstract
Chronotherapeutics aim at treating illnesses according to the endogenous biologic rhythms, which moderate xenobiotic metabolism and cellular drug response. The molecular clocks present in individual cells involve approximately fifteen clock genes interconnected in regulatory feedback loops. They are coordinated by the suprachiasmatic nuclei, a hypothalamic pacemaker, which also adjusts the circadian rhythms to environmental cycles. As a result, many mechanisms of diseases and drug effects are controlled by the circadian timing system. Thus, the tolerability of nearly 500 medications varies by up to fivefold according to circadian scheduling, both in experimental models and/or patients. Moreover, treatment itself disrupted, maintained, or improved the circadian timing system as a function of drug timing. Improved patient outcomes on circadian-based treatments (chronotherapy) have been demonstrated in randomized clinical trials, especially for cancer and inflammatory diseases. However, recent technological advances have highlighted large interpatient differences in circadian functions resulting in significant variability in chronotherapy response. Such findings advocate for the advancement of personalized chronotherapeutics through interdisciplinary systems approaches. Thus, the combination of mathematical, statistical, technological, experimental, and clinical expertise is now shaping the development of dedicated devices and diagnostic and delivery algorithms enabling treatment individualization. In particular, multiscale systems chronopharmacology approaches currently combine mathematical modeling based on cellular and whole-body physiology to preclinical and clinical investigations toward the design of patient-tailored chronotherapies. We review recent systems research works aiming to the individualization of disease treatment, with emphasis on both cancer management and circadian timing system–resetting strategies for improving chronic disease control and patient outcomes.
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Affiliation(s)
- Annabelle Ballesta
- Warwick Medical School (A.B., P.F.I., R.D., F.A.L.) and Warwick Mathematics Institute (A.B., D.A.R.), University of Warwick, Coventry, United Kingdom; Warwick Systems Biology and Infectious Disease Epidemiological Research Centre, Senate House, Coventry, United Kingdom (A.B., P.F.I., R.D., D.A.R., F.A.L.); INSERM-Warwick European Associated Laboratory "Personalising Cancer Chronotherapy through Systems Medicine" (C2SysMed), Unité mixte de Recherche Scientifique 935, Centre National de Recherche Scientifique Campus, Villejuif, France (A.B., P.F.I., R.D., D.A.R., F.A.L.); and Queen Elisabeth Hospital Birmingham, University Hospitals Birmingham National Health Service Foundation Trust, Cancer Unit, Edgbaston Birmingham, United Kingdom (P.F.I., F.A.L.)
| | - Pasquale F Innominato
- Warwick Medical School (A.B., P.F.I., R.D., F.A.L.) and Warwick Mathematics Institute (A.B., D.A.R.), University of Warwick, Coventry, United Kingdom; Warwick Systems Biology and Infectious Disease Epidemiological Research Centre, Senate House, Coventry, United Kingdom (A.B., P.F.I., R.D., D.A.R., F.A.L.); INSERM-Warwick European Associated Laboratory "Personalising Cancer Chronotherapy through Systems Medicine" (C2SysMed), Unité mixte de Recherche Scientifique 935, Centre National de Recherche Scientifique Campus, Villejuif, France (A.B., P.F.I., R.D., D.A.R., F.A.L.); and Queen Elisabeth Hospital Birmingham, University Hospitals Birmingham National Health Service Foundation Trust, Cancer Unit, Edgbaston Birmingham, United Kingdom (P.F.I., F.A.L.)
| | - Robert Dallmann
- Warwick Medical School (A.B., P.F.I., R.D., F.A.L.) and Warwick Mathematics Institute (A.B., D.A.R.), University of Warwick, Coventry, United Kingdom; Warwick Systems Biology and Infectious Disease Epidemiological Research Centre, Senate House, Coventry, United Kingdom (A.B., P.F.I., R.D., D.A.R., F.A.L.); INSERM-Warwick European Associated Laboratory "Personalising Cancer Chronotherapy through Systems Medicine" (C2SysMed), Unité mixte de Recherche Scientifique 935, Centre National de Recherche Scientifique Campus, Villejuif, France (A.B., P.F.I., R.D., D.A.R., F.A.L.); and Queen Elisabeth Hospital Birmingham, University Hospitals Birmingham National Health Service Foundation Trust, Cancer Unit, Edgbaston Birmingham, United Kingdom (P.F.I., F.A.L.)
| | - David A Rand
- Warwick Medical School (A.B., P.F.I., R.D., F.A.L.) and Warwick Mathematics Institute (A.B., D.A.R.), University of Warwick, Coventry, United Kingdom; Warwick Systems Biology and Infectious Disease Epidemiological Research Centre, Senate House, Coventry, United Kingdom (A.B., P.F.I., R.D., D.A.R., F.A.L.); INSERM-Warwick European Associated Laboratory "Personalising Cancer Chronotherapy through Systems Medicine" (C2SysMed), Unité mixte de Recherche Scientifique 935, Centre National de Recherche Scientifique Campus, Villejuif, France (A.B., P.F.I., R.D., D.A.R., F.A.L.); and Queen Elisabeth Hospital Birmingham, University Hospitals Birmingham National Health Service Foundation Trust, Cancer Unit, Edgbaston Birmingham, United Kingdom (P.F.I., F.A.L.)
| | - Francis A Lévi
- Warwick Medical School (A.B., P.F.I., R.D., F.A.L.) and Warwick Mathematics Institute (A.B., D.A.R.), University of Warwick, Coventry, United Kingdom; Warwick Systems Biology and Infectious Disease Epidemiological Research Centre, Senate House, Coventry, United Kingdom (A.B., P.F.I., R.D., D.A.R., F.A.L.); INSERM-Warwick European Associated Laboratory "Personalising Cancer Chronotherapy through Systems Medicine" (C2SysMed), Unité mixte de Recherche Scientifique 935, Centre National de Recherche Scientifique Campus, Villejuif, France (A.B., P.F.I., R.D., D.A.R., F.A.L.); and Queen Elisabeth Hospital Birmingham, University Hospitals Birmingham National Health Service Foundation Trust, Cancer Unit, Edgbaston Birmingham, United Kingdom (P.F.I., F.A.L.)
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Bayraktar G, Kreutz MR. Neuronal DNA Methyltransferases: Epigenetic Mediators between Synaptic Activity and Gene Expression? Neuroscientist 2017; 24:171-185. [PMID: 28513272 PMCID: PMC5846851 DOI: 10.1177/1073858417707457] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
DNMT3A and 3B are the main de novo DNA methyltransferases (DNMTs) in the brain that introduce new methylation marks to non-methylated DNA in postmitotic neurons. DNA methylation is a key epigenetic mark that is known to regulate important cellular processes in neuronal development and brain plasticity. Accumulating evidence disclosed rapid and dynamic changes in DNA methylation of plasticity-relevant genes that are important for learning and memory formation. To understand how DNMTs contribute to brain function and how they are regulated by neuronal activity is a prerequisite for a deeper appreciation of activity-dependent gene expression in health and disease. This review discusses the functional role of de novo methyltransferases and in particular DNMT3A1 in the adult brain with special emphasis on synaptic plasticity, memory formation, and brain disorders.
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Affiliation(s)
- Gonca Bayraktar
- 1 RG Neuroplasticity, Leibniz Institute for Neurobiology, Magdeburg, Germany
| | - Michael R Kreutz
- 1 RG Neuroplasticity, Leibniz Institute for Neurobiology, Magdeburg, Germany.,2 Leibniz Group "Dendritic Organelles and Synaptic Function", ZMNH, Magdeburg, Germany
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125
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Papazyan R, Zhang Y, Lazar MA. Genetic and epigenomic mechanisms of mammalian circadian transcription. Nat Struct Mol Biol 2017; 23:1045-1052. [PMID: 27922611 DOI: 10.1038/nsmb.3324] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 10/13/2016] [Indexed: 12/27/2022]
Abstract
The mammalian molecular clock comprises a complex network of transcriptional programs that integrates environmental signals with physiological pathways in a tissue-specific manner. Emerging technologies are extending knowledge of basic clock features by uncovering their underlying molecular mechanisms, thus setting the stage for a 'systems' view of the molecular clock. Here we discuss how recent data from genome-wide genetic and epigenetic studies have informed the understanding of clock function. In addition to its importance in human physiology and disease, the clock mechanism provides an ideal model to assess general principles of dynamic transcription regulation in vivo.
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Affiliation(s)
- Romeo Papazyan
- Division of Endocrinology, Diabetes, and Metabolism; Department of Medicine; Department of Genetics; and Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Yuxiang Zhang
- Division of Endocrinology, Diabetes, and Metabolism; Department of Medicine; Department of Genetics; and Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Mitchell A Lazar
- Division of Endocrinology, Diabetes, and Metabolism; Department of Medicine; Department of Genetics; and Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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126
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Stevenson TJ. Environmental and hormonal regulation of epigenetic enzymes in the hypothalamus. J Neuroendocrinol 2017; 29. [PMID: 28370682 DOI: 10.1111/jne.12471] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Revised: 03/09/2017] [Accepted: 03/25/2017] [Indexed: 12/13/2022]
Abstract
Neuroendocrine structures integrate a vast range of external cues and internal signals that, in turn, result in adaptive physiological responses. Emerging data indicate that light, social cues, stress and energy balance stimulate relatively short- and long-term genomic modifications in discrete neuroendocrine structures, which are mediated by epigenetic mechanisms. Moreover, environmentally-induced fluctuations in the synthesis of local hypothalamic and circulating hormones provide an internal signal that contributes to the extensive neuroendocrine genomic plasticity. This review examines the impact of environmental stimuli and endogenous hormonal signals on the regulation of epigenetic enzymes in key neuroendocrine structures. The data discussed are predominantly derived from studies in the neuroendocrine control of seasonal reproduction and the impact of social stress in rodent models. The perspective presented considers the role of oestrogen and glucocorticoids as the primary catalysts for inducing epigenetic modifications (eg, DNA methylation) in specific neuroendocrine structures. Oestrogen and glucocorticoid actions suggest: (i) a preferential action for specific epigenetic enzymes and (ii) nucleus- and cell-specific modifications. Untangling the complex web of hormonal regulation of methylation and acetylation will enhance our understanding of short- and long-term changes in epigenetic enzymes that generate adaptive and pathological neuroendocrine responses.
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Affiliation(s)
- T J Stevenson
- Institute for Biological and Environmental Sciences, University of Aberdeen, Aberdeen, UK
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127
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Mendoza-Viveros L, Chiang CK, Ong JLK, Hegazi S, Cheng AH, Bouchard-Cannon P, Fana M, Lowden C, Zhang P, Bothorel B, Michniewicz MG, Magill ST, Holmes MM, Goodman RH, Simonneaux V, Figeys D, Cheng HYM. miR-132/212 Modulates Seasonal Adaptation and Dendritic Morphology of the Central Circadian Clock. Cell Rep 2017; 19:505-520. [PMID: 28423315 PMCID: PMC5864111 DOI: 10.1016/j.celrep.2017.03.057] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Revised: 01/11/2017] [Accepted: 03/17/2017] [Indexed: 02/04/2023] Open
Abstract
The central circadian pacemaker, the suprachiasmatic nucleus (SCN), encodes day length information by mechanisms that are not well understood. Here, we report that genetic ablation of miR-132/212 alters entrainment to different day lengths and non-24 hr day-night cycles, as well as photoperiodic regulation of Period2 expression in the SCN. SCN neurons from miR-132/212-deficient mice have significantly reduced dendritic spine density, along with altered methyl CpG-binding protein (MeCP2) rhythms. In Syrian hamsters, a model seasonal rodent, day length regulates spine density on SCN neurons in a melatonin-independent manner, as well as expression of miR-132, miR-212, and their direct target, MeCP2. Genetic disruption of Mecp2 fully restores the level of dendritic spines of miR-132/212-deficient SCN neurons. Our results reveal that, by regulating the dendritic structure of SCN neurons through a MeCP2-dependent mechanism, miR-132/212 affects the capacity of the SCN to encode seasonal time.
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Affiliation(s)
- Lucia Mendoza-Viveros
- Department of Biology, University of Toronto Mississauga, 3359 Mississauga Road, Mississauga, ON L5L 1C6, Canada; Department of Cell and Systems Biology, University of Toronto, 25 Harbord Street, Toronto, ON M5S 3G5, Canada
| | - Cheng-Kang Chiang
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada
| | - Jonathan L K Ong
- Department of Biology, University of Toronto Mississauga, 3359 Mississauga Road, Mississauga, ON L5L 1C6, Canada
| | - Sara Hegazi
- Department of Biology, University of Toronto Mississauga, 3359 Mississauga Road, Mississauga, ON L5L 1C6, Canada; Department of Cell and Systems Biology, University of Toronto, 25 Harbord Street, Toronto, ON M5S 3G5, Canada
| | - Arthur H Cheng
- Department of Biology, University of Toronto Mississauga, 3359 Mississauga Road, Mississauga, ON L5L 1C6, Canada; Department of Cell and Systems Biology, University of Toronto, 25 Harbord Street, Toronto, ON M5S 3G5, Canada
| | - Pascale Bouchard-Cannon
- Department of Biology, University of Toronto Mississauga, 3359 Mississauga Road, Mississauga, ON L5L 1C6, Canada; Department of Cell and Systems Biology, University of Toronto, 25 Harbord Street, Toronto, ON M5S 3G5, Canada
| | - Michael Fana
- Department of Biology, University of Toronto Mississauga, 3359 Mississauga Road, Mississauga, ON L5L 1C6, Canada; Department of Cell and Systems Biology, University of Toronto, 25 Harbord Street, Toronto, ON M5S 3G5, Canada
| | - Christopher Lowden
- Department of Biology, University of Toronto Mississauga, 3359 Mississauga Road, Mississauga, ON L5L 1C6, Canada; Department of Cell and Systems Biology, University of Toronto, 25 Harbord Street, Toronto, ON M5S 3G5, Canada
| | - Peng Zhang
- Department of Biology, University of Toronto Mississauga, 3359 Mississauga Road, Mississauga, ON L5L 1C6, Canada
| | - Béatrice Bothorel
- Institut des Neurosciences Cellulaires et Intégratives, UPR CNRS 3212, Université de Strasbourg, 5 rue Blaise Pascal, 67084 Strasbourg, France
| | - Matthew G Michniewicz
- Department of Biology, University of Toronto Mississauga, 3359 Mississauga Road, Mississauga, ON L5L 1C6, Canada
| | - Stephen T Magill
- Vollum Institute, Oregon Health and Science University, Portland, OR 97239, USA
| | - Melissa M Holmes
- Department of Cell and Systems Biology, University of Toronto, 25 Harbord Street, Toronto, ON M5S 3G5, Canada; Department of Psychology, University of Toronto Mississauga, 3359 Mississauga Road, Mississauga, ON L5L 1C6, Canada
| | - Richard H Goodman
- Vollum Institute, Oregon Health and Science University, Portland, OR 97239, USA
| | - Valérie Simonneaux
- Institut des Neurosciences Cellulaires et Intégratives, UPR CNRS 3212, Université de Strasbourg, 5 rue Blaise Pascal, 67084 Strasbourg, France
| | - Daniel Figeys
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada; Canadian Institute for Advanced Research, 180 Dundas Street West, Toronto, ON M5G 1Z8, Canada
| | - Hai-Ying M Cheng
- Department of Biology, University of Toronto Mississauga, 3359 Mississauga Road, Mississauga, ON L5L 1C6, Canada; Department of Cell and Systems Biology, University of Toronto, 25 Harbord Street, Toronto, ON M5S 3G5, Canada.
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128
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Saino N, Ambrosini R, Albetti B, Caprioli M, De Giorgio B, Gatti E, Liechti F, Parolini M, Romano A, Romano M, Scandolara C, Gianfranceschi L, Bollati V, Rubolini D. Migration phenology and breeding success are predicted by methylation of a photoperiodic gene in the barn swallow. Sci Rep 2017; 7:45412. [PMID: 28361883 PMCID: PMC5374444 DOI: 10.1038/srep45412] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 02/16/2017] [Indexed: 02/07/2023] Open
Abstract
Individuals often considerably differ in the timing of their life-cycle events, with major consequences for individual fitness, and, ultimately, for population dynamics. Phenological variation can arise from genetic effects but also from epigenetic modifications in DNA expression and translation. Here, we tested if CpG methylation at the poly-Q and 5'-UTR loci of the photoperiodic Clock gene predicted migration and breeding phenology of long-distance migratory barn swallows (Hirundo rustica) that were tracked year-round using light-level geolocators. Increasing methylation at Clock poly-Q was associated with earlier spring departure from the African wintering area, arrival date at the European breeding site, and breeding date. Higher methylation levels also predicted increased breeding success. Thus, we showed for the first time in any species that CpG methylation at a candidate gene may affect phenology and breeding performance. Methylation at Clock may be a candidate mechanism mediating phenological responses of migratory birds to ongoing climate change.
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Affiliation(s)
- Nicola Saino
- Department of Biosciences, University of Milan, via Celoria 26, I-20133 Milan, Italy
| | - Roberto Ambrosini
- Department of Earth and Environmental Sciences (DISAT), University of Milano Bicocca, Piazza della Scienza, 1, I-20126 Milan, Italy
| | - Benedetta Albetti
- EPIGET - Epidemiology, Epigenetics and Toxicology Lab - Department of Clinical Sciences and Community Health, University of Milan, via San Barnaba 8, I-20122 Milan, Italy
| | - Manuela Caprioli
- Department of Biosciences, University of Milan, via Celoria 26, I-20133 Milan, Italy
| | - Barbara De Giorgio
- EPIGET - Epidemiology, Epigenetics and Toxicology Lab - Department of Clinical Sciences and Community Health, University of Milan, via San Barnaba 8, I-20122 Milan, Italy
| | - Emanuele Gatti
- Department of Earth and Environmental Sciences (DISAT), University of Milano Bicocca, Piazza della Scienza, 1, I-20126 Milan, Italy
| | - Felix Liechti
- Swiss Ornithological Insititute, Seerose 1, CH-6204, Sempach, Switzerland
| | - Marco Parolini
- Department of Biosciences, University of Milan, via Celoria 26, I-20133 Milan, Italy
| | - Andrea Romano
- Department of Biosciences, University of Milan, via Celoria 26, I-20133 Milan, Italy
| | - Maria Romano
- Department of Biosciences, University of Milan, via Celoria 26, I-20133 Milan, Italy
| | - Chiara Scandolara
- Department of Biosciences, University of Milan, via Celoria 26, I-20133 Milan, Italy
| | - Luca Gianfranceschi
- Department of Biosciences, University of Milan, via Celoria 26, I-20133 Milan, Italy
| | - Valentina Bollati
- EPIGET - Epidemiology, Epigenetics and Toxicology Lab - Department of Clinical Sciences and Community Health, University of Milan, via San Barnaba 8, I-20122 Milan, Italy
| | - Diego Rubolini
- Department of Biosciences, University of Milan, via Celoria 26, I-20133 Milan, Italy
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129
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Mendoza-Viveros L, Bouchard-Cannon P, Hegazi S, Cheng AH, Pastore S, Cheng HYM. Molecular modulators of the circadian clock: lessons from flies and mice. Cell Mol Life Sci 2017; 74:1035-1059. [PMID: 27689221 PMCID: PMC11107503 DOI: 10.1007/s00018-016-2378-8] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2016] [Revised: 09/03/2016] [Accepted: 09/22/2016] [Indexed: 12/16/2022]
Abstract
Circadian timekeeping is a ubiquitous mechanism that enables organisms to maintain temporal coordination between internal biological processes and time of the local environment. The molecular basis of circadian rhythms lies in a set of transcription-translation feedback loops (TTFLs) that drives the rhythmic transcription of core clock genes, whose level and phase of expression serve as the marker of circadian time. However, it has become increasingly evident that additional regulatory mechanisms impinge upon the TTFLs to govern the properties and behavior of the circadian clock. Such mechanisms include changes in chromatin architecture, interactions with other transcription factor networks, post-transcriptional control by RNA modifications, alternative splicing and microRNAs, and post-translational regulation of subcellular trafficking and protein degradation. In this review, we will summarize the current knowledge of circadian clock regulation-from transcriptional to post-translational-drawing from literature pertaining to the Drosophila and murine circadian systems.
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Affiliation(s)
- Lucia Mendoza-Viveros
- Department of Biology, University of Toronto Mississauga, 3359 Mississauga Road, Mississauga, ON, L5L 1C6, Canada
- Department of Cell and Systems Biology, University of Toronto, 25 Harbord Street, Toronto, ON, M5S 3G5, Canada
| | - Pascale Bouchard-Cannon
- Department of Biology, University of Toronto Mississauga, 3359 Mississauga Road, Mississauga, ON, L5L 1C6, Canada
- Department of Cell and Systems Biology, University of Toronto, 25 Harbord Street, Toronto, ON, M5S 3G5, Canada
| | - Sara Hegazi
- Department of Biology, University of Toronto Mississauga, 3359 Mississauga Road, Mississauga, ON, L5L 1C6, Canada
- Department of Cell and Systems Biology, University of Toronto, 25 Harbord Street, Toronto, ON, M5S 3G5, Canada
| | - Arthur H Cheng
- Department of Biology, University of Toronto Mississauga, 3359 Mississauga Road, Mississauga, ON, L5L 1C6, Canada
- Department of Cell and Systems Biology, University of Toronto, 25 Harbord Street, Toronto, ON, M5S 3G5, Canada
| | - Stephen Pastore
- Department of Biology, University of Toronto Mississauga, 3359 Mississauga Road, Mississauga, ON, L5L 1C6, Canada
- Department of Cell and Systems Biology, University of Toronto, 25 Harbord Street, Toronto, ON, M5S 3G5, Canada
| | - Hai-Ying Mary Cheng
- Department of Biology, University of Toronto Mississauga, 3359 Mississauga Road, Mississauga, ON, L5L 1C6, Canada.
- Department of Cell and Systems Biology, University of Toronto, 25 Harbord Street, Toronto, ON, M5S 3G5, Canada.
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130
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Stevenson TJ. Circannual and circadian rhythms of hypothalamic DNA methyltransferase and histone deacetylase expression in male Siberian hamsters (Phodopus sungorus). Gen Comp Endocrinol 2017; 243:130-137. [PMID: 27916575 DOI: 10.1016/j.ygcen.2016.11.011] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 11/29/2016] [Accepted: 11/30/2016] [Indexed: 12/20/2022]
Abstract
Precise timing of gene transcription is a fundamental component of many biological rhythms. DNA methylation and histone acetylation are two epigenetic modifications that can affect the probability of gene transcription and RNA expression. Enzymes involved in DNA methylation (dnmts) have been shown to exhibit photoperiodic rhythms in expression in the hypothalamus, which coincide with hypothalamic expression of deiodinase type III (dio3), a gene involved in the photoperiodic regulation of reproduction. It is currently unknown whether enzymes involved in histone deacetylation (hdacs) also vary in response to photoperiod, nor have seasonal changes in the circadian waveforms of methylation and/or acetylation enzymes been examined. The present work documents circadian and photoperiodic changes in dnmts and hdacs in whole hypothalamic dissections obtained from male Siberian hamsters (Phodopus sungorus) after 5-6weeks of exposure to SD. The data indicate that short days (SD) markedly inhibit dnmt3a expression, and that SD inhibition of dnmt3a was evident regardless of the alignment of circadian waveforms. Among hdacs, photoperiodic and circadian changes in expression were only observed in hdac4 expression. Recurrent temporal waveforms in epigenetic enzyme expression may provide molecular inputs to the timing systems that reprogram RNA expression to generate daily and annual phenotypic plasticity.
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Affiliation(s)
- Tyler J Stevenson
- Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, UK.
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131
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Azzi A, Evans JA, Leise T, Myung J, Takumi T, Davidson AJ, Brown SA. Network Dynamics Mediate Circadian Clock Plasticity. Neuron 2017; 93:441-450. [PMID: 28065650 DOI: 10.1016/j.neuron.2016.12.022] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Revised: 09/01/2016] [Accepted: 12/09/2016] [Indexed: 11/19/2022]
Abstract
A circadian clock governs most aspects of mammalian behavior. Although its properties are in part genetically determined, altered light-dark environment can change circadian period length through a mechanism requiring de novo DNA methylation. We show here that this mechanism is mediated not via cell-autonomous clock properties, but rather through altered networking within the suprachiasmatic nuclei (SCN), the circadian "master clock," which is DNA methylated in region-specific manner. DNA methylation is necessary to temporally reorganize circadian phasing among SCN neurons, which in turn changes the period length of the network as a whole. Interruption of neural communication by inhibiting neuronal firing or by physical cutting suppresses both SCN reorganization and period changes. Mathematical modeling suggests, and experiments confirm, that this SCN reorganization depends upon GABAergic signaling. Our results therefore show that basic circadian clock properties are governed by dynamic interactions among SCN neurons, with neuroadaptations in network function driven by the environment.
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Affiliation(s)
- Abdelhalim Azzi
- Institute of Pharmacology and Toxicology, University of Zurich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Jennifer A Evans
- Department of Biomedical Sciences, College of Health Sciences, Marquette University, 1250 W. Wisconsin Ave., Milwaukee, WI 53233, USA
| | - Tanya Leise
- Department of Mathematics and Statistics, Amherst College, 220 S. Pleasant St., Amherst, MA 01002, USA
| | - Jihwan Myung
- RIKEN Brain Science Institute (BSI), 2-1 Hirosawa Wako City, Saitama 351-0198, Japan
| | - Toru Takumi
- RIKEN Brain Science Institute (BSI), 2-1 Hirosawa Wako City, Saitama 351-0198, Japan
| | - Alec J Davidson
- Department of Neurobiology, Morehouse School of Medicine, 720 Westview Dr., Atlanta, GA 30310, USA
| | - Steven A Brown
- Institute of Pharmacology and Toxicology, University of Zurich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
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132
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Herzog ED, Hermanstyne T, Smyllie NJ, Hastings MH. Regulating the Suprachiasmatic Nucleus (SCN) Circadian Clockwork: Interplay between Cell-Autonomous and Circuit-Level Mechanisms. Cold Spring Harb Perspect Biol 2017; 9:9/1/a027706. [PMID: 28049647 DOI: 10.1101/cshperspect.a027706] [Citation(s) in RCA: 149] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The suprachiasmatic nucleus (SCN) is the principal circadian clock of the brain, directing daily cycles of behavior and physiology. SCN neurons contain a cell-autonomous transcription-based clockwork but, in turn, circuit-level interactions synchronize the 20,000 or so SCN neurons into a robust and coherent daily timer. Synchronization requires neuropeptide signaling, regulated by a reciprocal interdependence between the molecular clockwork and rhythmic electrical activity, which in turn depends on a daytime Na+ drive and nighttime K+ drag. Recent studies exploiting intersectional genetics have started to identify the pacemaking roles of particular neuronal groups in the SCN. They support the idea that timekeeping involves nonlinear and hierarchical computations that create and incorporate timing information through the interactions between key groups of neurons within the SCN circuit. The field is now poised to elucidate these computations, their underlying cellular mechanisms, and how the SCN clock interacts with subordinate circadian clocks across the brain to determine the timing and efficiency of the sleep-wake cycle, and how perturbations of this coherence contribute to neurological and psychiatric illness.
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Affiliation(s)
- Erik D Herzog
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri 63130-4899
| | - Tracey Hermanstyne
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri 63130-4899
| | - Nicola J Smyllie
- Division of Neurobiology, MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - Michael H Hastings
- Division of Neurobiology, MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
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133
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Baldanzi S, Watson R, McQuaid CD, Gouws G, Porri F. Epigenetic variation among natural populations of the South African sandhopper Talorchestia capensis. Evol Ecol 2016. [DOI: 10.1007/s10682-016-9877-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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134
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van Ee R, Van de Cruys S, Schlangen LJ, Vlaskamp BN. Circadian-Time Sickness: Time-of-Day Cue-Conflicts Directly Affect Health. Trends Neurosci 2016; 39:738-749. [DOI: 10.1016/j.tins.2016.09.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Revised: 09/06/2016] [Accepted: 09/13/2016] [Indexed: 10/20/2022]
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135
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Epigenome-Wide DNA Methylation Analysis of Monozygotic Twins Discordant for Diurnal Preference. Twin Res Hum Genet 2016; 18:662-9. [PMID: 26678051 DOI: 10.1017/thg.2015.78] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Diurnal preference is an individual's preference for daily activities and sleep timing and is strongly correlated with the underlying circadian clock and the sleep-wake cycle validating its use as an indirect circadian measure in humans. Recent research has implicated DNA methylation as a mechanism involved in the regulation of the circadian clock system in humans and other mammals. In order to evaluate the extent of epigenetic differences associated with diurnal preference, we examined genome-wide patterns of DNA methylation in DNA from monozygotic (MZ) twin-pairs discordant for diurnal preference. MZ twins were selected from a longitudinal twin study designed to investigate the interplay of genetic and environmental factors in the development of emotional and behavioral difficulties. Fifteen pairs of MZ twins were identified in which one member scored considerably higher on the Horne-Ostberg Morningness-Eveningness Questionnaire (MEQ) than the other. Genome-wide DNA methylation patterns were assessed in twins' buccal cell DNA using the Illumina Infinium HumanMethylation450 BeadChips. Quality control and data pre-processing was undertaken using the wateRmelon package. Differentially methylated probes (DMPs) were identified using an analysis strategy taking into account both the significance and the magnitude of DNA methylation differences. Our data indicate that DNA methylation differences are detectable in MZ twins discordant for diurnal preference. Moreover, downstream gene ontology (GO) enrichment analysis on the top-ranked diurnal preference associated DMPs revealed significant enrichment of pathways that have been previously associated with circadian rhythm regulation, including cell adhesion processes and calcium ion binding.
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136
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Tokuda IT, Ono D, Ananthasubramaniam B, Honma S, Honma KI, Herzel H. Coupling Controls the Synchrony of Clock Cells in Development and Knockouts. Biophys J 2016; 109:2159-70. [PMID: 26588574 DOI: 10.1016/j.bpj.2015.09.024] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Revised: 08/12/2015] [Accepted: 09/25/2015] [Indexed: 12/21/2022] Open
Abstract
In mammals, a network of coupled neurons within the hypothalamus coordinates physiological rhythms with daily changes in the environment. In each neuron, delayed negative transcriptional feedbacks generate oscillations, albeit noisy and unreliable ones. Coupling mediated by diffusible neuropeptides lends precision and robustness to circadian rhythms. The double knockout of Cryptochrome Cry turns adult mice arrhythmic. But, remarkably, double knockout neonates continue to show robust oscillation much like wild-type neonates and appear to lose rhythmicity with development. We study quantitatively dispersed neurons and brain slices from wild-type and Cry double knockout mice to understand the links between single cell rhythmicity and intercellular coupling. We quantify oscillator properties of dispersed cells using nonlinear regression and study bifurcations diagrams of network models. We find that varying just three parameters-oscillator strength, strength of coupling, and timing of coupling-can reproduce experimentally observed features. In particular, modeling reveals that minor changes in timing of coupling can destroy synchronization as observed in adult slices from knockout mice.
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Affiliation(s)
- Isao T Tokuda
- Department of Mechanical Engineering, Ritsumeikan University, Shiga, Japan.
| | - Daisuke Ono
- Photonic Bioimaging Section, Research Center for Cooperative Projects, Hokkaido University Graduate School of Medicine, Sapporo, Japan
| | | | - Sato Honma
- Department of Chronomedicine, Hokkaido University Graduate School of Medicine, Sapporo, Japan
| | - Ken-Ichi Honma
- Department of Chronomedicine, Hokkaido University Graduate School of Medicine, Sapporo, Japan
| | - Hanspeter Herzel
- Institute for Theoretical Biology, Humboldt University of Berlin, Berlin, Germany
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137
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Gupta T, Morgan HR, Bailey JA, Certel SJ. Functional conservation of MBD proteins: MeCP2 and Drosophila MBD proteins alter sleep. GENES BRAIN AND BEHAVIOR 2016; 15:757-774. [PMID: 27489246 DOI: 10.1111/gbb.12314] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Revised: 07/29/2016] [Accepted: 08/01/2016] [Indexed: 01/01/2023]
Abstract
Proteins containing a methyl-CpG-binding domain (MBD) bind 5mC and convert the methylation pattern information into appropriate functional cellular states. The correct readout of epigenetic marks is of particular importance in the nervous system where abnormal expression or compromised MBD protein function, can lead to disease and developmental disorders. Recent evidence indicates that the genome of Drosophila melanogaster is methylated and two MBD proteins, dMBD2/3 and dMBD-R2, are present. Are Drosophila MBD proteins required for neuronal function, and as MBD-containing proteins have diverged and evolved, does the MBD domain retain the molecular properties required for conserved cellular function across species? To address these questions, we expressed the human MBD-containing protein, hMeCP2, in distinct amine neurons and quantified functional changes in sleep circuitry output using a high throughput assay in Drosophila. hMeCP2 expression resulted in phase-specific sleep loss and sleep fragmentation with the hMeCP2-mediated sleep deficits requiring an intact MBD domain. Reducing endogenous dMBD2/3 and dMBD-R2 levels also generated sleep fragmentation, with an increase in sleep occurring upon dMBD-R2 reduction. To examine if hMeCP2 and dMBD-R2 are targeting common neuronal functions, we reduced dMBD-R2 levels in combination with hMeCP2 expression and observed a complete rescue of sleep deficits. Furthermore, chromosomal binding experiments indicate MBD-R2 and MeCP2 associate on shared genomic loci. Our results provide the first demonstration that Drosophila MBD-containing family members are required for neuronal function and suggest that the MBD domain retains considerable functional conservation at the whole organism level across species.
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Affiliation(s)
- T Gupta
- Neuroscience Graduate Program
| | - H R Morgan
- Division of Biological Sciences and Center for Structural and Functional Neuroscience, The University of Montana, Missoula, MT, USA
| | - J A Bailey
- Division of Biological Sciences and Center for Structural and Functional Neuroscience, The University of Montana, Missoula, MT, USA
| | - S J Certel
- Neuroscience Graduate Program.,Division of Biological Sciences and Center for Structural and Functional Neuroscience, The University of Montana, Missoula, MT, USA
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138
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Moulin L, Cenizo V, Antu AN, André V, Pain S, Sommer P, Debret R. Methylation of LOXL1 Promoter by DNMT3A in Aged Human Skin Fibroblasts. Rejuvenation Res 2016; 20:103-110. [PMID: 27396912 DOI: 10.1089/rej.2016.1832] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Lysyl oxidase-like 1 (LOXL1) is an amino-oxidase involved in maturation of elastic fibers. Its downregulation has been associated with elastic fibers repair loss in aging aorta, lung, ligament, and skin. Several evidences of LOXL1 epigenetic silencing by promoter methylation were reported in cancer and cutis laxa syndrome. We hypothesized that this mechanism could be implicated in skin aging process, as far as elastic fibers are also concerned. Anti-DNMT3A chromatin immunoprecipitation was conducted with nuclear extracts from skin fibroblasts isolated from young and elderly individuals, and showed a higher level of DNMT3A protein binding to the LOXL1 promoter in older cells concomitantly to the decrease of LOXL1 mRNA expression and the increase of LOXL1 promoter methylation. Using luciferase reporter assay driven by LOXL1 promoter in HEK293 cells, we demonstrated that LOXL1 transcriptional activity was dramatically reduced when a recombinant DNMT3A was concomitantly overexpressed. LOXL1 promoter transcriptional activity was restored in the presence of a broad-spectrum inhibitor of DNMT activity, 5-aza-2'-deoxycytidine. Finally, to assess whether the interplay between DNMT3A and LOXL1 promoter could be targeted to increase LOXL1 mRNA expression level, an Origanum majorana extract was selected among 43 plant extracts as a new inhibitor of human DNMT3A activity to restore LOXL1 secretion without cytotoxicity in aged skin fibroblasts.
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Affiliation(s)
- Léa Moulin
- 1 Laboratory of Tissue Biology and Therapeutic Engineering, UMR5305, CNRS, University Claude Bernard , Lyon, France
| | | | - Alengo Nyamay Antu
- 1 Laboratory of Tissue Biology and Therapeutic Engineering, UMR5305, CNRS, University Claude Bernard , Lyon, France
| | - Valérie André
- 2 BASF-Beauty Care Solutions France SAS , Lyon, France
| | - Sabine Pain
- 2 BASF-Beauty Care Solutions France SAS , Lyon, France
| | - Pascal Sommer
- 1 Laboratory of Tissue Biology and Therapeutic Engineering, UMR5305, CNRS, University Claude Bernard , Lyon, France
| | - Romain Debret
- 1 Laboratory of Tissue Biology and Therapeutic Engineering, UMR5305, CNRS, University Claude Bernard , Lyon, France
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139
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Heegaard NHH, Carlsen AL, Lilje B, Ng KL, Rønne ME, Jørgensen HL, Sennels H, Fahrenkrug J. Diurnal Variations of Human Circulating Cell-Free Micro-RNA. PLoS One 2016; 11:e0160577. [PMID: 27494182 PMCID: PMC4975411 DOI: 10.1371/journal.pone.0160577] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 07/21/2016] [Indexed: 12/26/2022] Open
Abstract
A 24-hour light and dark cycle-dependent rhythmicity pervades physiological processes in virtually all living organisms including humans. These regular oscillations are caused by external cues to endogenous, independent biological time-keeping systems (clocks). The rhythm is reflected by gene expression that varies in a circadian and specific fashion in different organs and tissues and is regulated largely by dynamic epigenetic and post-transcriptional mechanisms. This leads to well-documented oscillations of specific electrolytes, hormones, metabolites, and plasma proteins in blood samples. An emerging, important class of gene regulators is short single-stranded RNA (micro-RNA, miRNA) that interferes post-transcriptionally with gene expression and thus may play a role in the circadian variation of gene expression. MiRNAs are promising biomarkers by virtue of their disease-specific tissue expression and because of their presence as stable entities in the circulation. However, no studies have addressed the putative circadian rhythmicity of circulating, cell-free miRNAs. This question is important both for using miRNAs as biological markers and for clues to miRNA function in the regulation of circadian gene expression. Here, we investigate 92 miRNAs in plasma samples from 24 young male, healthy volunteers repeatedly sampled 9 times during a 24-hour stay in a regulated environment. We demonstrate that a third (26/79) of the measurable plasma miRNAs (using RT-qPCR on a microfluidic system) exhibit a rhythmic behavior and are distributed in two main phase patterns. Some of these miRNAs weakly target known clock genes and many have strong targets in intracellular MAPK signaling pathways. These novel findings highlight the importance of considering bio-oscillations in miRNA biomarker studies and suggest the further study of a set of specific circulating miRNAs in the regulation and functioning of biological clocks.
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Affiliation(s)
- Niels H. H. Heegaard
- Department of Autoimmunology and Biomarkers, Statens Serum Institut, Copenhagen, Denmark
- Department of Clinical Biochemistry and Pharmacology, Odense University Hospital, Odense, Denmark
- * E-mail:
| | - Anting Liu Carlsen
- Department of Autoimmunology and Biomarkers, Statens Serum Institut, Copenhagen, Denmark
- Department of Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Berit Lilje
- Department of Microbiology and Infection Control, Statens Serum Institut, Copenhagen, Denmark
| | - Kim Lee Ng
- Department of Microbiology and Infection Control, Statens Serum Institut, Copenhagen, Denmark
| | - Mette E. Rønne
- Department of Autoimmunology and Biomarkers, Statens Serum Institut, Copenhagen, Denmark
| | - Henrik L. Jørgensen
- Department of Clinical Biochemistry, Faculty of Health Science, Bispebjerg Hospital, University of Copenhagen, Denmark
| | - Henriette Sennels
- Department of Clinical Biochemistry, Faculty of Health Science, Rigshospitalet - Glostrup, University of Copenhagen, Copenhagen, Denmark
| | - Jan Fahrenkrug
- Department of Clinical Biochemistry, Faculty of Health Science, Bispebjerg Hospital, University of Copenhagen, Denmark
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140
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Deibel SH, Zelinski EL, Keeley RJ, Kovalchuk O, McDonald RJ. Epigenetic alterations in the suprachiasmatic nucleus and hippocampus contribute to age-related cognitive decline. Oncotarget 2016; 6:23181-203. [PMID: 26252151 PMCID: PMC4695111 DOI: 10.18632/oncotarget.4036] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Accepted: 12/31/1969] [Indexed: 12/16/2022] Open
Abstract
Circadian rhythm dysfunction and cognitive decline, specifically memory loss, frequently accompany natural aging. Circadian rhythms and memory are intertwined, as circadian rhythms influence memory formation and recall in young and old rodents. Although, the precise relationship between circadian rhythms and memory is still largely unknown, it is hypothesized that circadian rhythm disruption, which occurs during aging, contributes to age-associated cognitive decline, specifically memory loss. While there are a variety of mechanisms that could mediate this effect, changes in the epigenome that occur during aging has been proposed as a potential candidate. Interestingly, epigenetic mechanisms, such as DNA methylation and sirtuin1 (SIRT1) are necessary for both circadian rhythms and memory. During aging, similar alterations of epigenetic mechanisms occur in the suprachiasmatic nucleus (SCN) and hippocampus, which are necessary for circadian rhythm generation and memory, respectively. Recently, circadian rhythms have been linked to epigenetic function in the hippocampus, as some of these epigenetic mechanisms oscillate in the hippocampus and are disrupted by clock gene deletion. The current paper will review how circadian rhythms and memory change with age, and will suggest how epigenetic changes in these processes might contribute to age-related cognitive decline.
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Affiliation(s)
- Scott H Deibel
- Canadian Centre for Behavioural Neuroscience, Department of Neuroscience, University of Lethbridge, Lethbridge, AB, Canada
| | - Erin L Zelinski
- Canadian Centre for Behavioural Neuroscience, Department of Neuroscience, University of Lethbridge, Lethbridge, AB, Canada
| | - Robin J Keeley
- Canadian Centre for Behavioural Neuroscience, Department of Neuroscience, University of Lethbridge, Lethbridge, AB, Canada
| | - Olga Kovalchuk
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB, Canada
| | - Robert J McDonald
- Canadian Centre for Behavioural Neuroscience, Department of Neuroscience, University of Lethbridge, Lethbridge, AB, Canada
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141
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Samblas M, Milagro FI, Gómez-Abellán P, Martínez JA, Garaulet M. Methylation on the Circadian Gene BMAL1 Is Associated with the Effects of a Weight Loss Intervention on Serum Lipid Levels. J Biol Rhythms 2016; 31:308-17. [PMID: 26873744 DOI: 10.1177/0748730416629247] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The circadian clock system has been linked to the onset and development of obesity and some accompanying comorbidities. Epigenetic mechanisms, such as DNA methylation, are putatively involved in the regulation of the circadian clock system. The aim of this study was to investigate the influence of a weight loss intervention based on an energy-controlled Mediterranean dietary pattern in the methylation levels of 3 clock genes, BMAL1, CLOCK, and NR1D1, and the association between the methylation levels and changes induced in the serum lipid profile with the weight loss treatment. The study sample enrolled 61 women (body mass index = 28.6 ± 3.4 kg/m(2); age: 42.2 ± 11.4 years), who followed a nutritional program based on a Mediterranean dietary pattern. DNA was isolated from whole blood obtained at the beginning and end point. Methylation levels at different CpG sites of BMAL1, CLOCK, and NR1D1 were analyzed by Sequenom's MassArray. The energy-restricted intervention modified the methylation levels of different CpG sites in BMAL1 (CpGs 5, 6, 7, 9, 11, and 18) and NR1D1 (CpGs 1, 10, 17, 18, 19, and 22). Changes in cytosine methylation in the CpG 5 to 9 region of BMAL1 with the intervention positively correlated with the eveningness profile (p = 0.019). The baseline methylation of the CpG 5 to 9 region in BMAL1 positively correlated with energy (p = 0.047) and carbohydrate (p = 0.017) intake and negatively correlated with the effect of the weight loss intervention on total cholesterol (p = 0.032) and low-density lipoprotein cholesterol (p = 0.005). Similar significant and positive correlations were found between changes in methylation levels in the CpG 5 to 9 region of BMAL1 due to the intervention and changes in serum lipids (p < 0.05). This research describes apparently for the first time an association between changes in the methylation of the BMAL1 gene with the intervention and the effects of a weight loss intervention on blood lipids levels.
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Affiliation(s)
- Mirian Samblas
- Department of Nutrition, Food Science and Physiology, University of Navarra, Pamplona, Spain
| | - Fermin I Milagro
- Department of Nutrition, Food Science and Physiology, University of Navarra, Pamplona, Spain Centre for Nutrition Research, University of Navarra, Pamplona, Spain CIBERobn, Physiopathology of Obesity, Carlos III Institute, Madrid, Spain
| | | | - J Alfredo Martínez
- Department of Nutrition, Food Science and Physiology, University of Navarra, Pamplona, Spain Centre for Nutrition Research, University of Navarra, Pamplona, Spain CIBERobn, Physiopathology of Obesity, Carlos III Institute, Madrid, Spain IdiSNA, Navarra's Health Research Institute, Pamplona, Spain
| | - Marta Garaulet
- Department of Physiology, Faculty of Biology, University of Murcia, IMIB, Murcia, Spain
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142
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Lynch EWJ, Coyle CS, Lorgen M, Campbell EM, Bowman AS, Stevenson TJ. Cyclical DNA Methyltransferase 3a Expression Is a Seasonal and Estrus Timer in Reproductive Tissues. Endocrinology 2016; 157:2469-78. [PMID: 27105384 DOI: 10.1210/en.2015-1988] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
It is becoming clear that epigenetic modifications such as DNA methylation can be dynamic and, in many cases, reversible. Here we investigated the photoperiod and hormone regulation of DNA methylation in testes, ovaries, and uterine tissue across multiple time scales. We hypothesized that DNA methyltransferase 3a (dnmt3a) is driven by photoperiodic treatment and exhibits natural variation across the female reproductive cycle and that melatonin increases whereas estrogen reduces DNA methylation. We used Siberian hamsters (Phodopus sungorus) due to their robust changes in reproductive physiology across seasonal and estrus time scales. Our findings indicate that short-day (SD) winter-like conditions significantly increased global DNA methylation and dnmt3a expression in the testes. Using immunohistochemistry, we confirm that increased dnmt3a expression was primarily localized to spermatogonium. Conversely, the ovaries did not exhibit variation in DNA methylation or dnmt3a/3b expression. However, exposure to SD significantly increased uterine dnmt3a expression. We then determined that dnmt3a was significantly decreased during the estrus stage. Next, we ovariectomized females and subsequently identified that a single estrogen+progesterone injection was sufficient to rapidly inhibit dnmt3a and dnmt3b expression. Finally, we demonstrate that treatment of human embryonic kidney-293 cells with melatonin significantly increased both dnmt3a and dnmt3b expression, suggesting that long-duration nocturnal signaling in SD may be involved in the regulation of DNA methylation in both sexes. Overall, our data indicate that dnmt3a shows marked photoperiod and estrus plasticity that likely has broad downstream effects on the timing of the genomic control of reproductive function.
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Affiliation(s)
- Eloise W J Lynch
- Institute for Biological and Environmental Sciences, University of Aberdeen, Aberdeen AB24 2TZ, United Kingdom
| | - Chris S Coyle
- Institute for Biological and Environmental Sciences, University of Aberdeen, Aberdeen AB24 2TZ, United Kingdom
| | - Marlene Lorgen
- Institute for Biological and Environmental Sciences, University of Aberdeen, Aberdeen AB24 2TZ, United Kingdom
| | - Ewan M Campbell
- Institute for Biological and Environmental Sciences, University of Aberdeen, Aberdeen AB24 2TZ, United Kingdom
| | - Alan S Bowman
- Institute for Biological and Environmental Sciences, University of Aberdeen, Aberdeen AB24 2TZ, United Kingdom
| | - Tyler J Stevenson
- Institute for Biological and Environmental Sciences, University of Aberdeen, Aberdeen AB24 2TZ, United Kingdom
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143
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Affiliation(s)
- Valter Tucci
- Neuroscience and Brain Technologies Department, Istituto Italiano di Tecnologia (IIT), Genova, Italy
- * E-mail:
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144
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Abstract
Breast cancer is already the most common malignancy affecting women worldwide, and evidence is mounting that breast cancer induced by circadian disruption (CD) is a warranted concern. Numerous studies have investigated various aspects of the circadian clock in relation to breast cancer, and evidence from these studies indicates that melatonin and the core clock genes can play a crucial role in breast cancer development. Even though epigenetics has been increasingly recognized as a key player in the etiology of breast cancer and linked to circadian rhythms, and there is evidence of overlap between epigenetic deregulation and breast cancer induced by circadian disruption, only a handful of studies have directly investigated the role of epigenetics in CD-induced breast cancer. This review explores the circadian clock and breast cancer, and the growing role of epigenetics in breast cancer development and circadian rhythms. We also summarize the current knowledge and next steps for the investigation of the epigenetic link in CD-induced breast cancer.
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Affiliation(s)
- David Z Kochan
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB, Canada
| | - Olga Kovalchuk
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB, Canada
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145
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Reciprocal interactions between circadian clocks and aging. Mamm Genome 2016; 27:332-40. [PMID: 27137838 PMCID: PMC4935744 DOI: 10.1007/s00335-016-9639-6] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 04/14/2016] [Indexed: 12/24/2022]
Abstract
Virtually, all biological processes in the body are modulated by an internal circadian clock which optimizes physiological and behavioral performance according to the changing demands of the external 24-h world. This circadian clock undergoes a number of age-related changes, at both the physiological and molecular levels. While these changes have been considered to be part of the normal aging process, there is increasing evidence that disruptions to the circadian system can substantially impact upon aging and these impacts will have clear health implications. Here we review the current data of how both the physiological and core molecular clocks change with age and how feedback from external cues may modulate the aging of the circadian system.
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146
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Dallmann R, Okyar A, Lévi F. Dosing-Time Makes the Poison: Circadian Regulation and Pharmacotherapy. Trends Mol Med 2016; 22:430-445. [PMID: 27066876 DOI: 10.1016/j.molmed.2016.03.004] [Citation(s) in RCA: 162] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Accepted: 03/17/2016] [Indexed: 12/14/2022]
Abstract
Daily rhythms in physiology significantly modulate drug pharmacokinetics and pharmacodynamics according to the time-of-day, a finding that has led to the concept of chronopharmacology. The importance of biological clocks for xenobiotic metabolism has gained increased attention with the discovery of the molecular circadian clockwork. Mechanistic understanding of the cell-autonomous molecular circadian oscillator and the circadian timing system as a whole has opened new conceptual and methodological lines of investigation to understand first, the clock's impact on a specific drug's daily variations or the effects/side effects of environmental substances, and second, how clock-controlled pathways are coordinated within a given tissue or organism. Today, there is an increased understanding of the circadian modulation of drug effects. Moreover, several molecular strategies are being developed to treat disease-dependent and drug-induced clock disruptions in humans.
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Affiliation(s)
- Robert Dallmann
- Warwick Medical School, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, UK; Warwick Systems Biology Centre, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, UK.
| | - Alper Okyar
- Department of Pharmacology, Faculty of Pharmacy, Istanbul University, Beyazit-Istanbul, Turkey
| | - Francis Lévi
- Warwick Medical School, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, UK; Warwick Systems Biology Centre, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, UK
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147
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Greenwood MP, Greenwood M, Gillard BT, Loh SY, Paton JFR, Murphy D. Epigenetic Control of the Vasopressin Promoter Explains Physiological Ability to Regulate Vasopressin Transcription in Dehydration and Salt Loading States in the Rat. J Neuroendocrinol 2016; 28. [PMID: 26833868 PMCID: PMC4855680 DOI: 10.1111/jne.12371] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Revised: 01/06/2016] [Accepted: 01/23/2016] [Indexed: 02/06/2023]
Abstract
The synthesis of arginine vasopressin (AVP) in the supraoptic nucleus (SON) and paraventricular nucleus (PVN) of the hypothalamus is sensitive to increased plasma osmolality and a decreased blood volume, and thus is robustly increased by both dehydration (increased plasma osmolality and decreased blood volume) and salt loading (increased plasma osmolality). Both stimuli result in functional remodelling of the SON and PVN, a process referred to as functional-related plasticity. Such plastic changes in the brain have recently been associated with altered patterns of DNA methylation at CpG (cytosine-phosphate-guanine) residues, a process considered to be important for the regulation of gene transcription. In this regard, the proximal Avp promoter contains a number of CpG sites and is recognised as one of four CpG islands for the Avp gene, suggesting that methylation may be regulating Avp transcription. In the present study, we show that, in an immortalised hypothalamic cell line 4B, the proximal Avp promoter is highly methylated, and treatment of these cells with the DNA methyltransferase inhibitor 5-Aza-2'-deoxycytidine to demethylate DNA dramatically increases basal and stimulated Avp biosynthesis. We report no changes in the expression of DNA methyltransferases, Dnmt1 and Dnmt3a, whereas there is decreased expression of the demethylating enzyme ten-eleven-translocation 2, Tet2, in the SON by dehydration and salt loading. We found higher methylation of the SON Avp promoter in dehydrated but not salt-loaded rats. By analysis of individual CpG sites, we observed hypomethylation, hypermethylation and no change in methylation of specific CpGs in the SON Avp promoter of the dehydrated rat. Using reporter gene assays, we show that mutation of individual CpGs can result in altered Avp promoter activity. We propose that methylation of the SON Avp promoter is necessary to co-ordinate the duel inputs of increased plasma osmolality and decreased blood volume on Avp transcription in the chronically dehydrated rat.
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Affiliation(s)
- M P Greenwood
- School of Clinical Sciences, University of Bristol, Bristol, UK
| | - M Greenwood
- School of Clinical Sciences, University of Bristol, Bristol, UK
| | - B T Gillard
- School of Clinical Sciences, University of Bristol, Bristol, UK
| | - S Y Loh
- Department of Physiology, University of Malaya, Kuala Lumpur, Malaysia
| | - J F R Paton
- School of Physiology and Pharmacology, University of Bristol, Bristol, UK
| | - D Murphy
- School of Clinical Sciences, University of Bristol, Bristol, UK
- Department of Physiology, University of Malaya, Kuala Lumpur, Malaysia
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148
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Impey S, Pelz C, Tafessu A, Marzulla T, Turker MS, Raber J. Proton irradiation induces persistent and tissue-specific DNA methylation changes in the left ventricle and hippocampus. BMC Genomics 2016; 17:273. [PMID: 27036964 PMCID: PMC4815246 DOI: 10.1186/s12864-016-2581-x] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Accepted: 03/08/2016] [Indexed: 02/06/2023] Open
Abstract
Background Proton irradiation poses a potential hazard to astronauts during and following a mission, with post-mitotic cells at most risk because they cannot dilute resultant epigenetic changes via cell division. Persistent epigenetic changes that result from environmental exposures include gains or losses of DNA methylation of cytosine, which can impact gene expression. In the present study, we compared the long-term epigenetic effects of whole body proton irradiation in the mouse hippocampus and left ventricle. We used an unbiased genome-wide DNA methylation study, involving ChIP-seq with antibodies to 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) to identify DNA regions in which methylation levels have changed 22 weeks after a single exposure to proton irradiation. We used DIP-Seq to profile changes in genome-wide DNA methylation and hydroxymethylation following proton irradiation. In addition, we used published RNAseq data to assess whether differentially methylated regions were linked to changes in gene expression. Results The DNA methylation data showed tissue-dependent effects of proton irradiation and revealed significant major pathway changes in response to irradiation that are related to known pathophysiologic processes. Many regions affected in the ventricle mapped to genes involved in cardiovascular function pathways, whereas many regions affected in the hippocampus mapped to genes involved in neuronal functions. In the ventricle, increases in 5hmC were associated with decreases in 5mC. We also observed spatial overlap for regions where both epigenetic marks decreased in the ventricle. In hippocampus, increases in 5hmC were most significantly correlated (spatially) with regions that had increased 5mC, suggesting that deposition of hippocampal 5mC and 5hmC may be mechanistically coupled. Conclusions The results demonstrate long-term changes in DNA methylation patterns following a single proton irradiation, that these changes are tissue specific, and that they map to pathways consistent with tissue specific responses to proton irradiation. Further, the results suggest novel relationships between changes in 5mC and 5hmC. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2581-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Soren Impey
- Oregon Stem Cell Center and Department of Pediatrics, Oregon Health and Science University, Portland, OR, 97239, USA. .,Department of Cell, Developmental and Cancer Biology, Oregon Health and Science University, Portland, OR, 97239, USA. .,Department of Pediatric, L321, Oregon Health and Science University, 3181SW Sam Jackson Park Road, Portland, OR, 97239, USA.
| | - Carl Pelz
- Oregon Stem Cell Center and Department of Pediatrics, Oregon Health and Science University, Portland, OR, 97239, USA
| | - Amanuel Tafessu
- Oregon Stem Cell Center and Department of Pediatrics, Oregon Health and Science University, Portland, OR, 97239, USA
| | - Tessa Marzulla
- Department of Behavioral Neuroscience, L470, Oregon Health and Science University, 3181SW Sam Jackson Park Road, Portland, OR, 97239, USA
| | - Mitchell S Turker
- Oregon Institute of Occupational Health Sciences and Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, OR, 97239, USA
| | - Jacob Raber
- Department of Behavioral Neuroscience, L470, Oregon Health and Science University, 3181SW Sam Jackson Park Road, Portland, OR, 97239, USA. .,Departments of Neurology and Radiation Medicine, Division of Neuroscience ONPRC, Oregon Health and Science University, Portland, OR, 97239, USA. .,Knight Cardiovascular Institute, Oregon Health and Science University, Portland, OR, 97239, USA.
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149
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Temporally chimeric mice reveal flexibility of circadian period-setting in the suprachiasmatic nucleus. Proc Natl Acad Sci U S A 2016; 113:3657-62. [PMID: 26966234 PMCID: PMC4822582 DOI: 10.1073/pnas.1511351113] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
The suprachiasmatic nucleus (SCN) is the principal circadian clock of the mammalian brain. To function effectively, SCN neurons must operate as a synchronized circuit. How cell-autonomous and circuit-level circadian mechanisms interact to achieve this is unclear. Here, we used intersectional genetics to create temporally chimeric mice where both 24-h and 20-h clock neurons were present in the SCN, in different cell populations. The 24-h dopamine receptor-positive cells set the speed of the SCN, imposing their cell-autonomous 24-h period on all cells in the circuit. Exposure to a 20-h lighting cycle, however, inverted this dominance, reprograming the circuit to 20 h. These results show how robust circuit-level signaling underlies complex, nonlinear computations of circadian period that also exhibit a remarkable level of plasticity. The suprachiasmatic nucleus (SCN) is the master circadian clock controlling daily behavior in mammals. It consists of a heterogeneous network of neurons, in which cell-autonomous molecular feedback loops determine the period and amplitude of circadian oscillations of individual cells. In contrast, circuit-level properties of coherence, synchrony, and ensemble period are determined by intercellular signals and are embodied in a circadian wave of gene expression that progresses daily across the SCN. How cell-autonomous and circuit-level mechanisms interact in timekeeping is poorly understood. To explore this interaction, we used intersectional genetics to create temporally chimeric mice with SCN containing dopamine 1a receptor (Drd1a) cells with an intrinsic period of 24 h alongside non-Drd1a cells with 20-h clocks. Recording of circadian behavior in vivo alongside cellular molecular pacemaking in SCN slices in vitro demonstrated that such chimeric circuits form robust and resilient circadian clocks. It also showed that the computation of ensemble period is nonlinear. Moreover, the chimeric circuit sustained a wave of gene expression comparable to that of nonchimeric SCN, demonstrating that this circuit-level property is independent of differences in cell-intrinsic periods. The relative dominance of 24-h Drd1a and 20-h non-Drd1a neurons in setting ensemble period could be switched by exposure to resonant or nonresonant 24-h or 20-h lighting cycles. The chimeric circuit therefore reveals unanticipated principles of circuit-level operation underlying the emergent plasticity, resilience, and robustness of the SCN clock. The spontaneous and light-driven flexibility of period observed in chimeric mice provides a new perspective on the concept of SCN pacemaker cells.
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150
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Zhou D, Wang Y, Chen L, Jia L, Yuan J, Sun M, Zhang W, Wang P, Zuo J, Xu Z, Luan J. Evolving roles of circadian rhythms in liver homeostasis and pathology. Oncotarget 2016; 7:8625-39. [PMID: 26843619 PMCID: PMC4890992 DOI: 10.18632/oncotarget.7065] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 01/18/2016] [Indexed: 02/06/2023] Open
Abstract
Circadian clock in mammals is determined by a core oscillator in the suprachiasmatic nucleus (SCN) of the hypothalamus and synchronized peripheral clocks in other tissues. The coherent timing systems could sustain robust output of circadian rhythms in response to the entrainment controlled environmentally. Disparate approaches have discovered that clock genes and clock-controlled genes (CCGs) exist in nearly all mammalian cell types and are essential for establishing the mechanisms and complexity of internal time-keeping systems. Accumulating evidence demonstrates that the control of homeostasis and pathology in the liver involves intricate loops of transcriptional and post-translational regulation of clock genes expression. This review will focus on the recent advances with great importance concerning clock rhythms linking liver homeostasis and diseases. We particularly highlight what is currently known of the evolving insights into the mechanisms underlying circadian clock . Eventually , findings during recent years in the field might prompt new circadian-related chronotherapeutic strategies for the diagnosis and treatment of liver diseases by coupling these processes.
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Affiliation(s)
- Dexi Zhou
- Laboratory of Clinical Pharmacy of Wannan Medical College, Wuhu, Anhui Province, China
- Department of Pharmacy in Yijishan Hospital of Wannan Medical College, Wuhu, Anhui Province, China
| | - Yaqin Wang
- Laboratory of Clinical Pharmacy of Wannan Medical College, Wuhu, Anhui Province, China
- Department of Pharmacy in Yijishan Hospital of Wannan Medical College, Wuhu, Anhui Province, China
| | - Lu Chen
- Laboratory of Clinical Pharmacy of Wannan Medical College, Wuhu, Anhui Province, China
- Department of Pharmacy in Yijishan Hospital of Wannan Medical College, Wuhu, Anhui Province, China
| | - Leijuan Jia
- Laboratory of Clinical Pharmacy of Wannan Medical College, Wuhu, Anhui Province, China
- Department of Pharmacy in Yijishan Hospital of Wannan Medical College, Wuhu, Anhui Province, China
| | - Jie Yuan
- Laboratory of Clinical Pharmacy of Wannan Medical College, Wuhu, Anhui Province, China
- Department of Pharmacy in Yijishan Hospital of Wannan Medical College, Wuhu, Anhui Province, China
| | - Mei Sun
- Laboratory of Clinical Pharmacy of Wannan Medical College, Wuhu, Anhui Province, China
- Department of Pharmacy in Yijishan Hospital of Wannan Medical College, Wuhu, Anhui Province, China
| | - Wen Zhang
- Laboratory of Clinical Pharmacy of Wannan Medical College, Wuhu, Anhui Province, China
- Department of Pharmacy in Yijishan Hospital of Wannan Medical College, Wuhu, Anhui Province, China
| | - Peipei Wang
- Laboratory of Clinical Pharmacy of Wannan Medical College, Wuhu, Anhui Province, China
- Department of Pharmacy in Yijishan Hospital of Wannan Medical College, Wuhu, Anhui Province, China
| | - Jian Zuo
- Laboratory of Clinical Pharmacy of Wannan Medical College, Wuhu, Anhui Province, China
- Department of Pharmacy in Yijishan Hospital of Wannan Medical College, Wuhu, Anhui Province, China
| | - Zhenyu Xu
- Laboratory of Clinical Pharmacy of Wannan Medical College, Wuhu, Anhui Province, China
- Department of Pharmacy in Yijishan Hospital of Wannan Medical College, Wuhu, Anhui Province, China
| | - Jiajie Luan
- Laboratory of Clinical Pharmacy of Wannan Medical College, Wuhu, Anhui Province, China
- Department of Pharmacy in Yijishan Hospital of Wannan Medical College, Wuhu, Anhui Province, China
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