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Abstract
Circadian clocks are endogenous oscillators that control 24-h physiological and behavioral processes. The central circadian clock exerts control over myriad aspects of mammalian physiology, including the regulation of sleep, metabolism, and the immune system. Here, we review advances in understanding the genetic regulation of sleep through the circadian system, as well as the impact of dysregulated gene expression on metabolic function. We also review recent studies that have begun to unravel the circadian clock’s role in controlling the cardiovascular and nervous systems, gut microbiota, cancer, and aging. Such circadian control of these systems relies, in part, on transcriptional regulation, with recent evidence for genome-wide regulation of the clock through circadian chromosome organization. These novel insights into the genomic regulation of human physiology provide opportunities for the discovery of improved treatment strategies and new understanding of the biological underpinnings of human disease.
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102
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Emmett MJ, Lazar MA. Integrative regulation of physiology by histone deacetylase 3. Nat Rev Mol Cell Biol 2019; 20:102-115. [PMID: 30390028 DOI: 10.1038/s41580-018-0076-0] [Citation(s) in RCA: 98] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Cell-type-specific gene expression is physiologically modulated by the binding of transcription factors to genomic enhancer sequences, to which chromatin modifiers such as histone deacetylases (HDACs) are recruited. Drugs that inhibit HDACs are in clinical use but lack specificity. HDAC3 is a stoichiometric component of nuclear receptor co-repressor complexes whose enzymatic activity depends on this interaction. HDAC3 is required for many aspects of mammalian development and physiology, for example, for controlling metabolism and circadian rhythms. In this Review, we discuss the mechanisms by which HDAC3 regulates cell type-specific enhancers, the structure of HDAC3 and its function as part of nuclear receptor co-repressors, its enzymatic activity and its post-translational modifications. We then discuss the plethora of tissue-specific physiological functions of HDAC3.
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Affiliation(s)
- Matthew J Emmett
- Institute for Diabetes, Obesity, and Metabolism, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.,Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Mitchell A Lazar
- Institute for Diabetes, Obesity, and Metabolism, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA. .,Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.
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103
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Molecular mechanisms and physiological importance of circadian rhythms. Nat Rev Mol Cell Biol 2019; 21:67-84. [PMID: 31768006 DOI: 10.1038/s41580-019-0179-2] [Citation(s) in RCA: 523] [Impact Index Per Article: 104.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/19/2019] [Indexed: 12/12/2022]
Abstract
To accommodate daily recurring environmental changes, animals show cyclic variations in behaviour and physiology, which include prominent behavioural states such as sleep-wake cycles but also a host of less conspicuous oscillations in neurological, metabolic, endocrine, cardiovascular and immune functions. Circadian rhythmicity is created endogenously by genetically encoded molecular clocks, whose components cooperate to generate cyclic changes in their own abundance and activity, with a periodicity of about a day. Throughout the body, such molecular clocks convey temporal control to the function of organs and tissues by regulating pertinent downstream programmes. Synchrony between the different circadian oscillators and resonance with the solar day is largely enabled by a neural pacemaker, which is directly responsive to certain environmental cues and able to transmit internal time-of-day representations to the entire body. In this Review, we discuss aspects of the circadian clock in Drosophila melanogaster and mammals, including the components of these molecular oscillators, the function and mechanisms of action of central and peripheral clocks, their synchronization and their relevance to human health.
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104
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Cox KH, Takahashi JS. Circadian clock genes and the transcriptional architecture of the clock mechanism. J Mol Endocrinol 2019; 63:R93-R102. [PMID: 31557726 PMCID: PMC6872945 DOI: 10.1530/jme-19-0153] [Citation(s) in RCA: 201] [Impact Index Per Article: 40.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 09/26/2019] [Indexed: 12/12/2022]
Abstract
The mammalian circadian clock has evolved as an adaptation to the 24-h light/darkness cycle on earth. Maintaining cellular activities in synchrony with the activities of the organism (such as eating and sleeping) helps different tissue and organ systems coordinate and optimize their performance. The full extent of the mechanisms by which cells maintain the clock are still under investigation, but involve a core set of clock genes that regulate large networks of gene transcription both by direct transcriptional activation/repression as well as the recruitment of proteins that modify chromatin states more broadly.
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Affiliation(s)
- Kimberly H. Cox
- Department of Neuroscience, The University of Texas Southwestern Medical Center, Dallas, TX 75390-9111, USA
| | - Joseph S. Takahashi
- Department of Neuroscience, The University of Texas Southwestern Medical Center, Dallas, TX 75390-9111, USA
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390-9111, USA
- To whom correspondence should be addressed:
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105
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Cedernaes J, Waldeck N, Bass J. Neurogenetic basis for circadian regulation of metabolism by the hypothalamus. Genes Dev 2019; 33:1136-1158. [PMID: 31481537 PMCID: PMC6719618 DOI: 10.1101/gad.328633.119] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Circadian rhythms are driven by a transcription-translation feedback loop that separates anabolic and catabolic processes across the Earth's 24-h light-dark cycle. Central pacemaker neurons that perceive light entrain a distributed clock network and are closely juxtaposed with hypothalamic neurons involved in regulation of sleep/wake and fast/feeding states. Gaps remain in identifying how pacemaker and extrapacemaker neurons communicate with energy-sensing neurons and the distinct role of circuit interactions versus transcriptionally driven cell-autonomous clocks in the timing of organismal bioenergetics. In this review, we discuss the reciprocal relationship through which the central clock drives appetitive behavior and metabolic homeostasis and the pathways through which nutrient state and sleep/wake behavior affect central clock function.
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Affiliation(s)
- Jonathan Cedernaes
- Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
| | - Nathan Waldeck
- Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
| | - Joseph Bass
- Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
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106
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Circadian Clock Regulation of Hepatic Energy Metabolism Regulatory Circuits. BIOLOGY 2019; 8:biology8040079. [PMID: 31635079 PMCID: PMC6956161 DOI: 10.3390/biology8040079] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Revised: 10/13/2019] [Accepted: 10/15/2019] [Indexed: 01/03/2023]
Abstract
The liver is a critical organ of energy metabolism. At least 10% of the liver transcriptome demonstrates rhythmic expression, implying that the circadian clock regulates large programmes of hepatic genes. Here, we review the mechanisms by which this rhythmic regulation is conferred, with a particular focus on the transcription factors whose actions combine to impart liver- and time-specificity to metabolic gene expression.
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107
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Beytebiere JR, Greenwell BJ, Sahasrabudhe A, Menet JS. Clock-controlled rhythmic transcription: is the clock enough and how does it work? Transcription 2019; 10:212-221. [PMID: 31595813 DOI: 10.1080/21541264.2019.1673636] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Circadian clocks regulate the rhythmic expression of thousands of genes underlying the daily oscillations of biological functions. Here, we discuss recent findings showing that circadian clock rhythmic transcriptional outputs rely on additional mechanisms than just clock gene DNA binding, which may ultimately contribute to the plasticity of circadian transcriptional programs.
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Affiliation(s)
- Joshua R Beytebiere
- Department of Biology, Center for Biological Clock Research, Texas A&M University, TX, USA
| | - Ben J Greenwell
- Department of Biology, Center for Biological Clock Research, Texas A&M University, TX, USA.,Program of Genetics, Texas A&M University, College Station, TX, USA
| | - Aishwarya Sahasrabudhe
- Department of Biology, Center for Biological Clock Research, Texas A&M University, TX, USA
| | - Jerome S Menet
- Department of Biology, Center for Biological Clock Research, Texas A&M University, TX, USA.,Program of Genetics, Texas A&M University, College Station, TX, USA
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108
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Brunet A, Forsberg F, Fan Q, Sæther T, Collas P. Nuclear Lamin B1 Interactions With Chromatin During the Circadian Cycle Are Uncoupled From Periodic Gene Expression. Front Genet 2019; 10:917. [PMID: 31632442 PMCID: PMC6785633 DOI: 10.3389/fgene.2019.00917] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 08/30/2019] [Indexed: 12/17/2022] Open
Abstract
Many mammalian genes exhibit circadian expression patterns concordant with periodic binding of transcription factors, chromatin modifications, and chromosomal interactions. Here we investigate whether chromatin periodically associates with nuclear lamins. Entrainment of the circadian clock is accompanied, in mouse liver, by a net gain of lamin B1–chromatin interactions genome-wide, after which the majority of lamina-associated domains (LADs) are conserved during the circadian cycle. By tailoring a bioinformatics pipeline designed to identify periodic gene expression patterns, we also observe hundreds of variable lamin B1–chromatin interactions among which oscillations occur at 64 LADs, affecting one or both LAD extremities or entire LADs. Only a small subset of these oscillations however exhibit highly significant 12, 18, 24, or 30 h periodicity. These periodic LADs display oscillation asynchrony between their 5′ and 3′ borders, and are uncoupled from periodic gene expression within or in the vicinity of these LADs. Periodic gene expression is also unrelated to variations in gene-to-nearest LAD distances detected during the circadian cycle. Accordingly, periodic genes, including central clock-control genes, are located megabases away from LADs throughout circadian time, suggesting stable residence in a transcriptionally permissive chromatin environment. We conclude that periodic LADs are not a dominant feature of variable lamin B1–chromatin interactions during the circadian cycle in mouse liver. Our results also suggest that periodic hepatic gene expression is not regulated by rhythmic chromatin associations with the nuclear lamina.
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Affiliation(s)
- Annaël Brunet
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Frida Forsberg
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Qiong Fan
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Thomas Sæther
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Philippe Collas
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Oslo, Norway.,Department of Immunology and Transfusion Medicine, Oslo University Hospital, Oslo, Norway
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109
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Chu G, Zhou X, Hu Y, Shi S, Yang G. Rev-erbα Inhibits Proliferation and Promotes Apoptosis of Preadipocytes through the Agonist GSK4112. Int J Mol Sci 2019; 20:ijms20184524. [PMID: 31547330 PMCID: PMC6769707 DOI: 10.3390/ijms20184524] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 09/05/2019] [Accepted: 09/09/2019] [Indexed: 01/15/2023] Open
Abstract
Proliferation and apoptosis are important physiological processes of preadipocytes. Rev-erbα is a circadian clock gene, and its activity contributes to several physiological processes in various cells. Previous studies demonstrated that Rev-erbα promotes preadipocyte differentiation, but a role of Rev-erbα on preadipocyte proliferation and apoptosis has not been demonstrated. GSK4112 is often used as an agonist of Rev-erbα. In this study, we used GSK4112 to explore the effects of Rev-erbα on preadipocyte proliferation and apoptosis by RT-qPCR, Western blot, Cell Counting Kit-8 (CCK8) measurement, 5-Ethynyl-2′-deoxyuridine (EdU) staining, Annexin V-FITC/PI staining, and flow cytometry. These results revealed that GSK4112 inhibited the viability of 3T3-L1 preadipocytes and decreased cell numbers. There was also decreased expression of the proliferation-related gene Cyclin D and the canonical Wingless-type (Wnt) signaling effect factor β-catenin. Furthermore, palmitate (PA)-inducing cell apoptosis was promoted. Overall, these results reveal that Rev-erbα plays a role in proliferation and palmitate (PA)-inducing apoptosis of 3T3-L1 preadipocytes, and thus may be a new molecular target in efforts to prevent and treat obesity and related disease.
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Affiliation(s)
- Guiyan Chu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, Yangling 712100, China
- Laboratory of Animal Fat Deposition & Muscle Development, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Xiaoge Zhou
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, Yangling 712100, China
- Laboratory of Animal Fat Deposition & Muscle Development, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Yamei Hu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, Yangling 712100, China
- Laboratory of Animal Fat Deposition & Muscle Development, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Shengjie Shi
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, Yangling 712100, China
- Laboratory of Animal Fat Deposition & Muscle Development, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Gongshe Yang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, Yangling 712100, China.
- Laboratory of Animal Fat Deposition & Muscle Development, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China.
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110
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Zhao L, Wang S, Cao Z, Ouyang W, Zhang Q, Xie L, Zheng R, Guo M, Ma M, Hu Z, Sung WK, Zhang Q, Li G, Li X. Chromatin loops associated with active genes and heterochromatin shape rice genome architecture for transcriptional regulation. Nat Commun 2019; 10:3640. [PMID: 31409785 PMCID: PMC6692402 DOI: 10.1038/s41467-019-11535-9] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 07/19/2019] [Indexed: 02/06/2023] Open
Abstract
Insight into high-resolution three-dimensional genome organization and its effect on transcription remains largely elusive in plants. Here, using a long-read ChIA-PET approach, we map H3K4me3- and RNA polymerase II (RNAPII)-associated promoter-promoter interactions and H3K9me2-marked heterochromatin interactions at nucleotide/gene resolution in rice. The chromatin architecture is separated into different independent spatial interacting modules with distinct transcriptional potential and covers approximately 82% of the genome. Compared to inactive modules, active modules possess the majority of active loop genes with higher density and contribute to most of the transcriptional activity in rice. In addition, promoter-promoter interacting genes tend to be transcribed cooperatively. In contrast, the heterochromatin-mediated loops form relative stable structure domains in chromatin configuration. Furthermore, we examine the impact of genetic variation on chromatin interactions and transcription and identify a spatial correlation between the genetic regulation of eQTLs and e-traits. Thus, our results reveal hierarchical and modular 3D genome architecture for transcriptional regulation in rice.
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Affiliation(s)
- Lun Zhao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 1 Shizishan Street, Hongshan District, Wuhan, 430070, Hubei, China
| | - Shuangqi Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 1 Shizishan Street, Hongshan District, Wuhan, 430070, Hubei, China
| | - Zhilin Cao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 1 Shizishan Street, Hongshan District, Wuhan, 430070, Hubei, China.,Department of Resources and Environment, Henan University of Engineering, 1 Xianghe Road, Longhu Town, Zhengzhou, 451191, Henan, China
| | - Weizhi Ouyang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 1 Shizishan Street, Hongshan District, Wuhan, 430070, Hubei, China
| | - Qing Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 1 Shizishan Street, Hongshan District, Wuhan, 430070, Hubei, China
| | - Liang Xie
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 1 Shizishan Street, Hongshan District, Wuhan, 430070, Hubei, China
| | - Ruiqin Zheng
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 1 Shizishan Street, Hongshan District, Wuhan, 430070, Hubei, China
| | - Minrong Guo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 1 Shizishan Street, Hongshan District, Wuhan, 430070, Hubei, China
| | - Meng Ma
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 1 Shizishan Street, Hongshan District, Wuhan, 430070, Hubei, China
| | - Zhe Hu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, 1 Shizishan Street, Hongshan District, Wuhan, 430070, Hubei, China
| | - Wing-Kin Sung
- Department of Computer Science, National University of Singapore, 13 Computing Drive, Singapore, 117417, Singapore.,Genome Institute of Singapore, 60 Biopolis Street, Genome, Singapore, 138672, Singapore
| | - Qifa Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 1 Shizishan Street, Hongshan District, Wuhan, 430070, Hubei, China
| | - Guoliang Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 1 Shizishan Street, Hongshan District, Wuhan, 430070, Hubei, China. .,Hubei Key Laboratory of Agricultural Bioinformatics and Hubei Engineering Technology Research Center of Agricultural Big Data, Huazhong Agricultural University, 1 Shizishan Street, Hongshan District, Wuhan, 430070, Hubei, China.
| | - Xingwang Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 1 Shizishan Street, Hongshan District, Wuhan, 430070, Hubei, China.
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111
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Pacheco-Bernal I, Becerril-Pérez F, Aguilar-Arnal L. Circadian rhythms in the three-dimensional genome: implications of chromatin interactions for cyclic transcription. Clin Epigenetics 2019; 11:79. [PMID: 31092281 PMCID: PMC6521413 DOI: 10.1186/s13148-019-0677-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 04/29/2019] [Indexed: 12/20/2022] Open
Abstract
Circadian rhythms orchestrate crucial physiological functions and behavioral aspects around a day in almost all living forms. The circadian clock is a time tracking system that permits organisms to predict and anticipate periodic environmental fluctuations. The circadian system is hierarchically organized, and a master pacemaker located in the brain synchronizes subsidiary clocks in the rest of the organism. Adequate synchrony between central and peripheral clocks ensures fitness and potentiates a healthy state. Conversely, disruption of circadian rhythmicity is associated with metabolic diseases, psychiatric disorders, or cancer, amongst other pathologies. Remarkably, the molecular machinery directing circadian rhythms consists of an intricate network of feedback loops in transcription and translation which impose 24-h cycles in gene expression across all tissues. Interestingly, the molecular clock collaborates with multitude of epigenetic remodelers to fine tune transcriptional rhythms in a tissue-specific manner. Very exciting research demonstrate that three-dimensional properties of the genome have a regulatory role on circadian transcriptional rhythmicity, from bacteria to mammals. Unexpectedly, highly dynamic long-range chromatin interactions have been revealed during the circadian cycle in mammalian cells, where thousands of regulatory elements physically interact with promoter regions every 24 h. Molecular mechanisms directing circadian dynamics on chromatin folding are emerging, and the coordinated action between the core clock and epigenetic remodelers appears to be essential for these movements. These evidences reveal a critical epigenetic regulatory layer for circadian rhythms and pave the way to uncover molecular mechanisms triggering pathological states associated to circadian misalignment.
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Affiliation(s)
- Ignacio Pacheco-Bernal
- Instituto de Investigaciones Biomédicas, Departamento de Biología Celular y Fisiología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Fernando Becerril-Pérez
- Instituto de Investigaciones Biomédicas, Departamento de Biología Celular y Fisiología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Lorena Aguilar-Arnal
- Instituto de Investigaciones Biomédicas, Departamento de Biología Celular y Fisiología, Universidad Nacional Autónoma de México, Mexico City, Mexico.
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112
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Kim S, Dunham MJ, Shendure J. A combination of transcription factors mediates inducible interchromosomal contacts. eLife 2019; 8:e42499. [PMID: 31081754 PMCID: PMC6548505 DOI: 10.7554/elife.42499] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 05/11/2019] [Indexed: 12/30/2022] Open
Abstract
The genome forms specific three-dimensional contacts in response to cellular or environmental conditions. However, it remains largely unknown which proteins specify and mediate such contacts. Here we describe an assay, MAP-C (Mutation Analysis in Pools by Chromosome conformation capture), that simultaneously characterizes the effects of hundreds of cis or trans-acting mutations on a chromosomal contact. Using MAP-C, we show that inducible interchromosomal pairing between HAS1pr-TDA1pr alleles in saturated cultures of Saccharomyces yeast is mediated by three transcription factors, Leu3, Sdd4 (Ypr022c), and Rgt1. The coincident, combined binding of all three factors is strongest at the HAS1pr-TDA1pr locus and is also specific to saturated conditions. We applied MAP-C to further explore the biochemical mechanism of these contacts, and find they require the structured regulatory domain of Rgt1, but no known interaction partners of Rgt1. Altogether, our results demonstrate MAP-C as a powerful method for dissecting the mechanistic basis of chromosome conformation.
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Affiliation(s)
- Seungsoo Kim
- Department of Genome SciencesUniversity of WashingtonSeattleUnited States
| | - Maitreya J Dunham
- Department of Genome SciencesUniversity of WashingtonSeattleUnited States
| | - Jay Shendure
- Department of Genome SciencesUniversity of WashingtonSeattleUnited States
- Howard Hughes Medical InstituteSeattleUnited States
- Brotman Baty Institute for Precision MedicineSeattleUnited States
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113
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Schoenfelder S, Fraser P. Long-range enhancer–promoter contacts in gene expression control. Nat Rev Genet 2019; 20:437-455. [DOI: 10.1038/s41576-019-0128-0] [Citation(s) in RCA: 486] [Impact Index Per Article: 97.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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114
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Off the Clock: From Circadian Disruption to Metabolic Disease. Int J Mol Sci 2019; 20:ijms20071597. [PMID: 30935034 PMCID: PMC6480015 DOI: 10.3390/ijms20071597] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 03/20/2019] [Accepted: 03/27/2019] [Indexed: 12/18/2022] Open
Abstract
Circadian timekeeping allows appropriate temporal regulation of an organism’s internal metabolism to anticipate and respond to recurrent daily changes in the environment. Evidence from animal genetic models and from humans under circadian misalignment (such as shift work or jet lag) shows that disruption of circadian rhythms contributes to the development of obesity and metabolic disease. Inappropriate timing of food intake and high-fat feeding also lead to disruptions of the temporal coordination of metabolism and physiology and subsequently promote its pathogenesis. This review illustrates the impact of genetically or environmentally induced molecular clock disruption (at the level of the brain and peripheral tissues) and the interplay between the circadian system and metabolic processes. Here, we discuss some mechanisms responsible for diet-induced circadian desynchrony and consider the impact of nutritional cues in inter-organ communication, with a particular focus on the communication between peripheral organs and brain. Finally, we discuss the relay of environmental information by signal-dependent transcription factors to adjust the timing of gene oscillations. Collectively, a better knowledge of the mechanisms by which the circadian clock function can be compromised will lead to novel preventive and therapeutic strategies for obesity and other metabolic disorders arising from circadian desynchrony.
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115
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Abstract
This Outlook discusses Beytebiere et al.’s finding that the ability of BMAL1 to drive tissue-specific rhythmic transcription is associated with not only the activity of BMAL1-bound enhancers but also the activity of neighboring enhancers. The circadian clock in the suprachiasmatic nucleus (SCN) of mammals drives 24-h rhythms of sleep/wake cycles. Peripheral clocks present in other organs coordinate local and global physiology according to rhythmic signals from the SCN and via metabolic cues. The core circadian clockwork is identical in all cells. However, there is only a small amount of overlap of the circadian transcriptomes in different organs and tissues. A novel study by Beytebiere and colleagues (pp. 294–309) indicates that the regulation of tissue-specific rhythmic gene expression involves the cooperation of the circadian transcription factor (TF) BMAL1:CLOCK with tissue-specific TFs (ts-TFs) and correlates with the potential of BMAL1:CLOCK to facilitate rhythmic enhancer–enhancer interactions.
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Affiliation(s)
- Anton Shostak
- Heidelberg University Biochemistry Center, Heidelberg D-69120, Germany
| | - Michael Brunner
- Heidelberg University Biochemistry Center, Heidelberg D-69120, Germany
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116
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Beytebiere JR, Trott AJ, Greenwell BJ, Osborne CA, Vitet H, Spence J, Yoo SH, Chen Z, Takahashi JS, Ghaffari N, Menet JS. Tissue-specific BMAL1 cistromes reveal that rhythmic transcription is associated with rhythmic enhancer-enhancer interactions. Genes Dev 2019; 33:294-309. [PMID: 30804225 PMCID: PMC6411008 DOI: 10.1101/gad.322198.118] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 01/02/2019] [Indexed: 12/31/2022]
Abstract
The mammalian circadian clock relies on the transcription factor CLOCK:BMAL1 to coordinate the rhythmic expression of thousands of genes. Consistent with the various biological functions under clock control, rhythmic gene expression is tissue-specific despite an identical clockwork mechanism in every cell. Here we show that BMAL1 DNA binding is largely tissue-specific, likely because of differences in chromatin accessibility between tissues and cobinding of tissue-specific transcription factors. Our results also indicate that BMAL1 ability to drive tissue-specific rhythmic transcription is associated with not only the activity of BMAL1-bound enhancers but also the activity of neighboring enhancers. Characterization of physical interactions between BMAL1 enhancers and other cis-regulatory regions by RNA polymerase II chromatin interaction analysis by paired-end tag (ChIA-PET) reveals that rhythmic BMAL1 target gene expression correlates with rhythmic chromatin interactions. These data thus support that much of BMAL1 target gene transcription depends on BMAL1 capacity to rhythmically regulate a network of enhancers.
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Affiliation(s)
- Joshua R Beytebiere
- Department of Biology, Center for Biological Clocks Research, Texas A&M University, College Station, Texas 77843, USA
| | - Alexandra J Trott
- Department of Biology, Center for Biological Clocks Research, Texas A&M University, College Station, Texas 77843, USA
- Program of Genetics, Texas A&M University, College Station, Texas 77843, USA
| | - Ben J Greenwell
- Department of Biology, Center for Biological Clocks Research, Texas A&M University, College Station, Texas 77843, USA
- Program of Genetics, Texas A&M University, College Station, Texas 77843, USA
| | - Collin A Osborne
- Department of Biology, Center for Biological Clocks Research, Texas A&M University, College Station, Texas 77843, USA
- Program of Genetics, Texas A&M University, College Station, Texas 77843, USA
| | - Helene Vitet
- Department of Biology, Center for Biological Clocks Research, Texas A&M University, College Station, Texas 77843, USA
| | - Jessica Spence
- Department of Biology, Center for Biological Clocks Research, Texas A&M University, College Station, Texas 77843, USA
| | - Seung-Hee Yoo
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston, Houston, Texas 77030, USA
| | - Zheng Chen
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston, Houston, Texas 77030, USA
| | - Joseph S Takahashi
- Department of Neuroscience, Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Noushin Ghaffari
- Center for Bioinformatics and Genomic Systems Engineering (CBGSE), Texas A&M AgriLife Research, College Station, Texas 77845, USA
- AgriLife Genomics and Bioinformatics, Texas A&M AgriLife Research, College Station, Texas 77845, USA
| | - Jerome S Menet
- Department of Biology, Center for Biological Clocks Research, Texas A&M University, College Station, Texas 77843, USA
- Program of Genetics, Texas A&M University, College Station, Texas 77843, USA
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117
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Abstract
Circadian dysfunction is a common attribute of many neurodegenerative diseases, most of which are associated with neuroinflammation. Circadian rhythm dysfunction has been associated with inflammation in the periphery, but the role of the core clock in neuroinflammation remains poorly understood. Here we demonstrate that Rev-erbα, a nuclear receptor and circadian clock component, is a mediator of microglial activation and neuroinflammation. We observed time-of-day oscillation in microglial immunoreactivity in the hippocampus, which was disrupted in Rev-erbα-/- mice. Rev-erbα deletion caused spontaneous microglial activation in the hippocampus and increased expression of proinflammatory transcripts, as well as secondary astrogliosis. Transcriptomic analysis of hippocampus from Rev-erbα-/- mice revealed a predominant inflammatory phenotype and suggested dysregulated NF-κB signaling. Primary Rev-erbα-/- microglia exhibited proinflammatory phenotypes and increased basal NF-κB activation. Chromatin immunoprecipitation revealed that Rev-erbα physically interacts with the promoter regions of several NF-κB-related genes in primary microglia. Loss of Rev-erbα in primary astrocytes had no effect on basal activation but did potentiate the inflammatory response to lipopolysaccharide (LPS). In vivo, Rev-erbα-/- mice exhibited enhanced hippocampal neuroinflammatory responses to peripheral LPS injection, while pharmacologic activation of Rev-erbs with the small molecule agonist SR9009 suppressed LPS-induced hippocampal neuroinflammation. Rev-erbα deletion influenced neuronal health, as conditioned media from Rev-erbα-deficient primary glial cultures exacerbated oxidative damage in cultured neurons. Rev-erbα-/- mice also exhibited significantly altered cortical resting-state functional connectivity, similar to that observed in neurodegenerative models. Our results reveal Rev-erbα as a pharmacologically accessible link between the circadian clock and neuroinflammation.
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118
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Singh K, Jha NK, Thakur A. Spatiotemporal chromatin dynamics - A telltale of circadian epigenetic gene regulation. Life Sci 2019; 221:377-391. [PMID: 30721705 DOI: 10.1016/j.lfs.2019.02.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2018] [Revised: 01/27/2019] [Accepted: 02/01/2019] [Indexed: 01/08/2023]
Abstract
Over the course of evolution, nature has forced organisms under selection pressure to hardwire an internal time keeping device that defines 24 h of a daily cycle of physiological and behavioral rhythms, known as circadian rhythms. At the cellular level, the cycle is governed by significant fractions of transcriptomes, which are under the control of transcriptional and translational feedback loop of clock genes. Intriguingly, this feedback loop is regulated at multiple stratums such as at the transcriptional and translational levels, which direct a cell towards producing a robust rhythm by sustaining the repeated stoichiometry of protein products. Moreover, with the advent of state of the art paradigms, epigenetic regulation of circadian rhythms has been becoming more evident at present time. Light-induced recurring fluctuations in chromatin acetylation concurrent with the binding of RNA Pol II and integration of miRNAs monitor the chromatin modifiers or clock genes expression to drive temporal rhythmicity. Furthermore, CLOCK protein intrinsic histone acetyl transferase activity, the interaction of CLOCK-BMAL-1 with HAT enzymes, and the involvement of many histone deacetylases also maintain the rhythmic protein profile. Additionally, the critical role of the rhythmic methylation pattern of clock genes in battery of cancer and metabolic disorders also defines its importance. Therefore, in this review, we focused on accumulating all the present data available on epigenetics and circadian rhythms. Interestingly, we also gathered evidence from the available literature pinpointing towards the dynamic nature of chromatin architecture governed by long and short-range regulatory elements DNA contacts arising daily, that was thought to be steady otherwise.
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Affiliation(s)
- Kunal Singh
- Department of Biotechnology, Noida Institute of Engineering & Technology (NIET), Greater Noida, India.
| | - Niraj Kumar Jha
- Department of Biotechnology, Noida Institute of Engineering & Technology (NIET), Greater Noida, India
| | - Abhimanyu Thakur
- Department of Pharmaceutical Sciences and Technology, Birla Institute of Technology, Mesra, Ranchi, India
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119
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Sun F, Chronis C, Kronenberg M, Chen XF, Su T, Lay FD, Plath K, Kurdistani SK, Carey MF. Promoter-Enhancer Communication Occurs Primarily within Insulated Neighborhoods. Mol Cell 2019; 73:250-263.e5. [PMID: 30527662 PMCID: PMC6338517 DOI: 10.1016/j.molcel.2018.10.039] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Revised: 07/09/2018] [Accepted: 10/25/2018] [Indexed: 12/09/2022]
Abstract
Metazoan chromosomes are sequentially partitioned into topologically associating domains (TADs) and then into smaller sub-domains. One class of sub-domains, insulated neighborhoods, are proposed to spatially sequester and insulate the enclosed genes through self-association and chromatin looping. However, it has not been determined functionally whether promoter-enhancer interactions and gene regulation are broadly restricted to within these loops. Here, we employed published datasets from murine embryonic stem cells (mESCs) to identify insulated neighborhoods that confine promoter-enhancer interactions and demarcate gene regulatory regions. To directly address the functionality of these regions, we depleted estrogen-related receptor β (Esrrb), which binds the Mediator co-activator complex, to impair enhancers of genes within 222 insulated neighborhoods without causing mESC differentiation. Esrrb depletion reduces Mediator binding, promoter-enhancer looping, and expression of both nascent RNA and mRNA within the insulated neighborhoods without significantly affecting the flanking genes. Our data indicate that insulated neighborhoods represent functional regulons in mammalian genomes.
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MESH Headings
- Animals
- Binding Sites
- CCCTC-Binding Factor/genetics
- CCCTC-Binding Factor/metabolism
- Cell Cycle Proteins/genetics
- Cell Cycle Proteins/metabolism
- Cell Line
- Chromosomal Proteins, Non-Histone/genetics
- Chromosomal Proteins, Non-Histone/metabolism
- Chromosomes, Mammalian
- Databases, Genetic
- Down-Regulation
- Enhancer Elements, Genetic
- Insulator Elements
- Mice
- Mouse Embryonic Stem Cells/physiology
- Promoter Regions, Genetic
- Protein Binding
- RNA, Messenger/biosynthesis
- RNA, Messenger/genetics
- Receptors, Estrogen/genetics
- Receptors, Estrogen/metabolism
- Transcription, Genetic
- Cohesins
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Affiliation(s)
- Fei Sun
- Department of Biological Chemistry, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA 90095-1737, USA
| | - Constantinos Chronis
- Department of Biological Chemistry, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA 90095-1737, USA
| | - Michael Kronenberg
- Department of Biological Chemistry, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA 90095-1737, USA
| | - Xiao-Fen Chen
- Department of Biological Chemistry, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA 90095-1737, USA
| | - Trent Su
- Department of Biological Chemistry, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA 90095-1737, USA
| | - Fides D Lay
- Department of Molecular, Cellular and Developmental Biology, University of California at Los Angeles, Los Angeles, CA 90095, USA
| | - Kathrin Plath
- Department of Biological Chemistry, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA 90095-1737, USA
| | - Siavash K Kurdistani
- Department of Biological Chemistry, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA 90095-1737, USA
| | - Michael F Carey
- Department of Biological Chemistry, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA 90095-1737, USA.
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120
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Chapski DJ, Rosa-Garrido M, Hua N, Alber F, Vondriska TM. Spatial Principles of Chromatin Architecture Associated With Organ-Specific Gene Regulation. Front Cardiovasc Med 2019; 5:186. [PMID: 30697540 PMCID: PMC6341059 DOI: 10.3389/fcvm.2018.00186] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 12/10/2018] [Indexed: 11/13/2022] Open
Abstract
Packaging of the genome in the nucleus is a non-random process that is thought to directly contribute to cell type-specific transcriptomes, although this hypothesis remains untested. Epigenome architecture, as assayed by chromatin conformation capture techniques, such as Hi-C, has recently been described in the mammalian cardiac myocyte and found to be remodeled in the setting of heart failure. In the present study, we sought to determine whether the structural features of the epigenome are conserved between different cell types by investigating Hi-C and RNA-seq data from heart and liver. Investigation of genes with enriched expression in heart or liver revealed nuanced interaction paradigms between organs: first, the log2 ratios of heart:liver (or liver:heart) intrachromosomal interactions are higher in organ-specific gene sets (p = 0.009), suggesting that organ-specific genes have specialized chromatin structural features. Despite similar number of total interactions between cell types, intrachromosomal interaction profiles in heart but not liver demonstrate that genes forming promoter-to-transcription-end-site loops in the cardiac nucleus tend to be involved in cardiac-related pathways. The same analysis revealed an analogous organ-specific interaction profile for liver-specific loop genes. Investigation of A/B compartmentalization (marker of chromatin accessibility) revealed that in the heart, 66.7% of cardiac-specific genes are in compartment A, while 66.1% of liver-specific genes are found in compartment B, suggesting that there exists a cardiac chromatin topology that allows for expression of cardiac genes. Analyses of interchromosomal interactions revealed a relationship between interchromosomal interaction count and organ-specific gene localization (p = 2.2 × 10-16) and that, for both organs, regions of active or inactive chromatin tend to segregate in 3D space (i.e., active with active, inactive with inactive). 3D models of topologically associating domains (TADs) suggest that TADs tend to interact with regions of similar compartmentalization across chromosomes, revealing trans structural interactions contributing to genomic compartmentalization at distinct structural scales. These models reveal discordant nuclear compaction strategies, with heart packaging compartment A genes preferentially toward the center of the nucleus and liver exhibiting preferential arrangement toward the periphery. Taken together, our data suggest that intra- and interchromosomal chromatin architecture plays a role in orchestrating tissue-specific gene expression.
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Affiliation(s)
- Douglas J Chapski
- Departments of Anesthesiology, Physiology and Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| | - Manuel Rosa-Garrido
- Departments of Anesthesiology, Physiology and Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| | - Nan Hua
- Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA, United States
| | - Frank Alber
- Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA, United States
| | - Thomas M Vondriska
- Departments of Anesthesiology, Physiology and Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
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121
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Morales-Santana S, Morell S, Leon J, Carazo-Gallego A, Jimenez-Lopez JC, Morell M. An Overview of the Polymorphisms of Circadian Genes Associated With Endocrine Cancer. Front Endocrinol (Lausanne) 2019; 10:104. [PMID: 30873119 PMCID: PMC6401647 DOI: 10.3389/fendo.2019.00104] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Accepted: 02/04/2019] [Indexed: 12/17/2022] Open
Abstract
A major consequence of the world industrialized lifestyle is the increasing period of unnatural light in environments during the day and artificial lighting at night. This major change disrupts endogenous homeostasis with external circadian cues, which has been associated to higher risk of diseases affecting human health, mainly cancer among others. Circadian disruption promotes tumor development and accelerate its fast progression. The dysregulation mechanisms of circadian genes is greatly affected by the genetic variability of these genes. To date, several core circadian genes, also called circadian clock genes, have been identified, comprising the following: ARNTL, CLOCK, CRY1, CRY2, CSNK1E, NPAS2, NR1D1, NR1D2, PER1, PER2, PER3, RORA, and TIMELESS. The polymorphic variants of these circadian genes might contribute to an individual's risk to cancer. In this short review, we focused on clock circadian clock-related genes, major contributors of the susceptibility to endocrine-dependent cancers through affecting circadian clock, most likely affecting hormonal regulation. We examined polymorphisms affecting breast, prostate and ovarian carcinogenesis, in addition to pancreatic and thyroid cancer. Further study of the genetic composition in circadian clock-controlled tumors will be of great importance by establishing the foundation to discover novel genetic biomarkers for cancer prevention, prognosis and target therapies.
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Affiliation(s)
- Sonia Morales-Santana
- Proteomic Research Service, San Cecilio University Hospital, Instituto de Investigación Biosanitaria de Granada (Ibs.GRANADA), Granada, Spain
- *Correspondence: Sonia Morales-Santana
| | - Santiago Morell
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
- Santiago Morell
| | - Josefa Leon
- Clinical Management Unit of Digestive Disease, San Cecilio University Hospital, Instituto de Investigación Biosanitaria de Granada (Ibs.GRANADA), Granada, Spain
| | - Angel Carazo-Gallego
- Genomic Research Service, San Cecilio University Hospital, Instituto de Investigación Biosanitaria de Granada (Ibs.GRANADA), Granada, Spain
| | - Jose C. Jimenez-Lopez
- Department of Biochemistry, Cell and Molecular Biology of Plants, Estación Experimental del Zaidín, Spanish National Research Council (CSIC), Granada, Spain
- The UWA Institute of Agriculture and School of Agriculture and Environment, The University of Western Australia, Perth, WA, Australia
| | - María Morell
- Genomic Medicine Department, GENYO, Centre for Genomics and Oncological Research, Pfizer/University of Granada, Andalusian Regional Government, PTS Granada, Granada, Spain
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122
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Qu M, Duffy T, Hirota T, Kay SA. Nuclear receptor HNF4A transrepresses CLOCK:BMAL1 and modulates tissue-specific circadian networks. Proc Natl Acad Sci U S A 2018; 115:E12305-E12312. [PMID: 30530698 PMCID: PMC6310821 DOI: 10.1073/pnas.1816411115] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Either expression level or transcriptional activity of various nuclear receptors (NRs) have been demonstrated to be under circadian control. With a few exceptions, little is known about the roles of NRs as direct regulators of the circadian circuitry. Here we show that the nuclear receptor HNF4A strongly transrepresses the transcriptional activity of the CLOCK:BMAL1 heterodimer. We define a central role for HNF4A in maintaining cell-autonomous circadian oscillations in a tissue-specific manner in liver and colon cells. Not only transcript level but also genome-wide chromosome binding of HNF4A is rhythmically regulated in the mouse liver. ChIP-seq analyses revealed cooccupancy of HNF4A and CLOCK:BMAL1 at a wide array of metabolic genes involved in lipid, glucose, and amino acid homeostasis. Taken together, we establish that HNF4A defines a feedback loop in tissue-specific mammalian oscillators and demonstrate its recruitment in the circadian regulation of metabolic pathways.
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Affiliation(s)
- Meng Qu
- Keck School of Medicine, University of Southern California, Los Angeles, CA 90089
| | - Tomas Duffy
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037
| | - Tsuyoshi Hirota
- Institute of Transformative Bio-Molecules, Nagoya University, 464-8602 Nagoya, Japan
| | - Steve A Kay
- Keck School of Medicine, University of Southern California, Los Angeles, CA 90089;
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123
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Vermunt MW, Zhang D, Blobel GA. The interdependence of gene-regulatory elements and the 3D genome. J Cell Biol 2018; 218:12-26. [PMID: 30442643 PMCID: PMC6314554 DOI: 10.1083/jcb.201809040] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 10/29/2018] [Accepted: 10/29/2018] [Indexed: 01/12/2023] Open
Abstract
Vermunt et al. discuss the relationship between gene-regulatory elements and nuclear architectural features in transcription. Imaging studies, high-resolution chromatin conformation maps, and genome-wide occupancy data of architectural proteins have revealed that genome topology is tightly intertwined with gene expression. Cross-talk between gene-regulatory elements is often organized within insulated neighborhoods, and regulatory cues that induce transcriptional changes can reshape chromatin folding patterns and gene positioning within the nucleus. The cause–consequence relationship of genome architecture and gene expression is intricate, and its molecular mechanisms are under intense investigation. Here, we review the interdependency of transcription and genome organization with emphasis on enhancer–promoter contacts in gene regulation.
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Affiliation(s)
- Marit W Vermunt
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA
| | - Di Zhang
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA.,Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Gerd A Blobel
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA .,Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
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124
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Caldwell BA, Bartolomei MS. Mapping the diploid genome, one cell at a time. Nat Struct Mol Biol 2018; 25:994-995. [PMID: 30374084 DOI: 10.1038/s41594-018-0149-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Blake A Caldwell
- Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| | - Marisa S Bartolomei
- Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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125
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Yeung J, Naef F. Rhythms of the Genome: Circadian Dynamics from Chromatin Topology, Tissue-Specific Gene Expression, to Behavior. Trends Genet 2018; 34:915-926. [PMID: 30309754 DOI: 10.1016/j.tig.2018.09.005] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Revised: 08/31/2018] [Accepted: 09/10/2018] [Indexed: 11/18/2022]
Abstract
Circadian rhythms in physiology and behavior evolved to resonate with daily cycles in the external environment. In mammals, organs orchestrate temporal physiology over the 24-h day, which requires extensive gene expression rhythms targeted to the right tissue. Although a core set of gene products oscillates across virtually all cell types, gene expression profiling across tissues over the 24-h day showed that rhythmic gene expression programs are tissue specific. We highlight recent progress in uncovering how the circadian clock interweaves with tissue-specific gene regulatory networks involving functions such as xenobiotic metabolism, glucose homeostasis, and sleep. This progress hinges on not only comprehensive experimental approaches but also computational methods for multivariate analysis of periodic functional genomics data. We emphasize dynamic chromatin interactions as a novel regulatory layer underlying circadian gene transcription, core clock functions, and ultimately behavior. Finally, we discuss perspectives on extending the knowledge of the circadian clock in animals to human chronobiology.
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Affiliation(s)
- Jake Yeung
- The Institute of Bioengineering (IBI), School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Felix Naef
- The Institute of Bioengineering (IBI), School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
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126
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Kumar V, Sharma A. Common features of circadian timekeeping in diverse organisms. CURRENT OPINION IN PHYSIOLOGY 2018. [DOI: 10.1016/j.cophys.2018.07.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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127
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Wong DCS, O’Neill JS. Non-transcriptional processes in circadian rhythm generation. CURRENT OPINION IN PHYSIOLOGY 2018; 5:117-132. [PMID: 30596188 PMCID: PMC6302373 DOI: 10.1016/j.cophys.2018.10.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
'Biological clocks' orchestrate mammalian biology to a daily rhythm. Whilst 'clock gene' transcriptional circuits impart rhythmic regulation to myriad cellular systems, our picture of the biochemical mechanisms that determine their circadian (∼24 hour) period is incomplete. Here we consider the evidence supporting different models for circadian rhythm generation in mammalian cells in light of evolutionary factors. We find it plausible that the circadian timekeeping mechanism in mammalian cells is primarily protein-based, signalling biological timing information to the nucleus by the post-translational regulation of transcription factor activity, with transcriptional feedback imparting robustness to the oscillation via hysteresis. We conclude by suggesting experiments that might distinguish this model from competing paradigms.
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128
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Petrenko V, Philippe J, Dibner C. Time zones of pancreatic islet metabolism. Diabetes Obes Metab 2018; 20 Suppl 2:116-126. [PMID: 30230177 DOI: 10.1111/dom.13383] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 05/04/2018] [Accepted: 05/23/2018] [Indexed: 12/28/2022]
Abstract
Most living beings possess an intrinsic system of circadian oscillators, allowing anticipation of the Earth's rotation around its own axis. The mammalian circadian timing system orchestrates nearly all aspects of physiology and behaviour. Together with systemic signals originating from the central clock that resides in the hypothalamic suprachiasmatic nucleus, peripheral oscillators orchestrate tissue-specific fluctuations in gene transcription and translation, and posttranslational modifications, driving overt rhythms in physiology and behaviour. There is accumulating evidence of a reciprocal connection between the circadian oscillator and most aspects of physiology and metabolism, in particular as the circadian system plays a critical role in orchestrating body glucose homeostasis. Recent reports imply that circadian clocks operative in the endocrine pancreas regulate insulin secretion, and that islet clock perturbation in rodents leads to the development of overt type 2 diabetes. While whole islet clocks have been extensively studied during the last years, the heterogeneity of islet cell oscillators and the interplay between α- and β-cellular clocks for orchestrating glucagon and insulin secretion have only recently gained attention. Here, we review recent findings on the molecular makeup of the circadian clocks operative in pancreatic islet cells in rodents and in humans, and focus on the physiologically relevant synchronizers that are resetting these time-keepers. Moreover, the implication of islet clock functional outputs in the temporal coordination of metabolism in health and disease will be highlighted.
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Affiliation(s)
- Volodymyr Petrenko
- Division of Endocrinology, Diabetes, Hypertension and Nutrition, Department of Internal Medicine Specialties, University Hospital of Geneva, Geneva, Switzerland
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, Geneva, Switzerland
- Diabetes Center, Faculty of Medicine, University of Geneva, Geneva, Switzerland
- Institute of Genetics and Genomics in Geneva (iGE3), Geneva, Switzerland
| | - Jacques Philippe
- Division of Endocrinology, Diabetes, Hypertension and Nutrition, Department of Internal Medicine Specialties, University Hospital of Geneva, Geneva, Switzerland
- Diabetes Center, Faculty of Medicine, University of Geneva, Geneva, Switzerland
- Institute of Genetics and Genomics in Geneva (iGE3), Geneva, Switzerland
| | - Charna Dibner
- Division of Endocrinology, Diabetes, Hypertension and Nutrition, Department of Internal Medicine Specialties, University Hospital of Geneva, Geneva, Switzerland
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, Geneva, Switzerland
- Diabetes Center, Faculty of Medicine, University of Geneva, Geneva, Switzerland
- Institute of Genetics and Genomics in Geneva (iGE3), Geneva, Switzerland
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129
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Weidemann BJ, Ramsey KM, Bass J. A day in the life of chromatin: how enhancer-promoter loops shape daily behavior. Genes Dev 2018; 32:321-323. [PMID: 29593064 PMCID: PMC5900705 DOI: 10.1101/gad.314187.118] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
This Outlook by Weidemann et al. highlights two recent studies, one of which, by Mermet et al., is in this issue of Genes & Development. They examine how “time of day”-dependent changes in chromatin drive core clock oscillations and show that waking up involves highly dynamic changes in the three dimensional positioning of genes within the cell. Each spring, we get out of bed 1 h ahead of our biological wake-up time due to the misalignment of internal clocks with the light–dark cycle. Genetic discoveries revealed that clock genes encode transcription factors that are expressed throughout many tissues, yet a gap has remained in understanding the temporal dynamics of transcription. Two groups now apply circular chromosome conformation capture and high-throughput sequencing to dissect how “time of day”-dependent changes in chromatin drive core clock oscillations. A surprise is the finding that disruption of enhancer–promoter contacts within chromatin leads to an advance in the “wake-up” time of mice. Furthermore, the assembly of transcriptionally active domains of chromatin requires the ordered recruitment of core clock transcription factors each day. These studies show that waking up involves highly dynamic changes in the three-dimensional positioning of genes within the cell.
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Affiliation(s)
- Benjamin J Weidemann
- Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
| | - Kathryn Moynihan Ramsey
- Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
| | - Joseph Bass
- Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
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130
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Wang AW, Wangensteen KJ, Wang YJ, Zahm AM, Moss NG, Erez N, Kaestner KH. TRAP-seq identifies cystine/glutamate antiporter as a driver of recovery from liver injury. J Clin Invest 2018. [PMID: 29517978 DOI: 10.1172/jci95120] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Understanding the molecular basis of the regenerative response following hepatic injury holds promise for improved treatment of liver diseases. Here, we report an innovative method to profile gene expression specifically in the hepatocytes that regenerate the liver following toxic injury. We used the Fah-/- mouse, a model of hereditary tyrosinemia, which conditionally undergoes severe liver injury unless fumarylacetoacetate hydrolase (FAH) expression is reconstituted ectopically. We used translating ribosome affinity purification followed by high-throughput RNA sequencing (TRAP-seq) to isolate mRNAs specific to repopulating hepatocytes. We uncovered upstream regulators and important signaling pathways that are highly enriched in genes changed in regenerating hepatocytes. Specifically, we found that glutathione metabolism, particularly the gene Slc7a11 encoding the cystine/glutamate antiporter (xCT), is massively upregulated during liver regeneration. Furthermore, we show that Slc7a11 overexpression in hepatocytes enhances, and its suppression inhibits, repopulation following toxic injury. TRAP-seq allows cell type-specific expression profiling in repopulating hepatocytes and identified xCT, a factor that supports antioxidant responses during liver regeneration. xCT has potential as a therapeutic target for enhancing liver regeneration in response to liver injury.
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Affiliation(s)
| | - Kirk J Wangensteen
- Department of Genetics and.,Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | | | | | | | - Noam Erez
- Department of Genetics and.,Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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131
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Mallet de Lima CD, Göndör A. Circadian organization of the genome. Science 2018; 359:1212-1213. [PMID: 29590061 DOI: 10.1126/science.aat0934] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 02/22/2018] [Indexed: 12/11/2022]
Affiliation(s)
| | - Anita Göndör
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden.
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Mermet J, Yeung J, Hurni C, Mauvoisin D, Gustafson K, Jouffe C, Nicolas D, Emmenegger Y, Gobet C, Franken P, Gachon F, Naef F. Clock-dependent chromatin topology modulates circadian transcription and behavior. Genes Dev 2018; 32:347-358. [PMID: 29572261 PMCID: PMC5900709 DOI: 10.1101/gad.312397.118] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 03/02/2018] [Indexed: 12/27/2022]
Abstract
The circadian clock in animals orchestrates widespread oscillatory gene expression programs, which underlie 24-h rhythms in behavior and physiology. Several studies have shown the possible roles of transcription factors and chromatin marks in controlling cyclic gene expression. However, how daily active enhancers modulate rhythmic gene transcription in mammalian tissues is not known. Using circular chromosome conformation capture (4C) combined with sequencing (4C-seq), we discovered oscillatory promoter-enhancer interactions along the 24-h cycle in the mouse liver and kidney. Rhythms in chromatin interactions were abolished in arrhythmic Bmal1 knockout mice. Deleting a contacted intronic enhancer element in the Cryptochrome 1 (Cry1) gene was sufficient to compromise the rhythmic chromatin contacts in tissues. Moreover, the deletion reduced the daily dynamics of Cry1 transcriptional burst frequency and, remarkably, shortened the circadian period of locomotor activity rhythms. Our results establish oscillating and clock-controlled promoter-enhancer looping as a regulatory layer underlying circadian transcription and behavior.
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Affiliation(s)
- Jérôme Mermet
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Jake Yeung
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Clémence Hurni
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Daniel Mauvoisin
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Kyle Gustafson
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Céline Jouffe
- Nestle Institute of Health Sciences, CH-1015 Lausanne, Switzerland
| | - Damien Nicolas
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Yann Emmenegger
- Center for Integrative Genomics, University of Lausanne, CH-1015 Lausanne, Switzerland
| | - Cédric Gobet
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland.,Nestle Institute of Health Sciences, CH-1015 Lausanne, Switzerland
| | - Paul Franken
- Center for Integrative Genomics, University of Lausanne, CH-1015 Lausanne, Switzerland
| | - Frédéric Gachon
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland.,Nestle Institute of Health Sciences, CH-1015 Lausanne, Switzerland
| | - Félix Naef
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
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