1
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Zong W, Seney ML, Ketchesin KD, Gorczyca MT, Liu AC, Esser KA, Tseng GC, McClung CA, Huo Z. Experimental design and power calculation in omics circadian rhythmicity detection using the cosinor model. Stat Med 2023; 42:3236-3258. [PMID: 37265194 PMCID: PMC10425922 DOI: 10.1002/sim.9803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 03/27/2023] [Accepted: 05/09/2023] [Indexed: 06/03/2023]
Abstract
Circadian clocks are 24-h endogenous oscillators in physiological and behavioral processes. Though recent transcriptomic studies have been successful in revealing the circadian rhythmicity in gene expression, the power calculation for omics circadian analysis have not been fully explored. In this paper, we develop a statistical method, namely CircaPower, to perform power calculation for circadian pattern detection. Our theoretical framework is determined by three key factors in circadian gene detection: sample size, intrinsic effect size and sampling design. Via simulations, we systematically investigate the impact of these key factors on circadian power calculation. We not only demonstrate that CircaPower is fast and accurate, but also show its underlying cosinor model is robust against variety of violations of model assumptions. In real applications, we demonstrate the performance of CircaPower using mouse pan-tissue data and human post-mortem brain data, and illustrate how to perform circadian power calculation using mouse skeleton muscle RNA-Seq pilot as case study. Our method CircaPower has been implemented in an R package, which is made publicly available on GitHub ( https://github.com/circaPower/circaPower).
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Affiliation(s)
- Wei Zong
- Department of Biostatistics, University of Pittsburgh, PA, USA
| | - Marianne L. Seney
- Translational Neuroscience Program, Department of Psychiatry, Center for Neuroscience, University of Pittsburgh, PA, USA
| | - Kyle D. Ketchesin
- Translational Neuroscience Program, Department of Psychiatry, Center for Neuroscience, University of Pittsburgh, PA, USA
| | - Michael T. Gorczyca
- Department of Computational and Systems Biology, University of Pittsburgh, PA, USA
| | - Andrew C. Liu
- Department of Physiology and Aging, University of Florida, FL, USA
| | - Karyn A. Esser
- Department of Physiology and Aging, University of Florida, FL, USA
| | - George C. Tseng
- Department of Biostatistics, University of Pittsburgh, PA, USA
| | - Colleen A. McClung
- Translational Neuroscience Program, Department of Psychiatry, Center for Neuroscience, University of Pittsburgh, PA, USA
| | - Zhiguang Huo
- Department of Biostatistics, University of Florida, FL, USA
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2
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Oh VKS, Li RW. Temporal Dynamic Methods for Bulk RNA-Seq Time Series Data. Genes (Basel) 2021; 12:352. [PMID: 33673721 PMCID: PMC7997275 DOI: 10.3390/genes12030352] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 02/19/2021] [Accepted: 02/22/2021] [Indexed: 02/06/2023] Open
Abstract
Dynamic studies in time course experimental designs and clinical approaches have been widely used by the biomedical community. These applications are particularly relevant in stimuli-response models under environmental conditions, characterization of gradient biological processes in developmental biology, identification of therapeutic effects in clinical trials, disease progressive models, cell-cycle, and circadian periodicity. Despite their feasibility and popularity, sophisticated dynamic methods that are well validated in large-scale comparative studies, in terms of statistical and computational rigor, are less benchmarked, comparing to their static counterparts. To date, a number of novel methods in bulk RNA-Seq data have been developed for the various time-dependent stimuli, circadian rhythms, cell-lineage in differentiation, and disease progression. Here, we comprehensively review a key set of representative dynamic strategies and discuss current issues associated with the detection of dynamically changing genes. We also provide recommendations for future directions for studying non-periodical, periodical time course data, and meta-dynamic datasets.
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Affiliation(s)
- Vera-Khlara S. Oh
- Animal Genomics and Improvement Laboratory, United States Department of Agriculture, Agricultural Research Service, Beltsville, MD 20705, USA;
- Department of Computer Science and Statistics, College of Natural Sciences, Jeju National University, Jeju City 63243, Korea
| | - Robert W. Li
- Animal Genomics and Improvement Laboratory, United States Department of Agriculture, Agricultural Research Service, Beltsville, MD 20705, USA;
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3
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Affiliation(s)
- Yunong Li
- Department of Humanities and Science, Hunan Mechanical & Electrical Polytechnic, Changsha City, Hunan Province, China
| | - Wei Chen
- Department of Scientific Research, Hunan Sports Vocational College, Changsha City, Hunan Province, China
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4
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Wu G, Ruben MD, Lee Y, Li J, Hughes ME, Hogenesch JB. Genome-wide studies of time of day in the brain: Design and analysis. BRAIN SCIENCE ADVANCES 2020. [DOI: 10.26599/bsa.2020.9050005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Transcriptome profiling at different times of day is powerful for studying circadian regulation in model organisms and humans. To date, 24 h profiles from many tissue types suggest that about half of all genes are circadian-expressed somewhere in the body. However, few of these studies focused on the brain. Thus, despite known links between circadian disruption and neurological disease, we have virtually no mechanistic understanding. In the coming decade, we expect more genome-wide studies of time of day in different brain diseases, regions, and cell types. We expect just as many different approaches to the design and analysis of these studies. This review considers key principles of circadian tran scriptomics, with the goal of maximizing utility and reproducibility of future studies in the nervous system.
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Affiliation(s)
- Gang Wu
- Divisions of Human Genetics and Immunobiology, Center for Chronobiology, Department of Pediatrics, Cincinnati Children’s Hospital Medical Center, 240 Albert Sabin Way, Cincinnati, OH 45229, U.S.A
| | - Marc D. Ruben
- Divisions of Human Genetics and Immunobiology, Center for Chronobiology, Department of Pediatrics, Cincinnati Children’s Hospital Medical Center, 240 Albert Sabin Way, Cincinnati, OH 45229, U.S.A
| | - Yinyeng Lee
- Divisions of Human Genetics and Immunobiology, Center for Chronobiology, Department of Pediatrics, Cincinnati Children’s Hospital Medical Center, 240 Albert Sabin Way, Cincinnati, OH 45229, U.S.A
| | - Jiajia Li
- Division of Pulmonary and Critical Care Medicine, Washington University School of Medicine, St. Louis, MO 63310, U.S.A
| | - Michael E. Hughes
- Division of Pulmonary and Critical Care Medicine, Washington University School of Medicine, St. Louis, MO 63310, U.S.A
| | - John B. Hogenesch
- Divisions of Human Genetics and Immunobiology, Center for Chronobiology, Department of Pediatrics, Cincinnati Children’s Hospital Medical Center, 240 Albert Sabin Way, Cincinnati, OH 45229, U.S.A
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5
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Genome-wide circadian regulation: A unique system for computational biology. Comput Struct Biotechnol J 2020; 18:1914-1924. [PMID: 32774786 PMCID: PMC7385043 DOI: 10.1016/j.csbj.2020.07.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Revised: 06/30/2020] [Accepted: 07/02/2020] [Indexed: 01/20/2023] Open
Abstract
Circadian rhythms are 24-hour oscillations affecting an organism at multiple levels from gene expression all the way to tissues and organs. They have been observed in organisms across the kingdom of life, spanning from cyanobacteria to humans. In mammals, the master circadian pacemaker is located in the hypothalamic suprachiasmatic nuclei (SCN) in the brain where it synchronizes the peripheral oscillators that exist in other tissues. This system regulates the circadian activity of a large part of the transcriptome and recent findings indicate that almost every cell in the body has this clock at the molecular level. In this review, we briefly summarize the different factors that can influence the circadian transcriptome, including light, temperature, and food intake. We then summarize recently identified general principles governing genome-scale circadian regulation, as well as future lines of research. Genome-scale circadian activity represents a fascinating study model for computational biology. For this purpose, systems biology methods are promising exploratory tools to decode the global regulatory principles of circadian regulation.
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Key Words
- ABSR, Autoregressive Bayesian spectral regression
- AMPK, AMP-activated protein kinase
- AR, Arrhythmic feeding
- ARSER, Harmonic regression based on autoregressive spectral estimation
- BMAL1, The aryl hydrocarbon receptor nuclear translocator-like (ARNTL)
- CCD, Cortical collecting duct
- CR, Calorie-restricted diet
- CRY, Cryptochrome
- Circadian regulatory network
- Circadian rhythms
- Circadian transcriptome
- Cycling genes
- DCT/CNT, Distal convoluted tubule and connecting tubule
- DD, Dark: dark
- Energetic cost
- HF, High fat diet
- JTK_CYCLE, Jonckheere-Terpstra-Kendall (JTK) cycle
- KD, Ketogenic diet
- LB, Ad libitum
- LD, Light:dark
- LS, Lomb-Scargle
- Liver-RE, Liver clock reconstituted BMAL1-deficient mice
- NAD, Nicotinamide adenine dinucleotides
- ND, Normal diet
- NR, Night-restricted feeding
- PAS, PER-ARNT-SIM
- PER, Period
- RAIN, Rhythmicity Analysis Incorporating Nonparametric methods
- RF, Restricted feeding
- SCN, Suprachiasmatic nucleus
- SREBP, The sterol regulatory element binding protein
- TTFL, Transcriptional-translational feedback loop
- WT, Wild type
- eJTK_CYCLE, Empirical JTK_CYCLE
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6
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Ness-Cohn E, Iwanaszko M, Kath WL, Allada R, Braun R. TimeTrial: An Interactive Application for Optimizing the Design and Analysis of Transcriptomic Time-Series Data in Circadian Biology Research. J Biol Rhythms 2020; 35:439-451. [PMID: 32613882 PMCID: PMC7534021 DOI: 10.1177/0748730420934672] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The circadian rhythm drives the oscillatory expression of thousands of genes across all tissues, coordinating physiological processes. The effect of this rhythm on health has generated increasing interest in discovering genes under circadian control by searching for periodic patterns in transcriptomic time-series experiments. While algorithms for detecting cycling transcripts have advanced, there remains little guidance quantifying the effect of experimental design and analysis choices on cycling detection accuracy. We present TimeTrial, a user-friendly benchmarking framework using both real and synthetic data to investigate cycle detection algorithms’ performance and improve circadian experimental design. Results show that the optimal choice of analysis method depends on the sampling scheme, noise level, and shape of the waveform of interest and provides guidance on the impact of sampling frequency and duration on cycling detection accuracy. The TimeTrial software is freely available for download and may also be accessed through a web interface. By supplying a tool to vary and optimize experimental design considerations, TimeTrial will enhance circadian transcriptomics studies.
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Affiliation(s)
- Elan Ness-Cohn
- Biostatistics Division, Department of Preventive Medicine, Northwestern University, Chicago, Illinois, USA.,NSF-Simons Center for Quantitative Biology, Northwestern University, Evanston, Illinois, USA
| | - Marta Iwanaszko
- Biostatistics Division, Department of Preventive Medicine, Northwestern University, Chicago, Illinois, USA.,NSF-Simons Center for Quantitative Biology, Northwestern University, Evanston, Illinois, USA.,Silesian University of Technology, Department of Systems Biology and Engineering, Gliwice, Poland
| | - William L Kath
- NSF-Simons Center for Quantitative Biology, Northwestern University, Evanston, Illinois, USA.,Department of Engineering Sciences and Applied Mathematics, Northwestern University, Evanston, IL, USA.,Department of Neurobiology, Northwestern University, Evanston, IL, USA
| | - Ravi Allada
- NSF-Simons Center for Quantitative Biology, Northwestern University, Evanston, Illinois, USA.,Department of Neurobiology, Northwestern University, Evanston, IL, USA
| | - Rosemary Braun
- Biostatistics Division, Department of Preventive Medicine, Northwestern University, Chicago, Illinois, USA.,NSF-Simons Center for Quantitative Biology, Northwestern University, Evanston, Illinois, USA.,Department of Engineering Sciences and Applied Mathematics, Northwestern University, Evanston, IL, USA.,Department of Physics and Astronomy, Northwestern University, Evanston, Illinois, USA
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7
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Larriba Y, Rueda C, Fernández MA, Peddada SD. Order restricted inference in chronobiology. Stat Med 2020; 39:265-278. [PMID: 31769057 DOI: 10.1002/sim.8397] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Revised: 06/11/2019] [Accepted: 09/21/2019] [Indexed: 01/25/2023]
Abstract
This paper is motivated by applications in oscillatory systems where researchers are typically interested in discovering components of those systems that display rhythmic temporal patterns. The contributions of this paper are twofold. First, a methodology is developed based on a circular signal plus error model that is defined using order restrictions. This mathematical formulation of rhythmicity is simple, easily interpretable and very flexible, with the latter property derived from the nonparametric formulation of the signal. Second, we address various commonly encountered problems in the analysis of oscillatory systems data. Specifically, we propose a methodology for (a) detecting rhythmic signals in an oscillatory system and (b) estimating the unknown sampling time that occurs when tissues are obtained from subjects whose time of death is unknown. The proposed methodology is computationally efficient, outperforms the existing methods, and is broadly applicable to address a wide range of questions related to oscillatory systems.
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Affiliation(s)
- Yolanda Larriba
- Departamento de Estadística e Investigación Operativa, Universidad de Valladolid, Valladolid, Spain
| | - Cristina Rueda
- Departamento de Estadística e Investigación Operativa, Universidad de Valladolid, Valladolid, Spain
| | - Miguel A Fernández
- Departamento de Estadística e Investigación Operativa, Universidad de Valladolid, Valladolid, Spain
| | - Shyamal D Peddada
- Department of Biostatistics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania
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8
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Rahman S, Kraljević Pavelić S, Markova-Car E. Circadian (De)regulation in Head and Neck Squamous Cell Carcinoma. Int J Mol Sci 2019; 20:ijms20112662. [PMID: 31151182 PMCID: PMC6600143 DOI: 10.3390/ijms20112662] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 05/26/2019] [Accepted: 05/28/2019] [Indexed: 12/15/2022] Open
Abstract
Head and neck cancer encompass different malignancies that develop in and around the throat, larynx, nose, sinuses and mouth. Most head and neck cancers are squamous cell carcinomas (HNSCC) that arise in the flat squamous cells that makeup the thin layer of tissue on the surface of anatomical structures in the head and neck. Each year, HNSCC is diagnosed in more than 600,000 people worldwide, with about 50,000 new cases. HNSCC is considered extremely curable if detected early. But the problem remains in treatment of inoperable cases, residues or late stages. Circadian rhythm regulation has a big role in developing various carcinomas, and head and neck tumors are no exception. A number of studies have reported that alteration in clock gene expression is associated with several cancers, including HNSCC. Analyses on circadian clock genes and their association with HNSCC have shown that expression of PER1, PER2, PER3, CRY1, CRY2,CKIε, TIM, and BMAL1 are deregulated in HNSCC tissues. This review paper comprehensively presents data on deregulation of circadian genes in HNSCC and critically evaluates their potential diagnostics and prognostics role in this type of pathology.
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Affiliation(s)
- Sadia Rahman
- University of Rijeka, Department of Biotechnology, Centre for High-Throughput Technologies, 51000 Rijeka, Croatia.
| | - Sandra Kraljević Pavelić
- University of Rijeka, Department of Biotechnology, Centre for High-Throughput Technologies, 51000 Rijeka, Croatia.
| | - Elitza Markova-Car
- University of Rijeka, Department of Biotechnology, Centre for High-Throughput Technologies, 51000 Rijeka, Croatia.
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9
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Li J, Yu RY, Emran F, Chen BE, Hughes ME. Achilles-Mediated and Sex-Specific Regulation of Circadian mRNA Rhythms in Drosophila. J Biol Rhythms 2019; 34:131-143. [PMID: 30803307 DOI: 10.1177/0748730419830845] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The circadian clock is an evolutionarily conserved mechanism that generates the rhythmic expression of downstream genes. The core circadian clock drives the expression of clock-controlled genes, which in turn play critical roles in carrying out many rhythmic physiological processes. Nevertheless, the molecular mechanisms by which clock output genes orchestrate rhythmic signals from the brain to peripheral tissues are largely unknown. Here we explored the role of one rhythmic gene, Achilles, in regulating the rhythmic transcriptome in the fly head. Achilles is a clock-controlled gene in Drosophila that encodes a putative RNA-binding protein. Achilles expression is found in neurons throughout the fly brain using fluorescence in situ hybridization (FISH), and legacy data suggest it is not expressed in core clock neurons. Together, these observations argue against a role for Achilles in regulating the core clock. To assess its impact on circadian mRNA rhythms, we performed RNA sequencing (RNAseq) to compare the rhythmic transcriptomes of control flies and those with diminished Achilles expression in all neurons. Consistent with previous studies, we observe dramatic upregulation of immune response genes upon knock-down of Achilles. Furthermore, many circadian mRNAs lose their rhythmicity in Achilles knock-down flies, suggesting that a subset of the rhythmic transcriptome is regulated either directly or indirectly by Achilles. These Achilles-mediated rhythms are observed in genes involved in immune function and in neuronal signaling, including Prosap, Nemy and Jhl-21. A comparison of RNAseq data from control flies reveals that only 42.7% of clock-controlled genes in the fly brain are rhythmic in both males and females. As mRNA rhythms of core clock genes are largely invariant between the sexes, this observation suggests that sex-specific mechanisms are an important, and heretofore under-appreciated, regulator of the rhythmic transcriptome.
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Affiliation(s)
- Jiajia Li
- Division of Pulmonary and Critical Care Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Renee Yin Yu
- Centre for Research in Neuroscience, Research Institute of the McGill University Health Centre, Montreal General Hospital, Montréal, Québec, Canada
| | - Farida Emran
- Centre for Research in Neuroscience, Research Institute of the McGill University Health Centre, Montreal General Hospital, Montréal, Québec, Canada
| | - Brian E Chen
- Centre for Research in Neuroscience, Research Institute of the McGill University Health Centre, Montreal General Hospital, Montréal, Québec, Canada.,Departments of Medicine and Neurology and Neurosurgery, McGill University, Montréal, Quebec, Canada
| | - Michael E Hughes
- Division of Pulmonary and Critical Care Medicine, Washington University School of Medicine, St. Louis, MO, USA
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10
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Fontenot MR, Berto S, Liu Y, Werthmann G, Douglas C, Usui N, Gleason K, Tamminga CA, Takahashi JS, Konopka G. Novel transcriptional networks regulated by CLOCK in human neurons. Genes Dev 2017; 31:2121-2135. [PMID: 29196536 PMCID: PMC5749161 DOI: 10.1101/gad.305813.117] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Accepted: 11/07/2017] [Indexed: 01/01/2023]
Abstract
Fontenot et al. show that CLOCK regulates the expression of genes involved in neuronal migration. Dysregulation of CLOCK disrupts coexpressed networks of genes implicated in neuropsychiatric disorders, and the expression of these networks is driven by hub genes with human-specific patterns of expression. The molecular mechanisms underlying human brain evolution are not fully understood; however, previous work suggested that expression of the transcription factor CLOCK in the human cortex might be relevant to human cognition and disease. In this study, we investigated this novel transcriptional role for CLOCK in human neurons by performing chromatin immunoprecipitation sequencing for endogenous CLOCK in adult neocortices and RNA sequencing following CLOCK knockdown in differentiated human neurons in vitro. These data suggested that CLOCK regulates the expression of genes involved in neuronal migration, and a functional assay showed that CLOCK knockdown increased neuronal migratory distance. Furthermore, dysregulation of CLOCK disrupts coexpressed networks of genes implicated in neuropsychiatric disorders, and the expression of these networks is driven by hub genes with human-specific patterns of expression. These data support a role for CLOCK-regulated transcriptional cascades involved in human brain evolution and function.
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Affiliation(s)
- Miles R Fontenot
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Stefano Berto
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Yuxiang Liu
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Gordon Werthmann
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Connor Douglas
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Noriyoshi Usui
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Kelly Gleason
- Department of Psychiatry, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Carol A Tamminga
- Department of Psychiatry, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Joseph S Takahashi
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA.,Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Genevieve Konopka
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
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11
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Hughes ME, Abruzzi KC, Allada R, Anafi R, Arpat AB, Asher G, Baldi P, de Bekker C, Bell-Pedersen D, Blau J, Brown S, Ceriani MF, Chen Z, Chiu JC, Cox J, Crowell AM, DeBruyne JP, Dijk DJ, DiTacchio L, Doyle FJ, Duffield GE, Dunlap JC, Eckel-Mahan K, Esser KA, FitzGerald GA, Forger DB, Francey LJ, Fu YH, Gachon F, Gatfield D, de Goede P, Golden SS, Green C, Harer J, Harmer S, Haspel J, Hastings MH, Herzel H, Herzog ED, Hoffmann C, Hong C, Hughey JJ, Hurley JM, de la Iglesia HO, Johnson C, Kay SA, Koike N, Kornacker K, Kramer A, Lamia K, Leise T, Lewis SA, Li J, Li X, Liu AC, Loros JJ, Martino TA, Menet JS, Merrow M, Millar AJ, Mockler T, Naef F, Nagoshi E, Nitabach MN, Olmedo M, Nusinow DA, Ptáček LJ, Rand D, Reddy AB, Robles MS, Roenneberg T, Rosbash M, Ruben MD, Rund SSC, Sancar A, Sassone-Corsi P, Sehgal A, Sherrill-Mix S, Skene DJ, Storch KF, Takahashi JS, Ueda HR, Wang H, Weitz C, Westermark PO, Wijnen H, Xu Y, Wu G, Yoo SH, Young M, Zhang EE, Zielinski T, Hogenesch JB. Guidelines for Genome-Scale Analysis of Biological Rhythms. J Biol Rhythms 2017; 32:380-393. [PMID: 29098954 PMCID: PMC5692188 DOI: 10.1177/0748730417728663] [Citation(s) in RCA: 173] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Genome biology approaches have made enormous contributions to our understanding of biological rhythms, particularly in identifying outputs of the clock, including RNAs, proteins, and metabolites, whose abundance oscillates throughout the day. These methods hold significant promise for future discovery, particularly when combined with computational modeling. However, genome-scale experiments are costly and laborious, yielding “big data” that are conceptually and statistically difficult to analyze. There is no obvious consensus regarding design or analysis. Here we discuss the relevant technical considerations to generate reproducible, statistically sound, and broadly useful genome-scale data. Rather than suggest a set of rigid rules, we aim to codify principles by which investigators, reviewers, and readers of the primary literature can evaluate the suitability of different experimental designs for measuring different aspects of biological rhythms. We introduce CircaInSilico, a web-based application for generating synthetic genome biology data to benchmark statistical methods for studying biological rhythms. Finally, we discuss several unmet analytical needs, including applications to clinical medicine, and suggest productive avenues to address them.
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Affiliation(s)
- Michael E Hughes
- 1 Division of Pulmonary and Critical Care Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Katherine C Abruzzi
- 2 Department of Biology and Howard Hughes Medical Institute, Brandeis University, Waltham, Massachusetts, USA
| | - Ravi Allada
- 3 Department of Neurobiology, Northwestern University, Evanston, Illinois, USA
| | - Ron Anafi
- 4 Division of Sleep Medicine, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, USA
| | - Alaaddin Bulak Arpat
- 5 Center for Integrative Genomics, Génopode, University of Lausanne, Lausanne, Switzerland.,6 Vital-IT, Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Gad Asher
- 7 Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Pierre Baldi
- 8 Institute for Genomics and Bioinformatics, University of California, Irvine, USA
| | | | | | - Justin Blau
- 11 Department of Biology, New York University, New York, USA
| | - Steve Brown
- 12 Institute of Pharmacology and Toxicology, University of Zürich, Switzerland
| | - M Fernanda Ceriani
- 13 Laboratorio de Genética del Comportamiento, Fundación Instituto Leloir, IIBBA-CONICET, Buenos Aires, Argentina
| | - Zheng Chen
- 14 Department of Biochemistry and Molecular Biology, University of Texas Health Science Center, Houston, USA
| | - Joanna C Chiu
- 15 Department of Entomology and Nematology, University of California, Davis, USA
| | - Juergen Cox
- 16 Computational Systems Biochemistry, Max-Planck Institute of Biochemistry, Martinsried, Germany
| | - Alexander M Crowell
- 17 Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Jason P DeBruyne
- 18 Department of Pharmacology and Toxicology, Morehouse School of Medicine, Atlanta, Georgia, USA
| | - Derk-Jan Dijk
- 19 Surrey Sleep Research Centre, University of Surrey, Guildford, UK
| | - Luciano DiTacchio
- 20 The University of Kansas Medical Center, University of Kansas, Kansas City, USA
| | - Francis J Doyle
- 21 John A. Paulson School of Engineering and Applied Sciences, Harvard University, Boston, Massachusetts, USA
| | - Giles E Duffield
- 22 Department of Biological Sciences and Eck Institute for Global Health, University of Notre Dame, Notre Dame, Indiana, USA
| | - Jay C Dunlap
- 17 Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Kristin Eckel-Mahan
- 23 Institute of Molecular Medicine, McGovern Medical School, UT Health Houston, Houston, Texas, USA
| | - Karyn A Esser
- 24 Department of Physiology and Functional Genomics, University of Florida College of Medicine, Gainesville, USA
| | - Garret A FitzGerald
- 25 Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, USA
| | - Daniel B Forger
- 26 Department of Mathematics, University of Michigan, Ann Arbor, USA
| | - Lauren J Francey
- 27 Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Ying-Hui Fu
- 28 Kavli Institute for Fundamental Neuroscience, Weill Institute of Neuroscience, Department of Neurology, University of California, San Francisco, USA
| | - Frédéric Gachon
- 29 Department of Diabetes and Circadian Rhythms, Nestlé Institute of Health Sciences, Lausanne, Switzerland
| | - David Gatfield
- 5 Center for Integrative Genomics, Génopode, University of Lausanne, Lausanne, Switzerland
| | - Paul de Goede
- 30 Department of Endocrinology & Metabolism, Academic Medical Center, Amsterdam, the Netherlands
| | - Susan S Golden
- 31 Center for Circadian Biology and Division of Biological Sciences, University of California, San Diego, La Jolla, USA
| | - Carla Green
- 32 Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, USA
| | - John Harer
- 33 Department of Mathematics, Duke University, Durham, North Carolina, USA
| | - Stacey Harmer
- 34 Department of Plant Biology, University of California, Davis, USA
| | - Jeff Haspel
- 1 Division of Pulmonary and Critical Care Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Michael H Hastings
- 35 Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Hanspeter Herzel
- 36 Institute for Theoretical Biology, Charité-Universitätsmedizin Berlin, Germany
| | - Erik D Herzog
- 37 Department of Biology, Washington University in St. Louis, Missouri, USA
| | - Christy Hoffmann
- 1 Division of Pulmonary and Critical Care Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Christian Hong
- 27 Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Jacob J Hughey
- 38 Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Jennifer M Hurley
- 39 Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, New York, USA
| | | | - Carl Johnson
- 41 Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA
| | - Steve A Kay
- 42 Department of Cell and Molecular Biology, The Scripps Research Institute, University of California, San Diego, La Jolla, USA
| | - Nobuya Koike
- 43 Department of Physiology and Systems Bioscience, Kyoto Prefectural University of Medicine, Japan
| | - Karl Kornacker
- 44 Division of Sensory Biophysics, The Ohio State University, Columbus, USA
| | - Achim Kramer
- 45 Laboratory of Chronobiology, Charité Universitätsmedizin Berlin, Germany
| | - Katja Lamia
- 46 Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California, USA
| | - Tanya Leise
- 47 Department of Mathematics and Statistics, Amherst College, Amherst, Massachusetts, USA
| | - Scott A Lewis
- 1 Division of Pulmonary and Critical Care Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Jiajia Li
- 1 Division of Pulmonary and Critical Care Medicine, Washington University School of Medicine, St. Louis, Missouri, USA.,48 Department of Biology, University of Missouri-St. Louis, USA
| | - Xiaodong Li
- 49 Department of Cell Biology, College of Life Sciences at Wuhan University, China
| | - Andrew C Liu
- 50 Department of Biological Sciences, University of Memphis, Tennessee, USA
| | - Jennifer J Loros
- 51 Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Tami A Martino
- 52 Centre for Cardiovascular Investigations, Department of Biomedical Sciences, University of Guelph, Guelph, Ontario, Canada
| | - Jerome S Menet
- 10 Department of Biology, Texas A&M University, College Station, USA
| | - Martha Merrow
- 53 Institute of Medical Psychology, Faculty of Medicine, LMU Munich, Germany
| | - Andrew J Millar
- 54 SynthSys and School of Biological Sciences, University of Edinburgh, UK
| | - Todd Mockler
- 55 Donald Danforth Plant Science Center, St. Louis, Missouri, USA
| | - Felix Naef
- 56 The Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Switzerland
| | - Emi Nagoshi
- 57 Department of Genetics and Evolution, University of Geneva, Switzerland
| | - Michael N Nitabach
- 58 Department of Cellular and Molecular Physiology, Department of Genetics, Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, Connecticut, USA
| | - Maria Olmedo
- 59 Department of Genetics, University of Seville, Spain
| | - Dmitri A Nusinow
- 55 Donald Danforth Plant Science Center, St. Louis, Missouri, USA
| | - Louis J Ptáček
- 60 Department of Neurology, University of California, San Francisco, USA
| | - David Rand
- 61 Warwick Systems Biology and Mathematics Institute, University of Warwick, Conventry, UK
| | - Akhilesh B Reddy
- 62 The Francis Crick Institute, London, UK, and UCL Institute of Neurology, Queen Square, London, UK
| | - Maria S Robles
- 53 Institute of Medical Psychology, Faculty of Medicine, LMU Munich, Germany
| | - Till Roenneberg
- 53 Institute of Medical Psychology, Faculty of Medicine, LMU Munich, Germany
| | - Michael Rosbash
- 2 Department of Biology and Howard Hughes Medical Institute, Brandeis University, Waltham, Massachusetts, USA
| | - Marc D Ruben
- 27 Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Samuel S C Rund
- 63 Centre for Immunity, Infection and Evolution, University of Edinburgh, UK
| | - Aziz Sancar
- 64 Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, USA
| | - Paolo Sassone-Corsi
- 65 Department of Biological Chemistry, Center for Epigenetics and Metabolism, University of California, Irvine, USA
| | - Amita Sehgal
- 66 Howard Hughes Medical Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, USA
| | - Scott Sherrill-Mix
- 67 Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, USA
| | - Debra J Skene
- 68 Chronobiology, Faculty of Health and Medical Sciences, University of Surrey, Guildford, UK
| | - Kai-Florian Storch
- 69 Department of Psychiatry, Douglas Mental Health University Institute, McGill University, Montreal, Canada
| | - Joseph S Takahashi
- 70 Howard Hughes Medical Institute, Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, USA
| | - Hiroki R Ueda
- 71 Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan Laboratory for Synthetic Biology, RIKEN Quantitative Biology Center, Osaka, Japan
| | - Han Wang
- 72 Center for Circadian Clocks, Soochow University, Suzhou, Jiangsu, China
| | - Charles Weitz
- 73 Department of Neurobiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Pål O Westermark
- 74 Institute of Genetics and Biometry, Leibniz Institute for Farm Animal Biology, Dummerstorf, Germany
| | - Herman Wijnen
- 75 Biological Sciences and Institute for Life Sciences, University of Southampton, UK
| | - Ying Xu
- 76 Cam-Su GRC, Soochow University, Suzhou, China
| | - Gang Wu
- 27 Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Seung-Hee Yoo
- 14 Department of Biochemistry and Molecular Biology, University of Texas Health Science Center, Houston, USA
| | - Michael Young
- 77 Laboratory of Genetics, Rockefeller University, New York, New York, USA
| | | | - Tomasz Zielinski
- 54 SynthSys and School of Biological Sciences, University of Edinburgh, UK
| | - John B Hogenesch
- 27 Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
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12
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Krishnaiah SY, Wu G, Altman BJ, Growe J, Rhoades SD, Coldren F, Venkataraman A, Olarerin-George AO, Francey LJ, Mukherjee S, Girish S, Selby CP, Cal S, Er U, Sianati B, Sengupta A, Anafi RC, Kavakli IH, Sancar A, Baur JA, Dang CV, Hogenesch JB, Weljie AM. Clock Regulation of Metabolites Reveals Coupling between Transcription and Metabolism. Cell Metab 2017; 25:961-974.e4. [PMID: 28380384 PMCID: PMC5479132 DOI: 10.1016/j.cmet.2017.03.019] [Citation(s) in RCA: 107] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Revised: 01/12/2017] [Accepted: 03/22/2017] [Indexed: 01/09/2023]
Abstract
The intricate connection between the circadian clock and metabolism remains poorly understood. We used high temporal resolution metabolite profiling to explore clock regulation of mouse liver and cell-autonomous metabolism. In liver, ∼50% of metabolites were circadian, with enrichment of nucleotide, amino acid, and methylation pathways. In U2 OS cells, 28% were circadian, including amino acids and NAD biosynthesis metabolites. Eighteen metabolites oscillated in both systems and a subset of these in primary hepatocytes. These 18 metabolites were enriched in methylation and amino acid pathways. To assess clock dependence of these rhythms, we used genetic perturbation. BMAL1 knockdown diminished metabolite rhythms, while CRY1 or CRY2 perturbation generally shortened or lengthened rhythms, respectively. Surprisingly, CRY1 knockdown induced 8 hr rhythms in amino acid, methylation, and vitamin metabolites, decoupling metabolite from transcriptional rhythms, with potential impact on nutrient sensing in vivo. These results provide the first comprehensive views of circadian liver and cell-autonomous metabolism.
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Affiliation(s)
- Saikumari Y Krishnaiah
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute of Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Gang Wu
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Brian J Altman
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jacqueline Growe
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Seth D Rhoades
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute of Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Faith Coldren
- Institute of Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Anand Venkataraman
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Anthony O Olarerin-George
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Lauren J Francey
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Sarmistha Mukherjee
- Department of Physiology and Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Saiveda Girish
- Department of Physiology and Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Christopher P Selby
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Sibel Cal
- Chemical and Biological Engineering and Molecular Biology and Genetics, Koc University, Rumeli Feneri Yolu, 34450 Sariyer, Istanbul, Turkey
| | - Ubeydullah Er
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute of Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Bahareh Sianati
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute of Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Arjun Sengupta
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute of Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ron C Anafi
- Department of Medicine and Center for Sleep and Circadian Neurobiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - I Halil Kavakli
- Chemical and Biological Engineering and Molecular Biology and Genetics, Koc University, Rumeli Feneri Yolu, 34450 Sariyer, Istanbul, Turkey
| | - Aziz Sancar
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Joseph A Baur
- Department of Physiology and Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Chi V Dang
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - John B Hogenesch
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.
| | - Aalim M Weljie
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute of Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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13
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Abstract
This review summarizes various mathematical models of cell-autonomous mammalian circadian clock. We present the basics necessary for understanding of the cell-autonomous mammalian circadian oscillator, modern experimental data essential for its reconstruction and some special problems related to the validation of mathematical circadian oscillator models. This work compares existing mathematical models of circadian oscillator and the results of the computational studies of the oscillating systems. Finally, we discuss applications of the mathematical models of mammalian circadian oscillator for solving specific problems in circadian rhythm biology.
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14
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Torres M, Becquet D, Blanchard MP, Guillen S, Boyer B, Moreno M, Franc JL, François-Bellan AM. Paraspeckles as rhythmic nuclear mRNA anchorages responsible for circadian gene expression. Nucleus 2017; 8:249-254. [PMID: 28060565 DOI: 10.1080/19491034.2016.1277304] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Circadian clocks regulate rhythmic gene expression levels by means of mRNA oscillations that are mainly driven by post-transcriptional regulation. We identified a new post-transcriptional mechanism, which involves nuclear bodies called paraspeckles. Major components of paraspeckles including the long noncoding RNA Neat1, which is the structural component, and its major protein partners, as well as the number of paraspeckles, follow a circadian pattern in pituitary cells. Paraspeckles are known to retain within the nucleus RNAs containing inverted repeats of Alu sequences. We showed that a reporter gene in which these RNA duplex elements were inserted in the 3'-UTR region displayed a circadian expression. Moreover, circadian endogenous mRNA associated with paraspeckles lost their circadian pattern when paraspeckles were disrupted. This work not only highlights a new paraspeckle-based post-transcriptional mechanism involved in circadian gene expression but also provides the list of all mRNA associated with paraspeckles in the nucleus of pituitary cells.
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Affiliation(s)
- Manon Torres
- a Aix Marseille Université, CNRS, CRN2M-UMR7286, Faculté de Médecine Nord , Marseille , France
| | - Denis Becquet
- a Aix Marseille Université, CNRS, CRN2M-UMR7286, Faculté de Médecine Nord , Marseille , France
| | - Marie-Pierre Blanchard
- a Aix Marseille Université, CNRS, CRN2M-UMR7286, Faculté de Médecine Nord , Marseille , France
| | - Séverine Guillen
- a Aix Marseille Université, CNRS, CRN2M-UMR7286, Faculté de Médecine Nord , Marseille , France
| | - Bénédicte Boyer
- a Aix Marseille Université, CNRS, CRN2M-UMR7286, Faculté de Médecine Nord , Marseille , France
| | - Mathias Moreno
- a Aix Marseille Université, CNRS, CRN2M-UMR7286, Faculté de Médecine Nord , Marseille , France
| | - Jean-Louis Franc
- a Aix Marseille Université, CNRS, CRN2M-UMR7286, Faculté de Médecine Nord , Marseille , France
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15
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Larriba Y, Rueda C, Fernández MA, Peddada SD. Order restricted inference for oscillatory systems for detecting rhythmic signals. Nucleic Acids Res 2016; 44:e163. [PMID: 27596593 PMCID: PMC5159537 DOI: 10.1093/nar/gkw771] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Revised: 07/28/2016] [Accepted: 08/23/2016] [Indexed: 12/29/2022] Open
Abstract
MOTIVATION Many biological processes, such as cell cycle, circadian clock, menstrual cycles, are governed by oscillatory systems consisting of numerous components that exhibit rhythmic patterns over time. It is not always easy to identify such rhythmic components. For example, it is a challenging problem to identify circadian genes in a given tissue using time-course gene expression data. There is a great potential for misclassifying non-rhythmic as rhythmic genes and vice versa. This has been a problem of considerable interest in recent years. In this article we develop a constrained inference based methodology called Order Restricted Inference for Oscillatory Systems (ORIOS) to detect rhythmic signals. Instead of using mathematical functions (e.g. sinusoidal) to describe shape of rhythmic signals, ORIOS uses mathematical inequalities. Consequently, it is robust and not limited by the biologist's choice of the mathematical model. We studied the performance of ORIOS using simulated as well as real data obtained from mouse liver, pituitary gland and data from NIH3T3, U2OS cell lines. Our results suggest that, for a broad collection of patterns of gene expression, ORIOS has substantially higher power to detect true rhythmic genes in comparison to some popular methods, while also declaring substantially fewer non-rhythmic genes as rhythmic. AVAILABILITY AND IMPLEMENTATION A user friendly code implemented in R language can be downloaded from http://www.niehs.nih.gov/research/atniehs/labs/bb/staff/peddada/index.cfm CONTACT: peddada@niehs.nih.gov.
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Affiliation(s)
- Yolanda Larriba
- Departamento de Estadística e Investigación Operativa, Universidad de Valladolid, Paseo de Belén 7, 47011 Valladolid, Spain
| | - Cristina Rueda
- Departamento de Estadística e Investigación Operativa, Universidad de Valladolid, Paseo de Belén 7, 47011 Valladolid, Spain
| | - Miguel A Fernández
- Departamento de Estadística e Investigación Operativa, Universidad de Valladolid, Paseo de Belén 7, 47011 Valladolid, Spain
| | - Shyamal D Peddada
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences (NIEHS), Alexander Dr., RTP, NC 27709, USA
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16
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Torres M, Becquet D, Blanchard MP, Guillen S, Boyer B, Moreno M, Franc JL, François-Bellan AM. Circadian RNA expression elicited by 3'-UTR IRAlu-paraspeckle associated elements. eLife 2016; 5. [PMID: 27441387 PMCID: PMC4987140 DOI: 10.7554/elife.14837] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Accepted: 07/20/2016] [Indexed: 12/31/2022] Open
Abstract
Paraspeckles are nuclear bodies form around the long non-coding RNA, Neat1, and RNA-binding proteins. While their role is not fully understood, they are believed to control gene expression at a post-transcriptional level by means of the nuclear retention of mRNA containing in their 3’-UTR inverted repeats of Alu sequences (IRAlu). In this study, we found that, in pituitary cells, all components of paraspeckles including four major proteins and Neat1 displayed a circadian expression pattern. Furthermore the insertion of IRAlu at the 3’-UTR of the EGFP cDNA led to a rhythmic circadian nuclear retention of the egfp mRNA that was lost when paraspeckles were disrupted whereas insertion of a single antisense Alu had only a weak effect. Using real-time video-microscopy, these IRAlu were further shown to drive a circadian expression of EGFP protein. This study shows that paraspeckles, thanks to their circadian expression, control circadian gene expression at a post-transcriptional level. DOI:http://dx.doi.org/10.7554/eLife.14837.001 Many biological features of animals, including body temperature and hormone levels, follow daily rhythms that repeat every 24 hours. These so-called circadian rhythms are driven by an internal body clock and are essential for the organism to adapt to the daily cycle of light and dark. Circadian rhythms also take place inside individual cells – for example, the amount of a given protein in a cell often rises and falls over each 24-hour period. To generate these daily fluctuations, the processes used to make proteins based on the instructions encoded within a gene must be carefully controlled. Genes are first copied or ‘transcribed' into intermediate molecules called messenger RNAs (mRNAs). These mRNA molecules must then travel out of the cell’s nucleus before they can be de-coded to produce proteins. This means that daily fluctuations in mRNA and protein levels could occur because the rate at which the DNA is transcribed fluctuates or because controlling the steps that occur after transcription. However it is not clear how much these post-transcriptional steps contribute to circadian rhythms inside cells. Recently, structures called paraspeckles were seen inside the nucleus. These structures are made from a long RNA molecule that does not code for a protein, and a number of proteins that can bind mRNA molecules. Paraspeckles are thought to prevent certain mRNAs from leaving the nucleus and therefore stop them from being decoded to make proteins. Torres et al. have now investigated whether paraspeckles may play a role in circadian rhythms. Torres et al. looked at the long non-coding RNA and several proteins that are known to be components of paraspeckles in cells taken from the pituitary glands of rats using a variety of techniques. These cells were chosen because they were known to have a working circadian clock. The analysis showed that the levels of these components, as well as the number of paraspeckles within the nucleus, changed over the course of a daily cycle. Torres et al. then confirmed that mRNAs containing a sequence that is known to recruit mRNAs to paraspeckes (the IRAlu sequence) could be also retained in the nucleus or released with a circadian rhythm. This pattern was lost when the paraspeckles were disrupted. These findings suggest that daily fluctuations in protein levels can be post-transcriptionally controlled by paraspeckles rhythmically retaining mRNAs in the nucleus. Future studies could explore whether it may be possible to control circadian rhythms by targeting the paraspeckles, which could help to improve conditions where the internal body clock goes wrong. DOI:http://dx.doi.org/10.7554/eLife.14837.002
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Affiliation(s)
- Manon Torres
- Faculté de Médecine Nord, Aix Marseille Université, CNRS, CRN2M-UMR7286, Marseille, France
| | - Denis Becquet
- Faculté de Médecine Nord, Aix Marseille Université, CNRS, CRN2M-UMR7286, Marseille, France
| | - Marie-Pierre Blanchard
- Faculté de Médecine Nord, Aix Marseille Université, CNRS, CRN2M-UMR7286, Marseille, France
| | - Séverine Guillen
- Faculté de Médecine Nord, Aix Marseille Université, CNRS, CRN2M-UMR7286, Marseille, France
| | - Bénédicte Boyer
- Faculté de Médecine Nord, Aix Marseille Université, CNRS, CRN2M-UMR7286, Marseille, France
| | - Mathias Moreno
- Faculté de Médecine Nord, Aix Marseille Université, CNRS, CRN2M-UMR7286, Marseille, France
| | - Jean-Louis Franc
- Faculté de Médecine Nord, Aix Marseille Université, CNRS, CRN2M-UMR7286, Marseille, France
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17
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Yan L, Silver R. Neuroendocrine underpinnings of sex differences in circadian timing systems. J Steroid Biochem Mol Biol 2016; 160:118-26. [PMID: 26472554 PMCID: PMC4841755 DOI: 10.1016/j.jsbmb.2015.10.007] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Revised: 10/04/2015] [Accepted: 10/08/2015] [Indexed: 01/05/2023]
Abstract
There are compelling reasons to study the role of steroids and sex differences in the circadian timing system. A solid history of research demonstrates the ubiquity of circadian changes that impact virtually all behavioral and biological responses. Furthermore, steroid hormones can modulate every attribute of circadian responses including the period, amplitude and phase. Finally, desynchronization of circadian rhythmicity, and either enhancing or damping amplitude of various circadian responses can produce different effects in the sexes. Studies of the neuroendocrine underpinnings of circadian timing systems and underlying sex differences have paralleled the overall development of the field as a whole. Early experimental studies established the ubiquity of circadian rhythms by cataloging daily and seasonal changes in whole organism responses. The next generation of experiments demonstrated that daily changes are not a result of environmental synchronizing cues, and are internally orchestrated, and that these differ in the sexes. This work was followed by the revelation of molecular circadian rhythms within individual cells. At present, there is a proliferation of work on the consequences of these daily oscillations in health and in disease, and awareness that these may differ in the sexes. In the present discourse we describe the paradigms used to examine circadian oscillation, to characterize how these internal timing signals are synchronized to local environmental conditions, and how hormones of gonadal and/or adrenal origin modulate circadian responses. Evidence pointing to endocrinologically and genetically mediated sex differences in circadian timing systems can be seen at many levels of the neuroendocrine and endocrine systems, from the cell, the gland and organ, and to whole animal behavior, including sleep/wake or rest/activity cycles, responses to external stimuli, and responses to drugs. We review evidence indicating that the analysis of the circadian timing system is amenable to experimental analysis at many levels of the neuraxis, and on several different time scales, rendering it especially useful for the exploration of mechanisms associated with sex differences.
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Affiliation(s)
- Lily Yan
- Department of Psychology, Michigan State University, East Lansing, MI 48824, USA; Neuroscience Program, Michigan State University, East Lansing, MI 48824, USA.
| | - Rae Silver
- Psychology Department, Barnard College, New York, NY 10027, USA; Department of Psychology, Columbia University, New York, NY 10027, USA; Department of Pathology and Cell Biology, Columbia University Health Sciences, New York, NY 10032, USA
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18
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Schroder E, Hodge B, Riley L, Zhang X, Esser K. Reply from Elizabeth Schroder, Brian Hodge, Lance Riley, Xiping Zhang and Karyn Esser. J Physiol 2016; 594:3163-4. [DOI: 10.1113/jp272165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2016] [Accepted: 01/29/2016] [Indexed: 11/08/2022] Open
Affiliation(s)
- Elizabeth Schroder
- Center for Muscle Biology and Department of Physiology; College of Medicine, University of Kentucky; Lexington KY USA
| | - Brian Hodge
- Center for Muscle Biology and Department of Physiology; College of Medicine, University of Kentucky; Lexington KY USA
| | - Lance Riley
- Center for Muscle Biology and Department of Physiology; College of Medicine, University of Kentucky; Lexington KY USA
| | - Xiping Zhang
- Center for Muscle Biology and Department of Physiology; College of Medicine, University of Kentucky; Lexington KY USA
| | - Karyn Esser
- Center for Muscle Biology and Department of Physiology; College of Medicine, University of Kentucky; Lexington KY USA
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19
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Lück S, Westermark PO. Circadian mRNA expression: insights from modeling and transcriptomics. Cell Mol Life Sci 2016; 73:497-521. [PMID: 26496725 PMCID: PMC11108398 DOI: 10.1007/s00018-015-2072-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 10/13/2015] [Accepted: 10/14/2015] [Indexed: 01/08/2023]
Abstract
Circadian clocks synchronize organisms to the 24 h rhythms of the environment. These clocks persist under constant conditions, have their origin at the cellular level, and produce an output of rhythmic mRNA expression affecting thousands of transcripts in many mammalian cell types. Here, we review the charting of circadian output rhythms in mRNA expression, focusing on mammals. We emphasize the challenges in statistics, interpretation, and quantitative descriptions that such investigations have faced and continue to face, and outline remaining outstanding questions.
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Affiliation(s)
- Sarah Lück
- Institute for Theoretical Biology, Charité - Universitätsmedizin Berlin, Invalidenstrasse 43, 10115, Berlin, Germany
| | - Pål O Westermark
- Institute for Theoretical Biology, Charité - Universitätsmedizin Berlin, Invalidenstrasse 43, 10115, Berlin, Germany.
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20
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Abbondante S, Eckel-Mahan KL, Ceglia NJ, Baldi P, Sassone-Corsi P. Comparative Circadian Metabolomics Reveal Differential Effects of Nutritional Challenge in the Serum and Liver. J Biol Chem 2015; 291:2812-28. [PMID: 26644470 DOI: 10.1074/jbc.m115.681130] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Indexed: 01/07/2023] Open
Abstract
Diagnosis and therapeutic interventions in pathological conditions rely upon clinical monitoring of key metabolites in the serum. Recent studies show that a wide range of metabolic pathways are controlled by circadian rhythms whose oscillation is affected by nutritional challenges, underscoring the importance of assessing a temporal window for clinical testing and thereby questioning the accuracy of the reading of critical pathological markers in circulation. We have been interested in studying the communication between peripheral tissues under metabolic homeostasis perturbation. Here we present a comparative circadian metabolomic analysis on serum and liver in mice under high fat diet. Our data reveal that the nutritional challenge induces a loss of serum metabolite rhythmicity compared with liver, indicating a circadian misalignment between the tissues analyzed. Importantly, our results show that the levels of serum metabolites do not reflect the circadian liver metabolic signature or the effect of nutritional challenge. This notion reveals the possibility that misleading reads of metabolites in circulation may result in misdiagnosis and improper treatments. Our findings also demonstrate a tissue-specific and time-dependent disruption of metabolic homeostasis in response to altered nutrition.
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Affiliation(s)
- Serena Abbondante
- From the Center for Epigenetics and Metabolism, U904 INSERM, and the Department of Biological Chemistry, University of California, Irvine, California 92697-4625 and
| | - Kristin L Eckel-Mahan
- From the Center for Epigenetics and Metabolism, U904 INSERM, and the Department of Biological Chemistry, University of California, Irvine, California 92697-4625 and
| | - Nicholas J Ceglia
- the Department of Biological Chemistry, University of California, Irvine, California 92697-4625 and the Institute for Genomics and Bioinformatics, School of Information and Computer Sciences, University of California, Irvine, California 92697-3435
| | - Pierre Baldi
- the Department of Biological Chemistry, University of California, Irvine, California 92697-4625 and the Institute for Genomics and Bioinformatics, School of Information and Computer Sciences, University of California, Irvine, California 92697-3435
| | - Paolo Sassone-Corsi
- From the Center for Epigenetics and Metabolism, U904 INSERM, and the Department of Biological Chemistry, University of California, Irvine, California 92697-4625 and
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21
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Wu G, Zhu J, Yu J, Zhou L, Huang JZ, Zhang Z. Evaluation of five methods for genome-wide circadian gene identification. J Biol Rhythms 2015; 29:231-42. [PMID: 25238853 DOI: 10.1177/0748730414537788] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Identification of circadian-regulated genes based on temporal transcriptome data is important for studying the regulation mechanism of the circadian system. However, various computational methods adopting different strategies for the identification of cycling transcripts usually yield inconsistent results even for the same dataset, making it challenging to choose the optimal method for a specific circadian study. To address this challenge, we evaluate 5 popular methods, including ARSER (ARS), COSOPT (COS), Fisher's G test (FIS), HAYSTACK (HAY), and JTK_CYCLE (JTK), based on both simulated and empirical datasets. Our results show that increasing the number of total samples (through improving sampling frequency or lengthening the sampling time window) is beneficial for computational methods to accurately identify circadian transcripts and measure circadian phase. For a given number of total samples, higher sampling frequency is more important for HAY and JTK, and the longer sampling time window is more crucial for ARS and COS, as testified on simulated and empirical datasets from which circadian signals are computationally identified. In addition, the preference of higher sampling frequency or the longer sampling time window is also obvious for JTK, ARS, and COS in estimating circadian phases of simulated periodic profiles. Our results also indicate that attention should be paid to the significance threshold that is used for each method in selecting circadian genes, especially when analyzing the same empirical dataset with 2 or more methods. To summarize, for any study involving genome-wide identification of circadian genes from transcriptome data, our evaluation results provide suggestions for the selection of an optimal method based on specific goal and experimental design.
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Affiliation(s)
- Gang Wu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Jiang Zhu
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Jun Yu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Lan Zhou
- Department of Statistics, Texas A&M University, College Station, Texas, USA
| | - Jianhua Z Huang
- Department of Statistics, Texas A&M University, College Station, Texas, USA
| | - Zhang Zhang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
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22
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Hodge BA, Wen Y, Riley LA, Zhang X, England JH, Harfmann BD, Schroder EA, Esser KA. The endogenous molecular clock orchestrates the temporal separation of substrate metabolism in skeletal muscle. Skelet Muscle 2015; 5:17. [PMID: 26000164 PMCID: PMC4440511 DOI: 10.1186/s13395-015-0039-5] [Citation(s) in RCA: 111] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Accepted: 04/13/2015] [Indexed: 01/04/2023] Open
Abstract
Background Skeletal muscle is a major contributor to whole-body metabolism as it serves as a depot for both glucose and amino acids, and is a highly metabolically active tissue. Within skeletal muscle exists an intrinsic molecular clock mechanism that regulates the timing of physiological processes. A key function of the clock is to regulate the timing of metabolic processes to anticipate time of day changes in environmental conditions. The purpose of this study was to identify metabolic genes that are expressed in a circadian manner and determine if these genes are regulated downstream of the intrinsic molecular clock by assaying gene expression in an inducible skeletal muscle-specific Bmal1 knockout mouse model (iMS-Bmal1−/−). Methods We used circadian statistics to analyze a publicly available, high-resolution time-course skeletal muscle expression dataset. Gene ontology analysis was utilized to identify enriched biological processes in the skeletal muscle circadian transcriptome. We generated a tamoxifen-inducible skeletal muscle-specific Bmal1 knockout mouse model and performed a time-course microarray experiment to identify gene expression changes downstream of the molecular clock. Wheel activity monitoring was used to assess circadian behavioral rhythms in iMS-Bmal1−/− and control iMS-Bmal1+/+ mice. Results The skeletal muscle circadian transcriptome was highly enriched for metabolic processes. Acrophase analysis of circadian metabolic genes revealed a temporal separation of genes involved in substrate utilization and storage over a 24-h period. A number of circadian metabolic genes were differentially expressed in the skeletal muscle of the iMS-Bmal1−/− mice. The iMS-Bmal1−/− mice displayed circadian behavioral rhythms indistinguishable from iMS-Bmal1+/+ mice. We also observed a gene signature indicative of a fast to slow fiber-type shift and a more oxidative skeletal muscle in the iMS-Bmal1−/− model. Conclusions These data provide evidence that the intrinsic molecular clock in skeletal muscle temporally regulates genes involved in the utilization and storage of substrates independent of circadian activity. Disruption of this mechanism caused by phase shifts (that is, social jetlag) or night eating may ultimately diminish skeletal muscle’s ability to efficiently maintain metabolic homeostasis over a 24-h period. Electronic supplementary material The online version of this article (doi:10.1186/s13395-015-0039-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Brian A Hodge
- Department of Physiology, College of Medicine, University of Kentucky, MS 508, 800 Rose Street, Lexington, KY 40536 USA ; Center for Muscle Biology, University of Kentucky, 800 Rose Street, Lexington, KY 40536 USA
| | - Yuan Wen
- Department of Physiology, College of Medicine, University of Kentucky, MS 508, 800 Rose Street, Lexington, KY 40536 USA ; Center for Muscle Biology, University of Kentucky, 800 Rose Street, Lexington, KY 40536 USA
| | - Lance A Riley
- Department of Physiology, College of Medicine, University of Kentucky, MS 508, 800 Rose Street, Lexington, KY 40536 USA ; Center for Muscle Biology, University of Kentucky, 800 Rose Street, Lexington, KY 40536 USA
| | - Xiping Zhang
- Department of Physiology, College of Medicine, University of Kentucky, MS 508, 800 Rose Street, Lexington, KY 40536 USA ; Center for Muscle Biology, University of Kentucky, 800 Rose Street, Lexington, KY 40536 USA
| | - Jonathan H England
- Department of Physiology, College of Medicine, University of Kentucky, MS 508, 800 Rose Street, Lexington, KY 40536 USA ; Center for Muscle Biology, University of Kentucky, 800 Rose Street, Lexington, KY 40536 USA
| | - Brianna D Harfmann
- Department of Physiology, College of Medicine, University of Kentucky, MS 508, 800 Rose Street, Lexington, KY 40536 USA ; Center for Muscle Biology, University of Kentucky, 800 Rose Street, Lexington, KY 40536 USA
| | - Elizabeth A Schroder
- Department of Physiology, College of Medicine, University of Kentucky, MS 508, 800 Rose Street, Lexington, KY 40536 USA ; Center for Muscle Biology, University of Kentucky, 800 Rose Street, Lexington, KY 40536 USA
| | - Karyn A Esser
- Department of Physiology, College of Medicine, University of Kentucky, MS 508, 800 Rose Street, Lexington, KY 40536 USA ; Center for Muscle Biology, University of Kentucky, 800 Rose Street, Lexington, KY 40536 USA
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23
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Lin XW, Blum ID, Storch KF. Clocks within the Master Gland: Hypophyseal Rhythms and Their Physiological Significance. J Biol Rhythms 2015; 30:263-76. [PMID: 25926680 DOI: 10.1177/0748730415580881] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Various aspects of mammalian endocrine physiology show a time-of-day variation with a period of 24 h, which represents an adaptation to the daily environmental fluctuations resulting from the rotation of the earth. These 24-h rhythms in hormone abundance and consequently hormone function may rely on rhythmic signals produced by the master circadian clock, which resides in the suprachiasmatic nucleus and is thought to chiefly dictate the pattern of rest and activity in mammals in conjunction with the light/dark (LD) cycle. However, it is likely that clocks intrinsic to elements of the endocrine axes also contribute to the 24-h rhythms in hormone function. Here we review the evidence for rhythm generation in the endocrine master gland, the pituitary, and its physiological significance in the context of endocrine axes regulation and function.
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Affiliation(s)
- Xue-Wei Lin
- Department of Psychiatry, McGill University, Montreal, Quebec, Canada Douglas Mental Health University Institute, Montreal, Quebec, Canada Integrated Program in Neuroscience, McGill University, Montreal, Quebec, Canada
| | - Ian David Blum
- Department of Psychiatry, McGill University, Montreal, Quebec, Canada Douglas Mental Health University Institute, Montreal, Quebec, Canada Integrated Program in Neuroscience, McGill University, Montreal, Quebec, Canada
| | - Kai-Florian Storch
- Department of Psychiatry, McGill University, Montreal, Quebec, Canada Douglas Mental Health University Institute, Montreal, Quebec, Canada
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24
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Lin LL, Huang HC, Juan HF. Circadian systems biology in Metazoa. Brief Bioinform 2015; 16:1008-24. [PMID: 25758249 DOI: 10.1093/bib/bbv006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2014] [Indexed: 12/30/2022] Open
Abstract
Systems biology, which can be defined as integrative biology, comprises multistage processes that can be used to understand components of complex biological systems of living organisms and provides hierarchical information to decoding life. Using systems biology approaches such as genomics, transcriptomics and proteomics, it is now possible to delineate more complicated interactions between circadian control systems and diseases. The circadian rhythm is a multiscale phenomenon existing within the body that influences numerous physiological activities such as changes in gene expression, protein turnover, metabolism and human behavior. In this review, we describe the relationships between the circadian control system and its related genes or proteins, and circadian rhythm disorders in systems biology studies. To maintain and modulate circadian oscillation, cells possess elaborative feedback loops composed of circadian core proteins that regulate the expression of other genes through their transcriptional activities. The disruption of these rhythms has been reported to be associated with diseases such as arrhythmia, obesity, insulin resistance, carcinogenesis and disruptions in natural oscillations in the control of cell growth. This review demonstrates that lifestyle is considered as a fundamental factor that modifies circadian rhythm, and the development of dysfunctions and diseases could be regulated by an underlying expression network with multiple circadian-associated signals.
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25
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Abstract
Metabolism and physiology in animals show diurnal rhythm to adapt to the daily cycles of activity-rest and the associated rhythm in feeding and fasting. Accordingly, gene expression, protein activities, and numerous metabolites show daily rhythm in abundance. The significance of these rhythms in promoting healthy lifespan and preventing disease has recently come to light. Mice with genetic disruption of circadian rhythm, mice, and humans under shift-work paradigm, and mice fed high-fat diet ad libitum exhibit chronic disruption of feeding-fasting rhythm and dampened daily rhythms in physiology, metabolism, and gene expression. These dampened rhythms are associated with metabolic diseases. Conversely, time-restricted feeding, in which mice are fed for certain number of hours every day, restores rhythms and can prevent obesity and metabolic diseases even when mice are fed high-fat diet. These observations seek mechanistic explanations, which will require careful experiments in which feeding duration, genotype, nutrient, and feeding time relative to light:dark cycle will be manipulated and molecular changes in peripheral organs and a few brain regions will be assessed. This chapter will primarily focus on the use of mouse as an experimental animal and the experimental setup so that the molecular readouts can be better interpreted.
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Affiliation(s)
- Megumi Hatori
- School of Medicine, Keio University, Shinjuku-ku, Tokyo, Japan
| | - Satchidananda Panda
- Regulatory Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA.
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26
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Abstract
Circadian rhythms are daily endogenous oscillations of behavior, metabolism, and physiology. At a molecular level, these oscillations are generated by transcriptional-translational feedback loops composed of core clock genes. In turn, core clock genes drive the rhythmic accumulation of downstream outputs-termed clock-controlled genes (CCGs)-whose rhythmic translation and function ultimately underlie daily oscillations at a cellular and organismal level. Given the circadian clock's profound influence on human health and behavior, considerable efforts have been made to systematically identify CCGs. The recent development of next-generation sequencing has dramatically expanded our ability to study the expression, processing, and stability of rhythmically expressed mRNAs. Nevertheless, like any new technology, there are many technical issues to be addressed. Here, we discuss considerations for studying circadian rhythms using genome scale transcriptional profiling, with a particular emphasis on RNA sequencing. We make a number of practical recommendations-including the choice of sampling density, read depth, alignment algorithms, read-depth normalization, and cycling detection algorithms-based on computational simulations and our experience from previous studies. We believe that these results will be of interest to the circadian field and help investigators design experiments to derive most values from these large and complex data sets.
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Affiliation(s)
- Jiajia Li
- Department of Biology, University of Missouri-St. Louis, St. Louis, Missouri, USA
| | - Gregory R Grant
- Department of Genetics, University of Pennsylvania, Philadelphia, Pennsylvania, USA; Penn Center for Bioinformatics, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - John B Hogenesch
- Department of Pharmacology, Institute for Translational Medicine and Therapeutics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, USA
| | - Michael E Hughes
- Department of Biology, University of Missouri-St. Louis, St. Louis, Missouri, USA.
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27
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Kim JH, White SL, Devlin RH. Interaction of growth hormone overexpression and nutritional status on pituitary gland clock gene expression in coho salmon,Oncorhynchus kisutch. Chronobiol Int 2014; 32:113-27. [DOI: 10.3109/07420528.2014.958160] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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28
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Markova-Car EP, Jurišić D, Ilić N, Kraljević Pavelić S. Running for time: circadian rhythms and melanoma. Tumour Biol 2014; 35:8359-68. [PMID: 24729125 DOI: 10.1007/s13277-014-1904-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Accepted: 03/27/2014] [Indexed: 12/22/2022] Open
Abstract
Circadian timing system includes an input pathway transmitting environmental signals to a core oscillator that generates circadian signals responsible for the peripheral physiological or behavioural events. Circadian 24-h rhythms regulate diverse physiologic processes. Deregulation of these rhythms is associated with a number of pathogenic conditions including depression, diabetes, metabolic syndrome and cancer. Melanoma is a less common type of skin cancer yet more aggressive often with a lethal ending. However, little is known about circadian control in melanoma and exact functional associations between core clock genes and development of melanoma skin cancer. This paper, therefore, comprehensively analyses current literature data on the involvement of circadian clock components in melanoma development. In particular, the role of circadian rhythm deregulation is discussed in the context of DNA repair mechanisms and influence of UV radiation and artificial light exposure on cancer development. The role of arylalkylamine N-acetyltransferase (AANAT) enzyme and impact of melatonin, as a major output factor of circadian rhythm, and its protective role in melanoma are discussed in details. We hypothesise that further understanding of clock genes' involvement and circadian regulation might foster discoveries in the field of melanoma diagnostics and treatment.
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Affiliation(s)
- Elitza P Markova-Car
- Department of Biotechnology, University of Rijeka, Radmile Matejčić 2, 51000, Rijeka, Croatia,
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29
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Anafi RC, Lee Y, Sato TK, Venkataraman A, Ramanathan C, Kavakli IH, Hughes ME, Baggs JE, Growe J, Liu AC, Kim J, Hogenesch JB. Machine learning helps identify CHRONO as a circadian clock component. PLoS Biol 2014; 12:e1001840. [PMID: 24737000 PMCID: PMC3988006 DOI: 10.1371/journal.pbio.1001840] [Citation(s) in RCA: 95] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2013] [Accepted: 03/07/2014] [Indexed: 12/03/2022] Open
Abstract
Over the last decades, researchers have characterized a set of "clock genes" that drive daily rhythms in physiology and behavior. This arduous work has yielded results with far-reaching consequences in metabolic, psychiatric, and neoplastic disorders. Recent attempts to expand our understanding of circadian regulation have moved beyond the mutagenesis screens that identified the first clock components, employing higher throughput genomic and proteomic techniques. In order to further accelerate clock gene discovery, we utilized a computer-assisted approach to identify and prioritize candidate clock components. We used a simple form of probabilistic machine learning to integrate biologically relevant, genome-scale data and ranked genes on their similarity to known clock components. We then used a secondary experimental screen to characterize the top candidates. We found that several physically interact with known clock components in a mammalian two-hybrid screen and modulate in vitro cellular rhythms in an immortalized mouse fibroblast line (NIH 3T3). One candidate, Gene Model 129, interacts with BMAL1 and functionally represses the key driver of molecular rhythms, the BMAL1/CLOCK transcriptional complex. Given these results, we have renamed the gene CHRONO (computationally highlighted repressor of the network oscillator). Bi-molecular fluorescence complementation and co-immunoprecipitation demonstrate that CHRONO represses by abrogating the binding of BMAL1 to its transcriptional co-activator CBP. Most importantly, CHRONO knockout mice display a prolonged free-running circadian period similar to, or more drastic than, six other clock components. We conclude that CHRONO is a functional clock component providing a new layer of control on circadian molecular dynamics.
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Affiliation(s)
- Ron C. Anafi
- Division of Sleep Medicine, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
- Center for Sleep and Circadian Neurobiology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Yool Lee
- Department of Pharmacology and the Institute for Translational Medicine and Therapeutics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Trey K. Sato
- Department of Pharmacology and the Institute for Translational Medicine and Therapeutics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Anand Venkataraman
- Department of Pharmacology and the Institute for Translational Medicine and Therapeutics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Chidambaram Ramanathan
- Department of Biological Sciences, University of Memphis, Memphis, Tennessee, United States of America
| | - Ibrahim H. Kavakli
- Department of Chemical and Biological Engineering, Koc University, Istanbul, Turkey
| | - Michael E. Hughes
- Department of Biology, University of Missouri–St. Louis, St. Louis, Missouri, United States of America
| | - Julie E. Baggs
- Department of Pharmacology, Morehouse School of Medicine, Atlanta, Georgia, United States of America
| | - Jacqueline Growe
- Division of Sleep Medicine, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
- Center for Sleep and Circadian Neurobiology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Andrew C. Liu
- Department of Biological Sciences, University of Memphis, Memphis, Tennessee, United States of America
| | - Junhyong Kim
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - John B. Hogenesch
- Center for Sleep and Circadian Neurobiology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
- Department of Pharmacology and the Institute for Translational Medicine and Therapeutics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
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Karantanos T, Theodoropoulos G, Pektasides D, Gazouli M. Clock genes: Their role in colorectal cancer. World J Gastroenterol 2014; 20:1986-1992. [PMID: 24587674 PMCID: PMC3934468 DOI: 10.3748/wjg.v20.i8.1986] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/20/2013] [Revised: 09/23/2013] [Accepted: 01/20/2014] [Indexed: 02/07/2023] Open
Abstract
Clock genes create a complicated molecular time-keeping system consisting of multiple positive and negative feedback loops at transcriptional and translational levels. This circadian system coordinates and regulates multiple cellular procedures implicated in cancer development such as metabolism, cell cycle and DNA damage response. Recent data support that molecules such as CLOCK1, BMAL1 and PER and CRY proteins have various effects on c-Myc/p21 and Wnt/β-catenin pathways and influence multiple steps of DNA damage response playing a critical role in the preservation of genomic integrity in normal and cancer cells. Notably, all these events have already been related to the development and progression of colorectal cancer (CRC). Recent data highlight critical correlations between clock genes’ expression and pathogenesis, progression, aggressiveness and prognosis of CRC. Increased expression of positive regulators of this circadian system such as BMAL1 has been related to decrease overall survival while decreased expression of negative regulators such as PER2 and PER3 is connected with poorer differentiation, increased aggressiveness and worse prognosis. The implications of these molecules in DNA repair systems explain their involvement in the development of CRC but at the same time provide us with novel targets for modern therapeutic approaches for patients with advanced CRC.
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A contemporary view of genes and behavior: complex systems and interactions. ADVANCES IN CHILD DEVELOPMENT AND BEHAVIOR 2013; 44:285-306. [PMID: 23834009 DOI: 10.1016/b978-0-12-397947-6.00010-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Several large-scale searches for genes that influence complex human traits, such as intelligence and personality, in the normal range of variation have failed to identify even one gene that makes a significant difference. All previously published claims for genetic influences of this kind now appear to have been false positives. For more serious psychiatric and medical disorders such as schizophrenia and autism, several genes have been found where a rare mutation contributes to abnormal behavior, but in many instances they are de novo mutations not obtained from a parent. Despite the many disappointments in the search for genes influencing human behavior, the field of molecular genetics has made remarkable progress to the extent that several broadly applicable principles can now be affirmed. These principles show how development is regulated by networks of interacting genes that function in an environmental context. They invalidate several key assumptions of statistical genetic analysis that are made when estimating heritability. There is now a need to reform the teaching of genetics to our students and to restrict the funding of further searches for elusive genes that account for so little variance in normal behaviors.
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Abstract
Circadian rhythms occur in almost all species and control vital aspects of our physiology, from sleeping and waking to neurotransmitter secretion and cellular metabolism. Epidemiological studies from recent decades have supported a unique role for circadian rhythm in metabolism. As evidenced by individuals working night or rotating shifts, but also by rodent models of circadian arrhythmia, disruption of the circadian cycle is strongly associated with metabolic imbalance. Some genetically engineered mouse models of circadian rhythmicity are obese and show hallmark signs of the metabolic syndrome. Whether these phenotypes are due to the loss of distinct circadian clock genes within a specific tissue versus the disruption of rhythmic physiological activities (such as eating and sleeping) remains a cynosure within the fields of chronobiology and metabolism. Becoming more apparent is that from metabolites to transcription factors, the circadian clock interfaces with metabolism in numerous ways that are essential for maintaining metabolic homeostasis.
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33
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Circadian acetylome reveals regulation of mitochondrial metabolic pathways. Proc Natl Acad Sci U S A 2013; 110:3339-44. [PMID: 23341599 DOI: 10.1073/pnas.1217632110] [Citation(s) in RCA: 118] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The circadian clock is constituted by a complex molecular network that integrates a number of regulatory cues needed to maintain organismal homeostasis. To this effect, posttranslational modifications of clock proteins modulate circadian rhythms and are thought to convert physiological signals into changes in protein regulatory function. To explore reversible lysine acetylation that is dependent on the clock, we have characterized the circadian acetylome in WT and Clock-deficient (Clock(-/-)) mouse liver by quantitative mass spectrometry. Our analysis revealed that a number of mitochondrial proteins involved in metabolic pathways are heavily influenced by clock-driven acetylation. Pathways such as glycolysis/gluconeogenesis, citric acid cycle, amino acid metabolism, and fatty acid metabolism were found to be highly enriched hits. The significant number of metabolic pathways whose protein acetylation profile is altered in Clock(-/-) mice prompted us to link the acetylome to the circadian metabolome previously characterized in our laboratory. Changes in enzyme acetylation over the circadian cycle and the link to metabolite levels are discussed, revealing biological implications connecting the circadian clock to cellular metabolic state.
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Eckel-Mahan K, Sassone-Corsi P. Epigenetic Regulation of the Molecular Clockwork. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2013; 119:29-50. [DOI: 10.1016/b978-0-12-396971-2.00002-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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Wu G, Zhu J, He F, Wang W, Hu S, Yu J. Gene and genome parameters of mammalian liver circadian genes (LCGs). PLoS One 2012; 7:e46961. [PMID: 23071677 PMCID: PMC3468600 DOI: 10.1371/journal.pone.0046961] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2012] [Accepted: 09/07/2012] [Indexed: 11/19/2022] Open
Abstract
The mammalian circadian system controls various physiology processes and behavior responses by regulating thousands of circadian genes with rhythmic expressions. In this study, we redefined circadian-regulated genes based on published results in the mouse liver and compared them with other gene groups defined relative to circadian regulations, especially the non-circadian-regulated genes expressed in liver at multiple molecular levels from gene position to protein expression based on integrative analyses of different datasets from the literature. Based on the intra-tissue analysis, the liver circadian genes or LCGs show unique features when compared to other gene groups. First, LCGs in general have less neighboring genes and larger in both genomic and 3'-UTR lengths but shorter in CDS (coding sequence) lengths. Second, LCGs have higher mRNA and protein abundance, higher temporal expression variations, and shorter mRNA half-life. Third, more than 60% of LCGs form major co-expression clusters centered in four temporal windows: dawn, day, dusk, and night. In addition, larger and smaller LCGs are found mainly expressed in the day and night temporal windows, respectively, and we believe that LCGs are well-partitioned into the gene expression regulatory network that takes advantage of gene size, expression constraint, and chromosomal architecture. Based on inter-tissue analysis, more than half of LCGs are ubiquitously expressed in multiple tissues but only show rhythmical expression in one or limited number of tissues. LCGs show at least three-fold lower expression variations across the temporal windows than those among different tissues, and this observation suggests that temporal expression variations regulated by the circadian system is relatively subtle as compared with the tissue expression variations formed during development. Taken together, we suggest that the circadian system selects gene parameters in a cost effective way to improve tissue-specific functions by adapting temporal variations from the environment over evolutionary time scales.
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Affiliation(s)
- Gang Wu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- Graduate University of Chinese Academy of Sciences, Beijing, China
| | - Jiang Zhu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Fuhong He
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- Laboratory of Disease Genomics and Individualized Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Weiwei Wang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- Department of Medicine, University of Alberta, Edmonton, Alberta, Canada
| | - Songnian Hu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Jun Yu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- * E-mail:
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Hughes ME, Hong HK, Chong JL, Indacochea AA, Lee SS, Han M, Takahashi JS, Hogenesch JB. Brain-specific rescue of Clock reveals system-driven transcriptional rhythms in peripheral tissue. PLoS Genet 2012; 8:e1002835. [PMID: 22844252 PMCID: PMC3405989 DOI: 10.1371/journal.pgen.1002835] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2012] [Accepted: 05/29/2012] [Indexed: 11/17/2022] Open
Abstract
The circadian regulatory network is organized in a hierarchical fashion, with a central oscillator in the suprachiasmatic nuclei (SCN) orchestrating circadian oscillations in peripheral tissues. The nature of the relationship between central and peripheral oscillators, however, is poorly understood. We used the tetOFF expression system to specifically restore Clock function in the brains of Clock(Δ19) mice, which have compromised circadian clocks. Rescued mice showed normal locomotor rhythms in constant darkness, with activity period lengths approximating wildtype controls. We used microarray analysis to assess whether brain-specific rescue of circadian rhythmicity was sufficient to restore circadian transcriptional output in the liver. Compared to Clock mutants, Clock-rescue mice showed significantly larger numbers of cycling transcripts with appropriate phase and period lengths, including many components of the core circadian oscillator. This indicates that the SCN oscillator overcomes local circadian defects and signals directly to the molecular clock. Interestingly, the vast majority of core clock genes in liver were responsive to Clock expression in the SCN, suggesting that core clock genes in peripheral tissues are intrinsically sensitive to SCN cues. Nevertheless, most circadian output in the liver was absent or severely low-amplitude in Clock-rescue animals, demonstrating that the majority of peripheral transcriptional rhythms depend on a fully functional local circadian oscillator. We identified several new system-driven rhythmic genes in the liver, including Alas1 and Mfsd2. Finally, we show that 12-hour transcriptional rhythms (i.e., circadian "harmonics") are disrupted by Clock loss-of-function. Brain-specific rescue of Clock converted 12-hour rhythms into 24-hour rhythms, suggesting that signaling via the central circadian oscillator is required to generate one of the two daily peaks of expression. Based on these data, we conclude that 12-hour rhythms are driven by interactions between central and peripheral circadian oscillators.
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Affiliation(s)
- Michael E Hughes
- Department of Cellular and Molecular Physiology, Yale School of Medicine, New Haven, CT, USA
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Hughes ME, Grant GR, Paquin C, Qian J, Nitabach MN. Deep sequencing the circadian and diurnal transcriptome of Drosophila brain. Genome Res 2012; 22:1266-81. [PMID: 22472103 PMCID: PMC3396368 DOI: 10.1101/gr.128876.111] [Citation(s) in RCA: 145] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Eukaryotic circadian clocks include transcriptional/translational feedback loops that drive 24-h rhythms of transcription. These transcriptional rhythms underlie oscillations of protein abundance, thereby mediating circadian rhythms of behavior, physiology, and metabolism. Numerous studies over the last decade have used microarrays to profile circadian transcriptional rhythms in various organisms and tissues. Here we use RNA sequencing (RNA-seq) to profile the circadian transcriptome of Drosophila melanogaster brain from wild-type and period-null clock-defective animals. We identify several hundred transcripts whose abundance oscillates with 24-h periods in either constant darkness or 12 h light/dark diurnal cycles, including several noncoding RNAs (ncRNAs) that were not identified in previous microarray studies. Of particular interest are U snoRNA host genes (Uhgs), a family of diurnal cycling noncoding RNAs that encode the precursors of more than 50 box-C/D small nucleolar RNAs, key regulators of ribosomal biogenesis. Transcriptional profiling at the level of individual exons reveals alternative splice isoforms for many genes whose relative abundances are regulated by either period or circadian time, although the effect of circadian time is muted in comparison to that of period. Interestingly, period loss of function significantly alters the frequency of RNA editing at several editing sites, suggesting an unexpected link between a key circadian gene and RNA editing. We also identify tens of thousands of novel splicing events beyond those previously annotated by the modENCODE Consortium, including several that affect key circadian genes. These studies demonstrate extensive circadian control of ncRNA expression, reveal the extent of clock control of alternative splicing and RNA editing, and provide a novel, genome-wide map of splicing in Drosophila brain.
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Affiliation(s)
- Michael E Hughes
- Department of Cellular and Molecular Physiology, and Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale School of Medicine, New Haven, Connecticut 06520, USA
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Coordination of the transcriptome and metabolome by the circadian clock. Proc Natl Acad Sci U S A 2012; 109:5541-6. [PMID: 22431615 DOI: 10.1073/pnas.1118726109] [Citation(s) in RCA: 303] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The circadian clock governs a large array of physiological functions through the transcriptional control of a significant fraction of the genome. Disruption of the clock leads to metabolic disorders, including obesity and diabetes. As food is a potent zeitgeber (ZT) for peripheral clocks, metabolites are implicated as cellular transducers of circadian time for tissues such as the liver. From a comprehensive dataset of over 500 metabolites identified by mass spectrometry, we reveal the coordinate clock-controlled oscillation of many metabolites, including those within the amino acid and carbohydrate metabolic pathways as well as the lipid, nucleotide, and xenobiotic metabolic pathways. Using computational modeling, we present evidence of synergistic nodes between the circadian transcriptome and specific metabolic pathways. Validation of these nodes reveals that diverse metabolic pathways, including the uracil salvage pathway, oscillate in a circadian fashion and in a CLOCK-dependent manner. This integrated map illustrates the coherence within the circadian metabolome, transcriptome, and proteome and how these are connected through specific nodes that operate in concert to achieve metabolic homeostasis.
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Guillaumond F, Becquet D, Boyer B, Bosler O, Delaunay F, Franc JL, François-Bellan AM. DNA microarray analysis and functional profile of pituitary transcriptome under core-clock protein BMAL1 control. Chronobiol Int 2012; 29:103-30. [PMID: 22324551 DOI: 10.3109/07420528.2011.645707] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Although it is known to contain five cell types that synthesize and release hormones with a circadian pattern, the pituitary gland is poorly characterized as a circadian oscillator. By a differential microarray analysis, 252 genes were found to be differentially expressed in pituitaries from Bmal1(-/-) knockout versus wild-type mice. By integrative analyses of the data set with the Annotation, Visualization, and Integrated Discovery (DAVID) Bioinformatics Resources annotation analysis system, pituitary genes with altered expression in Bmal1(-/-) mice were dispatched among functional categories. Clusters of genes related to signaling and rhythmic processes as well as transcription regulators, in general, were found enriched in the data set, as were pathways such as circadian rhythm, transforming growth factor β (TGFβ) signaling, valine, leucine, and isoleucine degradation, and peroxisome proliferator-activated receptor (PPAR) signaling pathways. Gene Ontology term overrepresentation analyses revealed significant enrichment for genes involved in 10 key biological processes. To determine whether genes with altered expression in Bmal1(-/-) mice were actually circadian genes, we further characterized in the mouse pituitary gland the daily pattern of some of these genes, including core-clock genes. Core-clock genes and genes selected from three identified overrepresented biological processes, namely, hormone metabolic process, regulation of transcription from RNA polymerase II promoter, and cell adhesion, displayed a rhythmic pattern. Given the enrichment in genes dedicated to cell adhesion and their daily changes in the pituitary, it is hypothesized that cell-cell interactions could be involved in the transmission of information between endocrine cells, allowing rhythmic hormone outputs to be controlled in a temporally precise manner.
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Affiliation(s)
- F Guillaumond
- Aix-Marseille University , INSERM-U624, Marseille, France
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Zhou F, He X, Liu H, Zhu Y, Jin T, Chen C, Qu F, Li Y, Bao G, Chen Z, Xing J. Functional polymorphisms of circadian positive feedback regulation genes and clinical outcome of Chinese patients with resected colorectal cancer. Cancer 2012; 118:937-46. [PMID: 21773969 DOI: 10.1002/cncr.26348] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2011] [Revised: 04/25/2011] [Accepted: 05/16/2011] [Indexed: 12/14/2022]
Abstract
BACKGROUND Previous studies have demonstrated that circadian genes play a role in the development and progression of many cancers. This study aims to assess the effects of single nucleotide polymorphisms (SNPs) in circadian genes on recurrence and survival of colorectal cancer (CRC) patients. METHODS Nine functional SNPs in 3 genes (CLOCK, NPAS2, and BMAL1) on the circadian positive feedback loop were selected and genotyped using the Sequenom iPLEX genotyping system in a cohort of 411 resected Chinese CRC patients. Multivariate Cox proportional hazards model and Kaplan-Meier curve were used for the prognosis analysis. RESULTS The authors identified 2 SNPs in the CLOCK gene to be significantly associated with CRC overall survival. SNP rs3749474 exhibited a significant association with survival of CRC patients in the additive model (hazard ratio [HR], 0.55; 95% confidence interval [CI], 0.37-0.81; P = .003). In addition, patients carrying the heterozygous variant of rs1801260 had significantly increased overall survival compared with those carrying homozygous wild-type genotype (HR, 0.31; 95% CI, 0.11-0.88; P = .03). Findings from functional assay provided further biological support for these significant associations. Stratified analysis found no modifying effect of chemotherapy on the prognostic significance of both SNPs. Moreover, we observed cumulative effects of these 2 SNPs on CRC overall survival (P for trend = .01). Compared with patients carrying no unfavorable genotypes, those carrying 2 unfavorable genotypes had a 2.92-fold increased risk of death (P = .03). CONCLUSIONS The results suggest for the first time that CLOCK gene polymorphisms may serve as an independent prognostic marker for CRC patients.
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Affiliation(s)
- Feng Zhou
- Department of General Surgery, Tangdu Hospital, Xi'an, China
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Ozel AB, Srivannavit O, Rouillard JM, Gulari AE. Target concentration dependence of DNA melting temperature on oligonucleotide microarrays. Biotechnol Prog 2012; 28:556-66. [PMID: 22275183 DOI: 10.1002/btpr.1505] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2011] [Revised: 11/08/2011] [Indexed: 01/12/2023]
Abstract
The design of microarrays is currently based on studies focusing on DNA hybridization reaction in bulk solution. However, the presence of a surface to which the probe strand is attached can make the solution-based approximations invalid, resulting in sub-optimum hybridization conditions. To determine the effect of surfaces on DNA duplex formation, the authors studied the dependence of DNA melting temperature (T(m)) on target concentration. An automated system was developed to capture the melting profiles of a 25-mer perfect-match probe-target pair initially hybridized at 23°C. Target concentrations ranged from 0.0165 to 15 nM with different probe amounts (0.03-0.82 pmol on a surface area of 10(18) Å(2)), a constant probe density (5 × 10(12) molecules/cm(2)) and spacer length (15 dT). The authors found that T(m) for duplexes anchored to a surface is lower than in-solution, and this difference increases with increasing target concentration. In a representative set, a target concentration increase from 0.5 to 15 nM with 0.82 pmol of probe on the surface resulted in a T(m) decrease of 6°C when compared with a 4°C increase in solution. At very low target concentrations, a multi-melting process was observed in low temperature domains of the curves. This was attributed to the presence of truncated or mismatch probes.
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Affiliation(s)
- Ayse Bilge Ozel
- Dept. of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
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Layana C, Diambra L. Time-course analysis of cyanobacterium transcriptome: detecting oscillatory genes. PLoS One 2011; 6:e26291. [PMID: 22028849 PMCID: PMC3196541 DOI: 10.1371/journal.pone.0026291] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2011] [Accepted: 09/23/2011] [Indexed: 11/18/2022] Open
Abstract
The microarray technique allows the simultaneous measurements of the expression levels of thousands of mRNAs. By mining these data one can identify the dynamics of the gene expression time series. The detection of genes that are periodically expressed is an important step that allows us to study the regulatory mechanisms associated with the circadian cycle. The problem of finding periodicity in biological time series poses many challenges. Such challenge occurs due to the fact that the observed time series usually exhibit non-idealities, such as noise, short length, outliers and unevenly sampled time points. Consequently, the method for finding periodicity should preferably be robust against such anomalies in the data. In this paper, we propose a general and robust procedure for identifying genes with a periodic signature at a given significance level. This identification method is based on autoregressive models and the information theory. By using simulated data we show that the suggested method is capable of identifying rhythmic profiles even in the presence of noise and when the number of data points is small. By recourse of our analysis, we uncover the circadian rhythmic patterns underlying the gene expression profiles from Cyanobacterium Synechocystis.
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Affiliation(s)
- Carla Layana
- Centro Regional de Estudios Genómicos (CREG), Universidad Nacional de La Plata, Florencio Varela, Argentina
| | - Luis Diambra
- Centro Regional de Estudios Genómicos (CREG), Universidad Nacional de La Plata, Florencio Varela, Argentina
- * E-mail:
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Guillaumond F, Boyer B, Becquet D, Guillen S, Kuhn L, Garin J, Belghazi M, Bosler O, Franc J, François‐Bellan A. Chromatin remodeling as a mechanism for circadian prolactin transcription: rhythmic NONO and SFPQ recruitment to HLTF. FASEB J 2011; 25:2740-56. [DOI: 10.1096/fj.10-178616] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Fabienne Guillaumond
- Institut des Sciences Moleculaires de Marseille (ISM2)UMR6263 Université Aix‐Marseille IIIMarseilleFrance
| | - Benedicte Boyer
- Centre de Recherche en Neurobiologie et Neurophysiologie de Marseille (CRN2M)Centre National de la Recherche Scientifique (CNRS) Unité Mixte de Recherche (UMR) 6231Université Aix‐Marseille II, IIIMarseilleFrance
| | - Denis Becquet
- Centre de Recherche en Neurobiologie et Neurophysiologie de Marseille (CRN2M)Centre National de la Recherche Scientifique (CNRS) Unité Mixte de Recherche (UMR) 6231Université Aix‐Marseille II, IIIMarseilleFrance
| | - Severine Guillen
- Centre de Recherche en Neurobiologie et Neurophysiologie de Marseille (CRN2M)Centre National de la Recherche Scientifique (CNRS) Unité Mixte de Recherche (UMR) 6231Université Aix‐Marseille II, IIIMarseilleFrance
| | - Lauriane Kuhn
- Plateforme Étude de la Dynamique des Protéomes (EDyP)‐ServiceGrenobleFrance
| | - Jerome Garin
- Centre d'Analyse Protéomique de MarseilleInstitut Fédératif de Recherche (IFR) Jean‐RocheMarseilleFrance
| | - Maya Belghazi
- Plateforme Protéomique de l'Esplanade Institut de Biologie Moléculaire et Cellulaire (IBMC)StrasbourgFrance
| | - Olivier Bosler
- Centre de Recherche en Neurobiologie et Neurophysiologie de Marseille (CRN2M)Centre National de la Recherche Scientifique (CNRS) Unité Mixte de Recherche (UMR) 6231Université Aix‐Marseille II, IIIMarseilleFrance
| | - Jean‐Louis Franc
- Centre de Recherche en Neurobiologie et Neurophysiologie de Marseille (CRN2M)Centre National de la Recherche Scientifique (CNRS) Unité Mixte de Recherche (UMR) 6231Université Aix‐Marseille II, IIIMarseilleFrance
| | - Anne‐Marie François‐Bellan
- Centre de Recherche en Neurobiologie et Neurophysiologie de Marseille (CRN2M)Centre National de la Recherche Scientifique (CNRS) Unité Mixte de Recherche (UMR) 6231Université Aix‐Marseille II, IIIMarseilleFrance
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Baggs JE, Hogenesch JB. Genomics and systems approaches in the mammalian circadian clock. Curr Opin Genet Dev 2011; 20:581-7. [PMID: 20926286 DOI: 10.1016/j.gde.2010.08.009] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2010] [Revised: 08/11/2010] [Accepted: 08/31/2010] [Indexed: 11/26/2022]
Abstract
The circadian clock is an endogenous oscillator that regulates daily rhythms in behavior and physiology. In recent years, systems biology and genomics approaches re-shaped our view of the clock. Our understanding of outputs that regulate behavior and physiology has been enhanced through gene expression profiling and proteomic analyses. Systems approaches uncovered underlying principles of transcriptional regulation and robustness of the oscillator through perturbation analysis and synthetic methods. Finally, new clock components and modifiers were identified through cell-based screening efforts and proteomics.
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Affiliation(s)
- Julie E Baggs
- Department of Pharmacology, Institute for Translational Medicine and Therapeutics, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, United States
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Hughes ME, Hogenesch JB, Kornacker K. JTK_CYCLE: an efficient nonparametric algorithm for detecting rhythmic components in genome-scale data sets. J Biol Rhythms 2011; 25:372-80. [PMID: 20876817 DOI: 10.1177/0748730410379711] [Citation(s) in RCA: 743] [Impact Index Per Article: 57.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Circadian rhythms are oscillations of physiology, behavior, and metabolism that have period lengths near 24 hours. In several model organisms and humans, circadian clock genes have been characterized and found to be transcription factors. Because of this, researchers have used microarrays to characterize global regulation of gene expression and algorithmic approaches to detect cycling. This article presents a new algorithm, JTK_CYCLE, designed to efficiently identify and characterize cycling variables in large data sets. Compared with COSOPT and the Fisher's G test, two commonly used methods for detecting cycling transcripts, JTK_CYCLE distinguishes between rhythmic and nonrhythmic transcripts more reliably and efficiently. JTK_CYCLE's increased resistance to outliers results in considerably greater sensitivity and specificity. Moreover, JTK_CYCLE accurately measures the period, phase, and amplitude of cycling transcripts, facilitating downstream analyses. Finally, JTK_CYCLE is several orders of magnitude faster than COSOPT, making it ideal for large-scale data sets. JTK_CYCLE was used to analyze legacy data sets including NIH3T3 cells, which have comparatively low amplitude oscillations. JTK_CYCLE's improved power led to the identification of a novel cluster of RNA-interacting genes whose abundance is under clear circadian regulation. These data suggest that JTK_CYCLE is an ideal tool for identifying and characterizing oscillations in genome-scale data sets.
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Affiliation(s)
- Michael E Hughes
- Department of Cellular and Molecular Physiology, Yale School of Medicine, New Haven, CT, USA
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Bur IM, Zouaoui S, Fontanaud P, Coutry N, Molino F, Martin AO, Mollard P, Bonnefont X. The comparison between circadian oscillators in mouse liver and pituitary gland reveals different integration of feeding and light schedules. PLoS One 2010; 5:e15316. [PMID: 21179516 PMCID: PMC3002272 DOI: 10.1371/journal.pone.0015316] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2010] [Accepted: 11/09/2010] [Indexed: 12/28/2022] Open
Abstract
The mammalian circadian system is composed of multiple peripheral clocks that are synchronized by a central pacemaker in the suprachiasmatic nuclei of the hypothalamus. This system keeps track of the external world rhythms through entrainment by various time cues, such as the light-dark cycle and the feeding schedule. Alterations of photoperiod and meal time modulate the phase coupling between central and peripheral oscillators. In this study, we used real-time quantitative PCR to assess circadian clock gene expression in the liver and pituitary gland from mice raised under various photoperiods, or under a temporal restricted feeding protocol. Our results revealed unexpected differences between both organs. Whereas the liver oscillator always tracked meal time, the pituitary circadian clockwork showed an intermediate response, in between entrainment by the light regimen and the feeding-fasting rhythm. The same composite response was also observed in the pituitary gland from adrenalectomized mice under daytime restricted feeding, suggesting that circulating glucocorticoids do not inhibit full entrainment of the pituitary clockwork by meal time. Altogether our results reveal further aspects in the complexity of phase entrainment in the circadian system, and suggest that the pituitary may host oscillators able to integrate multiple time cues.
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Affiliation(s)
- Isabelle M. Bur
- CNRS, UMR 5203, Institut de Génomique Fonctionnelle, Montpellier, France
- INSERM, U661, Montpellier, France
- Université Montpellier, Montpellier, France
| | - Sonia Zouaoui
- CNRS, UMR 5203, Institut de Génomique Fonctionnelle, Montpellier, France
- INSERM, U661, Montpellier, France
- Université Montpellier, Montpellier, France
| | - Pierre Fontanaud
- CNRS, UMR 5203, Institut de Génomique Fonctionnelle, Montpellier, France
- INSERM, U661, Montpellier, France
- Université Montpellier, Montpellier, France
| | - Nathalie Coutry
- CNRS, UMR 5203, Institut de Génomique Fonctionnelle, Montpellier, France
- INSERM, U661, Montpellier, France
- Université Montpellier, Montpellier, France
| | - François Molino
- CNRS, UMR 5203, Institut de Génomique Fonctionnelle, Montpellier, France
- INSERM, U661, Montpellier, France
- Université Montpellier, Montpellier, France
| | - Agnès O. Martin
- CNRS, UMR 5203, Institut de Génomique Fonctionnelle, Montpellier, France
- INSERM, U661, Montpellier, France
- Université Montpellier, Montpellier, France
| | - Patrice Mollard
- CNRS, UMR 5203, Institut de Génomique Fonctionnelle, Montpellier, France
- INSERM, U661, Montpellier, France
- Université Montpellier, Montpellier, France
| | - Xavier Bonnefont
- CNRS, UMR 5203, Institut de Génomique Fonctionnelle, Montpellier, France
- INSERM, U661, Montpellier, France
- Université Montpellier, Montpellier, France
- * E-mail:
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Hayes KR, Beatty M, Meng X, Simmons CR, Habben JE, Danilevskaya ON. Maize global transcriptomics reveals pervasive leaf diurnal rhythms but rhythms in developing ears are largely limited to the core oscillator. PLoS One 2010; 5:e12887. [PMID: 20886102 PMCID: PMC2944807 DOI: 10.1371/journal.pone.0012887] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2010] [Accepted: 08/17/2010] [Indexed: 11/19/2022] Open
Abstract
Background Plant diurnal rhythms are vital environmental adaptations to coordinate internal physiological responses to alternating day-night cycles. A comprehensive view of diurnal biology has been lacking for maize (Zea mays), a major world crop. Methodology A photosynthetic tissue, the leaf, and a non-photosynthetic tissue, the developing ear, were sampled under natural field conditions. Genome-wide transcript profiling was conducted on a high-density 105 K Agilent microarray to investigate diurnal rhythms. Conclusions In both leaves and ears, the core oscillators were intact and diurnally cycling. Maize core oscillator genes are found to be largely conserved with their Arabidopsis counterparts. Diurnal gene regulation occurs in leaves, with some 23% of expressed transcripts exhibiting a diurnal cycling pattern. These transcripts can be assigned to over 1700 gene ontology functional terms, underscoring the pervasive impact of diurnal rhythms on plant biology. Considering the peak expression time for each diurnally regulated gene, and its corresponding functional assignment, most gene functions display temporal enrichment in the day, often with distinct patterns, such as dawn or midday preferred, indicating that there is a staged procession of biological events undulating with the diurnal cycle. Notably, many gene functions display a bimodal enrichment flanking the midday photosynthetic maximum, with an initial peak in mid-morning followed by another peak during the afternoon/evening. In contrast to leaves, in developing ears as few as 47 gene transcripts are diurnally regulated, and this set of transcripts includes primarily the core oscillators. In developing ears, which are largely shielded from light, the core oscillator therefore is intact with little outward effect on transcription.
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Affiliation(s)
- Kevin R. Hayes
- Pioneer Hi-Bred International, a DuPont Company, Johnston, Iowa, United States of America
| | - Mary Beatty
- Pioneer Hi-Bred International, a DuPont Company, Johnston, Iowa, United States of America
| | - Xin Meng
- Pioneer Hi-Bred International, a DuPont Company, Johnston, Iowa, United States of America
| | - Carl R. Simmons
- Pioneer Hi-Bred International, a DuPont Company, Johnston, Iowa, United States of America
| | - Jeffrey E. Habben
- Pioneer Hi-Bred International, a DuPont Company, Johnston, Iowa, United States of America
| | - Olga N. Danilevskaya
- Pioneer Hi-Bred International, a DuPont Company, Johnston, Iowa, United States of America
- * E-mail:
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Bozek K, Rosahl AL, Gaub S, Lorenzen S, Herzel H. Circadian transcription in liver. Biosystems 2010; 102:61-9. [PMID: 20655353 DOI: 10.1016/j.biosystems.2010.07.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2010] [Accepted: 07/15/2010] [Indexed: 02/02/2023]
Abstract
Circadian rhythms regulate a wide range of cellular, physiological, metabolic and behavioral activities in mammals. The complexity of tissue- and day-time specific regulation of thousands of clock controlled genes (CCGs) suggests that many transcriptional regulators are involved. Our bioinformatic analysis is based on two published DNA-array studies from mouse liver. We search overrepresented transcription factor binding sites in promoter regions of CCGs using GC-matched controls. Analyzing a large set of CCG promoters, we find known motifs such as E-boxes, D-boxes and cAMP responsive elements. In addition, we find overrepresented GC-rich motifs (Sp1, ETF, Nrf1), AT-rich motifs (TBP, Fox04, MEF-2), Y-box motifs (NF-Y, C/EBP) and cell cycle regulators (E2F, Elk-1). In a subset of system-driven genes, we find overrepresented motifs of the serum response factor SRF and the estrogen receptor ER. The analysis of published ChIP data reveals that some of our predicted regulators (C/EBP, E2F, HNF-1, Myc, MEF-2) target relatively many clock controlled genes. Our analysis of CCG promoters contributes to an understanding of the complex transcriptional regulation of circadian rhythms in liver.
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Affiliation(s)
- K Bozek
- Max Planck Institute for Informatics, Stuhlsatzenhausweg 85, 66123 Saarbrücken, Germany
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Circadian control of XPA and excision repair of cisplatin-DNA damage by cryptochrome and HERC2 ubiquitin ligase. Proc Natl Acad Sci U S A 2010; 107:4890-5. [PMID: 20304803 DOI: 10.1073/pnas.0915085107] [Citation(s) in RCA: 177] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Cisplatin is one of the most commonly used anticancer drugs. It kills cancer cells by damaging their DNA, and hence cellular DNA repair capacity is an important determinant of its efficacy. Here, we investigated the repair of cisplatin-induced DNA damage in mouse liver and testis tissue extracts prepared at regular intervals over the course of a day. We find that the XPA protein, which plays an essential role in repair of cisplatin damage by nucleotide excision repair, exhibits circadian oscillation in the liver but not in testis. Consequently, removal of cisplatin adducts in liver extracts, but not in testis extracts, exhibits a circadian pattern with zenith at approximately 5 pm and nadir at approximately 5 am. Furthermore, we find that the circadian oscillation of XPA is achieved both by regulation of transcription by the core circadian clock proteins including cryptochrome and by regulation at the posttranslational level by the HERC2 ubiquitin ligase. These findings may be used as a guide for timing of cisplatin chemotherapy.
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50
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Sancar A, Lindsey-Boltz LA, Kang TH, Reardon JT, Lee JH, Ozturk N. Circadian clock control of the cellular response to DNA damage. FEBS Lett 2010; 584:2618-25. [PMID: 20227409 DOI: 10.1016/j.febslet.2010.03.017] [Citation(s) in RCA: 182] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2010] [Revised: 03/08/2010] [Accepted: 03/10/2010] [Indexed: 11/18/2022]
Abstract
Mammalian cells possess a cell-autonomous molecular clock which controls the timing of many biochemical reactions and hence the cellular response to environmental stimuli including genotoxic stress. The clock consists of an autoregulatory transcription-translation feedback loop made up of four genes/proteins, BMal1, Clock, Cryptochrome, and Period. The circadian clock has an intrinsic period of about 24 h, and it dictates the rates of many biochemical reactions as a function of the time of the day. Recently, it has become apparent that the circadian clock plays an important role in determining the strengths of cellular responses to DNA damage including repair, checkpoints, and apoptosis. These new insights are expected to guide development of novel mechanism-based chemotherapeutic regimens.
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Affiliation(s)
- Aziz Sancar
- Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, NC 27599-7260, USA.
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