1
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Huang Y, Qi Z, Li J, You J, Zhang X, Wang M. Genetic interrogation of phenotypic plasticity informs genome-enabled breeding in cotton. J Genet Genomics 2023; 50:971-982. [PMID: 37211312 DOI: 10.1016/j.jgg.2023.05.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 04/19/2023] [Accepted: 05/04/2023] [Indexed: 05/23/2023]
Abstract
Phenotypic plasticity, or the ability to adapt to and thrive in changing climates and variable environments, is essential for developmental programs in plants. Despite its importance, the genetic underpinnings of phenotypic plasticity for key agronomic traits remain poorly understood in many crops. In this study, we aim to fill this gap by using genome-wide association studies to identify genetic variations associated with phenotypic plasticity in upland cotton (Gossypium hirsutum L.). We identified 73 additive quantitative trait loci (QTLs), 32 dominant QTLs, and 6799 epistatic QTLs associated with 20 traits. We also identified 117 additive QTLs, 28 dominant QTLs, and 4691 epistatic QTLs associated with phenotypic plasticity in 19 traits. Our findings reveal new genetic factors, including additive, dominant, and epistatic QTLs, that are linked to phenotypic plasticity and agronomic traits. Meanwhile, we find that the genetic factors controlling the mean phenotype and phenotypic plasticity are largely independent in upland cotton, indicating the potential for simultaneous improvement. Additionally, we envision a genomic design strategy by utilizing the identified QTLs to facilitate cotton breeding. Taken together, our study provides new insights into the genetic basis of phenotypic plasticity in cotton, which should be valuable for future breeding.
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Affiliation(s)
- Yuefan Huang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Zhengyang Qi
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Jianying Li
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Jiaqi You
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Xianlong Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei 430070, China.
| | - Maojun Wang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei 430070, China.
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2
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Schirmer AE, Kumar V, Schook A, Song EJ, Marshall MS, Takahashi JS. Cry1 expression during postnatal development is critical for the establishment of normal circadian period. Front Neurosci 2023; 17:1166137. [PMID: 37389366 PMCID: PMC10300422 DOI: 10.3389/fnins.2023.1166137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 05/23/2023] [Indexed: 07/01/2023] Open
Abstract
The mammalian circadian system generates an approximate 24-h rhythm through a complex autoregulatory feedback loop. Four genes, Period1 (Per1), Period2 (Per2), Cryptochrome1 (Cry1), and Cryptochrome2 (Cry2), regulate the negative feedback within this loop. Although these proteins have distinct roles within the core circadian mechanism, their individual functions are poorly understood. Here, we used a tetracycline trans-activator system (tTA) to examine the role of transcriptional oscillations in Cry1 and Cry2 in the persistence of circadian activity rhythms. We demonstrate that rhythmic Cry1 expression is an important regulator of circadian period. We then define a critical period from birth to postnatal day 45 (PN45) where the level of Cry1 expression is critical for setting the endogenous free running period in the adult animal. Moreover, we show that, although rhythmic Cry1 expression is important, in animals with disrupted circadian rhythms overexpression of Cry1 is sufficient to restore normal behavioral periodicity. These findings provide new insights into the roles of the Cryptochrome proteins in circadian rhythmicity and further our understanding of the mammalian circadian clock.
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Affiliation(s)
- Aaron E. Schirmer
- Department of Neurobiology, Northwestern University, Evanston, IL, United States
- Department of Biology, Northeastern Illinois University, Chicago, IL, United States
| | - Vivek Kumar
- Department of Neurobiology, Northwestern University, Evanston, IL, United States
- The Jackson Laboratory, Bar Harbor, ME, United States
| | - Andrew Schook
- Department of Neurobiology, Northwestern University, Evanston, IL, United States
| | - Eun Joo Song
- Department of Neurobiology, Northwestern University, Evanston, IL, United States
| | - Michael S. Marshall
- Department of Neurobiology, Northwestern University, Evanston, IL, United States
- Department of Pathology, Massachusetts General Hospital, Boston, MA, United States
- Harvard Medical School, Boston, MA, United States
| | - Joseph S. Takahashi
- Department of Neurobiology, Northwestern University, Evanston, IL, United States
- Department of Neuroscience, Peter O’Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX, United States
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, United States
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3
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Harbison ST. What have we learned about sleep from selective breeding strategies? Sleep 2022; 45:zsac147. [PMID: 36111812 PMCID: PMC9644121 DOI: 10.1093/sleep/zsac147] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 06/19/2022] [Indexed: 09/18/2023] Open
Abstract
Selective breeding is a classic technique that enables an experimenter to modify a heritable target trait as desired. Direct selective breeding for extreme sleep and circadian phenotypes in flies successfully alters these behaviors, and sleep and circadian perturbations emerge as correlated responses to selection for other traits in mice, rats, and dogs. The application of sequencing technologies to the process of selective breeding identifies the genetic network impacting the selected trait in a holistic way. Breeding techniques preserve the extreme phenotypes generated during selective breeding, generating community resources for further functional testing. Selective breeding is thus a unique strategy that can explore the phenotypic limits of sleep and circadian behavior, discover correlated responses of traits having shared genetic architecture with the target trait, identify naturally-occurring genomic variants and gene expression changes that affect trait variability, and pinpoint genes with conserved roles.
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Affiliation(s)
- Susan T Harbison
- Laboratory of Systems Genetics, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD,USA
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4
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Strain and Age Dependent Entrainable Range of Circadian Behavior in C57BL/6 and BALB/c Mice. Physiol Behav 2022; 255:113917. [PMID: 35853482 DOI: 10.1016/j.physbeh.2022.113917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 07/14/2022] [Accepted: 07/14/2022] [Indexed: 11/22/2022]
Abstract
The mammalian circadian system has a plasticity in a certain range, rather than a strict 24-hour cycle, with considerable variations among species, strains, and ages. As the most widely used mouse strains in circadian research, C57BL/6 and BALB/c mice were well known to have different internal periods and responses to various non-24-hour light-dark cycles. However, their entrainable range of circadian behavior was not specifically studied, neither was the effect of aging. Besides, it is not well known if mice with appeared behavioral adaptation are really healthy. In the current study, we exposed C57BL/6 and BALB/c mice at 3 months and 18 months old to a series of short (T cycles < 24 h) and long (T cycles > 24 h) light-dark cycles. Wheel running activities were monitored continuously for calculation of the entrainable range and glucose homeostasis was investigated to reflect their health status. Our results showed that the range in both young and old C57BL/6 mice is between T23 and T26. By contrast, due to the strong adaptability to extreme LD cycles, the entrainable range on a circadian scale in both young and old BALB/c mice cannot be well determined. Despite the adaptation appeared at the behavioral level, glucose homeostasis revealed by glucose tolerance test and insulin tolerance test was impaired in mice upon T cycle treatment. In summary, our study explored the entrainment range in two popular mouse strains and suggested that behavioral adaptation may not well reflect their health status.
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5
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Vijaya Shankara J, Horsley KG, Cheng N, Rho JM, Antle MC. Circadian Responses to Light in the BTBR Mouse. J Biol Rhythms 2022; 37:498-515. [PMID: 35722987 PMCID: PMC9452857 DOI: 10.1177/07487304221102279] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Animals with altered freerunning periods are valuable in understanding properties of the circadian clock. Understanding the relationship between endogenous clock properties, entrainment, and influence of light in terms of parametric and non-parametric models can help us better understand how different populations adapt to external light cycles. Many clinical populations often show significant changes in circadian properties that in turn cause sleep and circadian problems, possibly exacerbating their underlying clinical condition. BTBR T+Itpr3tf/J (BTBR) mice are a model commonly used for the study of autism spectrum disorders (ASD). Adults and adolescents with ASD frequently exhibit profound sleep and circadian disruptions, including increased latency to sleep, insomnia, advanced and delayed sleep phase disorders, and sleep fragmentation. Here, we investigated the circadian phenotype of BTBR mice in freerunning and light-entrained conditions and found that this strain of mice showed noticeably short freerunning periods (~22.75 h). In addition, when compared to C57BL/6J controls, BTBR mice also showed higher levels of activity even though this activity was compressed into a shorter active phase. Phase delays and phase advances to light were significantly larger in BTBR mice. Despite the short freerunning period, BTBR mice exhibited normal entrainment in light-dark cycles and accelerated entrainment to both advanced and delayed light cycles. Their ability to entrain to skeleton photoperiods of 1 min suggests that this entrainment cannot be attributed to masking. Period differences were also correlated with differences in the number of vasoactive intestinal polypeptide–expressing cells in the suprachiasmatic nucleus (SCN). Overall, the BTBR model, with their unique freerunning and entrainment properties, makes an interesting model to understand the underlying circadian clock.
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Affiliation(s)
- Jhenkruthi Vijaya Shankara
- Department of Psychology, University of Calgary, Calgary, AB, Canada.,Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Katelyn G Horsley
- Department of Psychology, University of Calgary, Calgary, AB, Canada.,Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Ning Cheng
- Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada.,Department of Comparative Biology & Experimental Medicine, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Jong M Rho
- Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada.,Departments of Neurosciences and Pediatrics, University of California, San Diego and Rady Children's Hospital, San Diego, California, USA
| | - Michael C Antle
- Department of Psychology, University of Calgary, Calgary, AB, Canada.,Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada.,Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
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6
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Pfeffer M, von Gall C, Wicht H, Korf HW. The Role of the Melatoninergic System in Circadian and Seasonal Rhythms—Insights From Different Mouse Strains. Front Physiol 2022; 13:883637. [PMID: 35492605 PMCID: PMC9039042 DOI: 10.3389/fphys.2022.883637] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 03/22/2022] [Indexed: 01/01/2023] Open
Abstract
The melatoninergic system comprises the neurohormone melatonin and its molecular targets. The major source of melatonin is the pineal organ where melatonin is rhythmically produced during darkness. In mammals, melatonin biosynthesis is controlled by the central circadian rhythm generator in the suprachiasmatic nucleus (SCN) and photoreceptors in the retina. Melatonin elicits its function principally through two specific receptors called MT1 and MT2. MT1 is highly expressed in the SCN and the hypophysial pars tuberalis (PT), an important interface for control of seasonal functions. The expression of the MT2 is more widespread. The role of the melatoninergic system in the control of seasonal functions, such as reproduction, has been known for more than 4 decades, but investigations on its impact on the circadian system under normal (entrained) conditions started 2 decades later by comparing mouse strains with a fully functional melatoninergic system with mouse strains which either produce insufficient amounts of melatonin or lack the melatonin receptors MT1 and MT2. These studies revealed that an intact melatoninergic system is not required for the generation or maintenance of rhythmic behavior under physiological entrained conditions. As shown by jet lag experiments, the melatoninergic system facilitated faster re-entrainment of locomotor activity accompanied by a more rapid adaptation of the molecular clock work in the SCN. This action depended on MT2. Further studies indicated that the endogenous melatoninergic system stabilizes the locomotor activity under entrained conditions. Notably, these effects of the endogenous melatoninergic system are subtle, suggesting that other signals such as corticosterone or temperature contribute to the synchronization of locomotor activity. Outdoor experiments lasting for a whole year indicate a seasonal plasticity of the chronotype which depends on the melatoninergic system. The comparison between mice with an intact or a compromised melatoninergic system also points toward an impact of this system on sleep, memory and metabolism.
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Affiliation(s)
- Martina Pfeffer
- Institute of Anatomy II, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
- *Correspondence: Martina Pfeffer,
| | - Charlotte von Gall
- Institute of Anatomy II, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
| | - Helmut Wicht
- Dr. Senckenbergische Anatomie II, Fachbereich Medizin der Goethe-Universität, Frankfurt am Main, Germany
| | - Horst-Werner Korf
- Institute of Anatomy I, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
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7
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Aung O, Weber ET. Differential effects of time-restricted feeding on circadian locomotor activity, food intake and body weight gain in BALB/cJ and C57BL/6J mice. BIOL RHYTHM RES 2021. [DOI: 10.1080/09291016.2021.1970395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- O Aung
- Department of Biology, Behavioral Neuroscience and Health Sciences, Rider University, Lawrenceville, NJ, USA
| | - E. Todd Weber
- Department of Biology, Behavioral Neuroscience and Health Sciences, Rider University, Lawrenceville, NJ, USA
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8
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Abstract
Circadian rhythms, present in most phyla across life, are biological oscillations occurring on a daily cycle. Since the discovery of their molecular foundations in model organisms, many inputs that modify this tightly controlled system in humans have been identified. Polygenic variations and environmental factors influence each person's circadian rhythm, contributing to the trait known as chronotype, which manifests as the degree of morning or evening preference in an individual. Despite normal variation in chronotype, much of society operates on a "one size fits all" schedule that can be difficult to adjust to, especially for certain individuals whose endogenous circadian phase is extremely advanced or delayed. This is a public health concern, as phase misalignment in humans is associated with a number of adverse health outcomes. Additionally, modern technology (such as electric lights and computer, tablet, and phone screens that emit blue light) and lifestyles (such as shift or irregular work schedules) are disrupting circadian consistency in an increasing number of people. Though medical and lifestyle interventions can alleviate some of these issues, growing research on endogenous circadian variability and sensitivity suggests that broader social changes may be necessary to minimize the impact of circadian misalignment on health.
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Affiliation(s)
| | | | - Ying-Hui Fu
- Department of Neurology
- Institute for Human Genetics
- Weill Institute for Neurosciences, and
- Kavli Institute for Fundamental Neuroscience, UCSF, San Francisco, California, USA
| | - Louis J. Ptáček
- Department of Neurology
- Institute for Human Genetics
- Weill Institute for Neurosciences, and
- Kavli Institute for Fundamental Neuroscience, UCSF, San Francisco, California, USA
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9
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Hillis DA, Yadgary L, Weinstock GM, Pardo-Manuel de Villena F, Pomp D, Fowler AS, Xu S, Chan F, Garland T. Genetic Basis of Aerobically Supported Voluntary Exercise: Results from a Selection Experiment with House Mice. Genetics 2020; 216:781-804. [PMID: 32978270 PMCID: PMC7648575 DOI: 10.1534/genetics.120.303668] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 09/18/2020] [Indexed: 12/14/2022] Open
Abstract
The biological basis of exercise behavior is increasingly relevant for maintaining healthy lifestyles. Various quantitative genetic studies and selection experiments have conclusively demonstrated substantial heritability for exercise behavior in both humans and laboratory rodents. In the "High Runner" selection experiment, four replicate lines of Mus domesticus were bred for high voluntary wheel running (HR), along with four nonselected control (C) lines. After 61 generations, the genomes of 79 mice (9-10 from each line) were fully sequenced and single nucleotide polymorphisms (SNPs) were identified. We used nested ANOVA with MIVQUE estimation and other approaches to compare allele frequencies between the HR and C lines for both SNPs and haplotypes. Approximately 61 genomic regions, across all somatic chromosomes, showed evidence of differentiation; 12 of these regions were differentiated by all methods of analysis. Gene function was inferred largely using Panther gene ontology terms and KO phenotypes associated with genes of interest. Some of the differentiated genes are known to be associated with behavior/motivational systems and/or athletic ability, including Sorl1, Dach1, and Cdh10 Sorl1 is a sorting protein associated with cholinergic neuron morphology, vascular wound healing, and metabolism. Dach1 is associated with limb bud development and neural differentiation. Cdh10 is a calcium ion binding protein associated with phrenic neurons. Overall, these results indicate that selective breeding for high voluntary exercise has resulted in changes in allele frequencies for multiple genes associated with both motivation and ability for endurance exercise, providing candidate genes that may explain phenotypic changes observed in previous studies.
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Affiliation(s)
- David A Hillis
- Genetics, Genomics, and Bioinformatics Graduate Program, University of California, Riverside, California 92521
| | - Liran Yadgary
- Department of Genetics, University of North Carolina at Chapel Hill, North Carolina 27599
| | - George M Weinstock
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut 06032
| | | | - Daniel Pomp
- Department of Genetics, University of North Carolina at Chapel Hill, North Carolina 27599
| | - Alexandra S Fowler
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, California 92521
| | - Shizhong Xu
- Department of Botany and Plant Sciences, University of California, Riverside, California 92521
| | - Frank Chan
- Friedrich Miescher Laboratory of the Max Planck Society, 72076 Tübingen, Germany
| | - Theodore Garland
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, California 92521
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10
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Chalfant JM, Howatt DA, Tannock LR, Daugherty A, Pendergast JS. Circadian disruption with constant light exposure exacerbates atherosclerosis in male ApolipoproteinE-deficient mice. Sci Rep 2020; 10:9920. [PMID: 32555251 PMCID: PMC7303111 DOI: 10.1038/s41598-020-66834-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 05/20/2020] [Indexed: 01/07/2023] Open
Abstract
Disruption of the circadian system caused by disordered exposure to light is pervasive in modern society and increases the risk of cardiovascular disease. The mechanisms by which this happens are largely unknown. ApolipoproteinE-deficient (ApoE−/−) mice are studied commonly to elucidate mechanisms of atherosclerosis. In this study, we determined the effects of light-induced circadian disruption on atherosclerosis in ApoE−/− mice. We first characterized circadian rhythms of behavior, light responsiveness, and molecular timekeeping in tissues from ApoE−/− mice that were indistinguishable from rhythms in ApoE+/+ mice. These data showed that ApoE−/− mice had no inherent circadian disruption and therefore were an appropriate model for our study. We next induced severe disruption of circadian rhythms by exposing ApoE−/− mice to constant light for 12 weeks. Constant light exposure exacerbated atherosclerosis in male, but not female, ApoE−/− mice. Male ApoE−/− mice exposed to constant light had increased serum cholesterol concentrations due to increased VLDL/LDL fractions. Taken together, these data suggest that ApoE−/− mice are an appropriate model for studying light-induced circadian disruption and that exacerbated dyslipidemia may mediate atherosclerotic lesion formation caused by constant light exposure.
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Affiliation(s)
| | - Deborah A Howatt
- Saha Cardiovascular Research Center, University of Kentucky, Lexington, Kentucky, USA
| | - Lisa R Tannock
- Saha Cardiovascular Research Center, University of Kentucky, Lexington, Kentucky, USA.,Department of Veterans Affairs, Lexington, Kentucky, USA.,Department of Internal Medicine, University of Kentucky, Lexington, Kentucky, USA.,Barnstable Brown Diabetes Center, University of Kentucky, Lexington, Kentucky, USA
| | - Alan Daugherty
- Saha Cardiovascular Research Center, University of Kentucky, Lexington, Kentucky, USA.,Department of Physiology, University of Kentucky, Lexington, Kentucky, USA
| | - Julie S Pendergast
- Department of Biology, University of Kentucky, Lexington, Kentucky, USA. .,Saha Cardiovascular Research Center, University of Kentucky, Lexington, Kentucky, USA. .,Barnstable Brown Diabetes Center, University of Kentucky, Lexington, Kentucky, USA.
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11
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Abstract
Sleep is a ubiquitous and complex behavior in both its manifestation and regulation. Despite its essential role in maintaining optimal performance, health, and well-being, the genetic mechanisms underlying sleep remain poorly understood. Here, we review the forward genetic approaches undertaken in the last four years to elucidate the genes and gene pathways affecting sleep and its regulation. Despite an increasing number of studies and mining large databases, a coherent picture on “sleep” genes has yet to emerge. We highlight the results achieved by using unbiased genetic screens mainly in humans, mice, and fruit flies with an emphasis on normal sleep and make reference to lessons learned from the circadian field.
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Affiliation(s)
- Maxime Jan
- Centre for Integrative Genomics, University of Lausanne, Lausanne, 1015, Switzerland
| | - Bruce F O'Hara
- Department of Biology, University of Kentucky, Lexington, 40515, USA
| | - Paul Franken
- Centre for Integrative Genomics, University of Lausanne, Lausanne, 1015, Switzerland
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12
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Appiakannan HS, Rasimowicz ML, Harrison CB, Weber ET. Differential effects of high-fat diet on glucose tolerance, food intake, and glucocorticoid regulation in male C57BL/6J and BALB/cJ mice. Physiol Behav 2020; 215:112773. [DOI: 10.1016/j.physbeh.2019.112773] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 12/10/2019] [Accepted: 12/10/2019] [Indexed: 12/12/2022]
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13
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Metzger J, Wicht H, Korf HW, Pfeffer M. Seasonal Variations of Locomotor Activity Rhythms in Melatonin-Proficient and -Deficient Mice under Seminatural Outdoor Conditions. J Biol Rhythms 2019; 35:58-71. [PMID: 31625428 DOI: 10.1177/0748730419881922] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Locomotor activity patterns of laboratory mice are widely used to analyze circadian mechanisms, but most investigations have been performed under standardized laboratory conditions. Outdoors, animals are exposed to daily changes in photoperiod and other abiotic cues that might influence their circadian system. To investigate how the locomotor activity patterns under outdoor conditions compare to controlled laboratory conditions, we placed 2 laboratory mouse strains (melatonin-deficient C57Bl and melatonin-proficient C3H) in the garden of the Dr. Senckenbergische Anatomie in Frankfurt am Main. The mice were kept singly in cages equipped with an infrared locomotion detector, a hiding box, nesting material, and with food and water ad libitum. The locomotor activity of each mouse was recorded for 1 year, together with data on ambient temperature, light, and humidity. Chronotype, chronotype stability, total daily activity, duration of the activity period, and daily diurnality indices were determined from the actograms. C3H mice showed clear seasonal differences in the chronotype, its stability, the total daily activity, and the duration of the activity period. These pronounced seasonal differences were not observed in the C57Bl. In both strains, the onset of the main activity period was mainly determined by the evening dusk, whereas the offset was influenced by the ambient temperature. The actograms did not reveal infra-, ultradian, or lunar rhythms or a weekday/weekend pattern. Under outdoor conditions, the 2 strains retained their nocturnal locomotor identity as observed in the laboratory. Our results indicate that the chronotype displays a seasonal plasticity that may depend on the melatoninergic system. Photoperiod and ambient temperature are the most potent abiotic entraining cues. The timing of the evening dusk mainly affects the onset of the activity period; the ambient temperature during this period influences the latter's duration. Humidity, overall light intensities, and human activities do not affect the locomotor behavior.
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Affiliation(s)
- Joshua Metzger
- Dr. Senckenbergische Anatomie II, Fachbereich Medizin, Goethe-Universität Frankfurt, Frankfurt am Main, Germany
| | - Helmut Wicht
- Dr. Senckenbergische Anatomie II, Fachbereich Medizin, Goethe-Universität Frankfurt, Frankfurt am Main, Germany
| | - Horst-Werner Korf
- Institut für Anatomie I, Fachbereich Medizin, Heinrich Heine Universität, Düsseldorf, Germany
| | - Martina Pfeffer
- Institut für Anatomie II, Fachbereich Medizin, Heinrich Heine Universität, Düsseldorf, Germany
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14
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Neuronal Myocyte-Specific Enhancer Factor 2D (MEF2D) Is Required for Normal Circadian and Sleep Behavior in Mice. J Neurosci 2019; 39:7958-7967. [PMID: 31420455 DOI: 10.1523/jneurosci.0411-19.2019] [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] [Received: 02/20/2019] [Revised: 07/08/2019] [Accepted: 08/10/2019] [Indexed: 11/21/2022] Open
Abstract
The transcription factor, myocyte enhancer factor-2 (MEF2), is required for normal circadian behavior in Drosophila; however, its role in the mammalian circadian system has not been established. Of the four mammalian Mef2 genes, Mef2d is highly expressed in the suprachiasmatic nucleus (SCN) of the hypothalamus, a region critical for coordinating peripheral circadian clocks. Using both conventional and brain-specific Mef2d KO (Mef2d -/-) mouse lines, we demonstrate that MEF2D is essential for maintaining the length of the circadian free-running period of locomotor activity and normal sleep patterns in male mice. Crossing Mef2d -/- with Per2::luc reporter mice, we show that these behavioral changes are achieved without altering the endogenous period of the master circadian oscillator in the SCN. Together, our data suggest that alterations in behavior in Mef2d -/- mice may be the result of an effect on SCN output, rather than an effect on timekeeping within the SCN itself. These findings add to the growing body of evidence that MEF2 proteins play important roles in the brain.SIGNIFICANCE STATEMENT These studies are the first to show a role for MEF2 proteins in the brain outside of the hippocampus, and our findings suggest that these proteins may play diverse roles in the CNS. It is important to continue to build on our understanding of the roles of proteins acting in the SCN because SCN dysfunction underlies jet lag in humans and influences the response to shift work schedules, which are now known as risk factors for the development of cancer. Our work on MEF2D could be the basis for opening new lines of research in the development and regulation of circadian rhythms.
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15
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Abstract
In mammals, genetic influences of circadian rhythms occur at many levels. A set of core "clock genes" have been identified that form a feedback loop of gene transcription and translation. The core genetic clockwork generates circadian rhythms in cells throughout the body. Polymorphisms in both core clock genes and interacting genes contribute to individual differences in the expression and properties of circadian rhythms. The circadian clock profoundly influences the patterns of gene expression and cellular functions, providing a mechanistic basis for the impact of the genetic circadian system on normal physiological processes as well as the development of diseases.
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Affiliation(s)
- Martha Hotz Vitaterna
- Center for Sleep and Circadian Biology; Department of Neurobiology, Weinberg College of Arts and Sciences, Northwestern University, 2205 Tech Drive, Evanston, IL 60208, USA.
| | - Kazuhiro Shimomura
- Center for Sleep and Circadian Biology; Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, 420 East Superior Street, Chicago, IL 60611, USA
| | - Peng Jiang
- Center for Sleep and Circadian Biology; Department of Neurobiology, Weinberg College of Arts and Sciences, Northwestern University, 2205 Tech Drive, Evanston, IL 60208, USA
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16
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de Groot MHM, Castorena CM, Cox KH, Kumar V, Mohawk JA, Ahmed NI, Takahashi JS. A novel mutation in Slc2a4 as a mouse model of fatigue. GENES BRAIN AND BEHAVIOR 2019; 18:e12578. [PMID: 31059591 DOI: 10.1111/gbb.12578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 05/01/2019] [Accepted: 05/02/2019] [Indexed: 11/28/2022]
Abstract
Chronic fatigue is a debilitating disorder with widespread consequences, but effective treatment strategies are lacking. Novel genetic mouse models of fatigue may prove invaluable for studying its underlying physiological mechanisms and for testing treatments and interventions. In a screen of voluntary wheel-running behavior in N-ethyl-N-nitrosourea mutagenized C57BL/6J mice, we discovered two lines with low body weights and aberrant wheel-running patterns suggestive of a fatigue phenotype. Affected progeny from these lines had lower daily activity levels and exhibited low amplitude circadian rhythm alterations. Their aberrant behavior was characterized by frequent interruptions and periods of inactivity throughout the dark phase of the light-dark cycle and increased levels of activity during the rest or light phase. Expression of the behavioral phenotypes in offspring of strategic crosses was consistent with a recessive inheritance pattern. Mapping of phenotypic abnormalities showed linkage with a single locus on chromosome 1, and whole exome sequencing identified a single point mutation in the Slc2a4 gene encoding the GLUT4 insulin-responsive glucose transporter. The single nucleotide change (A-T, which we named "twiggy") was in the distal end of exon 10 and resulted in a premature stop (Y440*). Additional metabolic phenotyping confirmed that these mice recapitulate phenotypes found in GLUT4 knockout mice. However, to the best of our knowledge, this is the first time a mutation in this gene has been shown to result in extensive changes in general behavioral patterns. These findings suggest that GLUT4 may be involved in circadian behavioral abnormalities and could provide insights into fatigue in humans.
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Affiliation(s)
- Marleen H M de Groot
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, Texas.,Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Carlos M Castorena
- Department of Internal Medicine, Division of Hypothalamic Research, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Kimberly H Cox
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Vivek Kumar
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Jennifer A Mohawk
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, Texas.,Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Newaz I Ahmed
- Department of Internal Medicine, Division of Hypothalamic Research, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Joseph S Takahashi
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, Texas.,Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas
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17
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Srivastava M, Varma V, Abhilash L, Sharma VK, Sheeba V. Circadian Clock Properties and Their Relationships as a Function of Free-Running Period in Drosophila melanogaster. J Biol Rhythms 2019; 34:231-248. [PMID: 30939971 DOI: 10.1177/0748730419837767] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The stability of circadian clock mechanisms under cyclic environments contributes to increased Darwinian fitness by accurately timing daily behavior and physiology. Earlier studies on biological clocks speculated that the timing of behavior and its accuracy are determined by the intrinsic period (τ) of the circadian clock under constant conditions, its stability, the period of the external cycle (T), and resetting of the clock by environmental time cues. However, most of these previous studies suffered from certain limitations, the major ones being a narrow range of examined τ values and a non-uniformity in the genetic background across the individuals tested. We present data that rigorously test the following hypotheses by employing Drosophila melanogaster fruit flies with τ ranging from 17 to 30 h in a uniform genetic background. We tested whether 1) precision (day-to-day stability of τ) is greater for clocks with τ close to 24 h; 2) accuracy (i.e., day-to-day stability of the phase relationship (ψ), where ψ is the duration between a phase of the rhythm and a phase of the external cycle) is greater for clocks with τ close to 24 h; 3) Ψ is delayed with an increase in τ; and 4) Ψ becomes more advanced with an increase in length of zeitgeber cycle (T). We show that precision is not always maximum for ~24-h clocks, but that accuracy is greatest when τ approximates T. Further, flies exhibit a delayed phase relationship with increasing τ and an advanced phase relationship under long T-cycles as compared with shorter T-cycles. We also describe relationships between activity and rest durations and how our observations fit predictions from models of circadian entrainment. Overall, we confirm that accuracy and phase of entrained rhythm are governed by both intrinsic clock period and the length of the external cycle; however, we find that the relationship between intrinsic period and precision does not fit previous predictions.
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Affiliation(s)
- Manishi Srivastava
- Chronobiology Laboratory, Evolutionary and Integrative Biology Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, Karnataka India
| | - Vishwanath Varma
- Chronobiology Laboratory, Evolutionary and Integrative Biology Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, Karnataka India
| | - Lakshman Abhilash
- Chronobiology Laboratory, Evolutionary and Integrative Biology Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, Karnataka India
| | - Vijay Kumar Sharma
- Chronobiology Laboratory, Evolutionary and Integrative Biology Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, Karnataka India
| | - Vasu Sheeba
- Behavioural Neurogenetics Laboratory, Neurosciences Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, Karnataka India
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18
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Corty RW, Kumar V, Tarantino LM, Takahashi JS, Valdar W. Mean-Variance QTL Mapping Identifies Novel QTL for Circadian Activity and Exploratory Behavior in Mice. G3 (BETHESDA, MD.) 2018; 8:3783-3790. [PMID: 30389793 PMCID: PMC6288835 DOI: 10.1534/g3.118.200194] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 10/11/2018] [Indexed: 12/11/2022]
Abstract
We illustrate, through two case studies, that "mean-variance QTL mapping"-QTL mapping that models effects on the mean and the variance simultaneously-can discover QTL that traditional interval mapping cannot. Mean-variance QTL mapping is based on the double generalized linear model, which extends the standard linear model used in interval mapping by incorporating not only a set of genetic and covariate effects for mean but also set of such effects for the residual variance. Its potential for use in QTL mapping has been described previously, but it remains underutilized, with certain key advantages undemonstrated until now. In the first case study, a reduced complexity intercross of C57BL/6J and C57BL/6N mice examining circadian behavior, our reanalysis detected a mean-controlling QTL for circadian wheel running activity that interval mapping did not; mean-variance QTL mapping was more powerful than interval mapping at the QTL because it accounted for the fact that mice homozygous for the C57BL/6N allele had less residual variance than other mice. In the second case study, an intercross between C57BL/6J and C58/J mice examining anxiety-like behaviors, our reanalysis detected a variance-controlling QTL for rearing behavior; interval mapping did not identify this QTL because it does not target variance QTL. We believe that the results of these reanalyses, which in other respects largely replicated the original findings, support the use of mean-variance QTL mapping as standard practice.
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Affiliation(s)
- Robert W Corty
- Department of Genetics
- Bioinformatics and Computational Biology Curriculum
| | | | | | - Joseph S Takahashi
- Howard Hughes Medical Institute, Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - William Valdar
- Department of Genetics
- Bioinformatics and Computational Biology Curriculum
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
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19
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Harbison ST, Kumar S, Huang W, McCoy LJ, Smith KR, Mackay TFC. Genome-Wide Association Study of Circadian Behavior in Drosophila melanogaster. Behav Genet 2018; 49:60-82. [PMID: 30341464 PMCID: PMC6326971 DOI: 10.1007/s10519-018-9932-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 10/04/2018] [Indexed: 12/31/2022]
Abstract
Circadian rhythms influence physiological processes from sleep–wake cycles to body temperature and are controlled by highly conserved cycling molecules. Although the mechanistic basis of the circadian clock has been known for decades, the extent to which circadian rhythms vary in nature and the underlying genetic basis for that variation is not well understood. We measured circadian period (Ʈ) and rhythmicity index in the Drosophila Genetic Reference Panel (DGRP) and observed extensive genetic variation in both. Seven DGRP lines had sexually dimorphic arrhythmicity and one line had an exceptionally long Ʈ. Genome-wide analyses identified 584 polymorphisms in 268 genes. We observed differences among transcripts for nine genes predicted to interact among themselves and canonical clock genes in the long period line and a control. Mutations/RNAi knockdown targeting these genes also affected circadian behavior. Our observations reveal that complex genetic interactions influence high levels of variation in circadian phenotypes.
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Affiliation(s)
- Susan T Harbison
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA. .,Laboratory of Systems Genetics, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA. .,Laboratory of Systems Genetics, National Heart Lung and Blood Institute, Building 10, Room 7D13, 10 Center Drive, Bethesda, MD, 20892-1640, USA.
| | - Shailesh Kumar
- Laboratory of Systems Genetics, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Wen Huang
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA.,Genetics Program and W. M. Keck Center for Behavioral Biology, North Carolina State University, Raleigh, NC, USA.,Department of Animal Science, Michigan State University, East Lansing, MI, USA
| | - Lenovia J McCoy
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
| | - Kirklin R Smith
- Laboratory of Systems Genetics, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Trudy F C Mackay
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA.,Genetics Program and W. M. Keck Center for Behavioral Biology, North Carolina State University, Raleigh, NC, USA.,Center for Human Genetics and Department of Genetics and Biochemistry, Clemson University, 114 Gregor Mendel Circle, Greenwood, SC, 29646, USA
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20
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On the Relationship Between High-Order Linkage Disequilibrium and Epistasis. G3-GENES GENOMES GENETICS 2018; 8:2817-2824. [PMID: 29945968 PMCID: PMC6071592 DOI: 10.1534/g3.118.200513] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
A plausible explanation for statistical epistasis revealed in genome wide association analyses is the presence of high order linkage disequilibrium (LD) between the genotyped markers tested for interactions and unobserved functional polymorphisms. Based on findings in experimental data, it has been suggested that high order LD might be a common explanation for statistical epistasis inferred between local polymorphisms in the same genomic region. Here, we empirically evaluate how prevalent high order LD is between local, as well as distal, polymorphisms in the genome. This could provide insights into whether we should account for this when interpreting results from genome wide scans for statistical epistasis. An extensive and strong genome wide high order LD was revealed between pairs of markers on the high density 250k SNP-chip and individual markers revealed by whole genome sequencing in the Arabidopsis thaliana 1001-genomes collection. The high order LD was found to be more prevalent in smaller populations, but present also in samples including several hundred individuals. An empirical example illustrates that high order LD might be an even greater challenge in cases when the genetic architecture is more complex than the common assumption of bi-allelic loci. The example shows how significant statistical epistasis is detected for a pair of markers in high order LD with a complex multi allelic locus. Overall, our study illustrates the importance of considering also other explanations than functional genetic interactions when genome wide statistical epistasis is detected, in particular when the results are obtained in small populations of inbred individuals.
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21
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Davies B, Brown LA, Cais O, Watson J, Clayton AJ, Chang VT, Biggs D, Preece C, Hernandez-Pliego P, Krohn J, Bhomra A, Twigg SRF, Rimmer A, Kanapin A, Sen A, Zaiwalla Z, McVean G, Foster R, Donnelly P, Taylor JC, Blair E, Nutt D, Aricescu AR, Greger IH, Peirson SN, Flint J, Martin HC. A point mutation in the ion conduction pore of AMPA receptor GRIA3 causes dramatically perturbed sleep patterns as well as intellectual disability. Hum Mol Genet 2018; 26:3869-3882. [PMID: 29016847 PMCID: PMC5639461 DOI: 10.1093/hmg/ddx270] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Accepted: 07/06/2017] [Indexed: 01/19/2023] Open
Abstract
The discovery of genetic variants influencing sleep patterns can shed light on the physiological processes underlying sleep. As part of a large clinical sequencing project, WGS500, we sequenced a family in which the two male children had severe developmental delay and a dramatically disturbed sleep-wake cycle, with very long wake and sleep durations, reaching up to 106-h awake and 48-h asleep. The most likely causal variant identified was a novel missense variant in the X-linked GRIA3 gene, which has been implicated in intellectual disability. GRIA3 encodes GluA3, a subunit of AMPA-type ionotropic glutamate receptors (AMPARs). The mutation (A653T) falls within the highly conserved transmembrane domain of the ion channel gate, immediately adjacent to the analogous residue in the Grid2 (glutamate receptor) gene, which is mutated in the mouse neurobehavioral mutant, Lurcher. In vitro, the GRIA3(A653T) mutation stabilizes the channel in a closed conformation, in contrast to Lurcher. We introduced the orthologous mutation into a mouse strain by CRISPR-Cas9 mutagenesis and found that hemizygous mutants displayed significant differences in the structure of their activity and sleep compared to wild-type littermates. Typically, mice are polyphasic, exhibiting multiple sleep bouts of sleep several minutes long within a 24-h period. The Gria3A653T mouse showed significantly fewer brief bouts of activity and sleep than the wild-types. Furthermore, Gria3A653T mice showed enhanced period lengthening under constant light compared to wild-type mice, suggesting an increased sensitivity to light. Our results suggest a role for GluA3 channel activity in the regulation of sleep behavior in both mice and humans.
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Affiliation(s)
- Benjamin Davies
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, Oxfordshire OX3 7BN, UK
| | - Laurence A Brown
- Nuffield Department of Clinical Neurosciences, Sleep and Circadian Neuroscience Institute, University of Oxford, Oxford, Oxfordshire OX3 9DU, UK
| | - Ondrej Cais
- Medical Research Council (MRC) Laboratory of Molecular Biology, Neurobiology Division, Cambridge, Cambridgeshire CB2 0QH, UK
| | - Jake Watson
- Medical Research Council (MRC) Laboratory of Molecular Biology, Neurobiology Division, Cambridge, Cambridgeshire CB2 0QH, UK
| | - Amber J Clayton
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, Oxfordshire OX3 7BN, UK
| | - Veronica T Chang
- Medical Research Council (MRC) Laboratory of Molecular Biology, Neurobiology Division, Cambridge, Cambridgeshire CB2 0QH, UK
| | - Daniel Biggs
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, Oxfordshire OX3 7BN, UK
| | - Christopher Preece
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, Oxfordshire OX3 7BN, UK
| | | | - Jon Krohn
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, Oxfordshire OX3 7BN, UK
| | - Amarjit Bhomra
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, Oxfordshire OX3 7BN, UK
| | - Stephen R F Twigg
- Clinical Genetics Group, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, Oxfordshire OX3 9DS, UK
| | | | - Alexander Kanapin
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, Oxfordshire OX3 7BN, UK.,Department of Oncology, University of Oxford, Oxford, Oxfordshire OX3 7DQ, UK
| | | | - Arjune Sen
- Oxford Epilepsy Research Group, NIHR Biomedical Research Centre, Nuffield Department of Clinical Neuroscience, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | - Zenobia Zaiwalla
- Department of Neuroscience, John Radcliffe Hospital, Oxford, Oxfordshire OX3 9DU, UK
| | - Gil McVean
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, Oxfordshire OX3 7BN, UK.,Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, Oxfordshire OX3 7FZ, UK
| | - Russell Foster
- Nuffield Department of Clinical Neurosciences, Sleep and Circadian Neuroscience Institute, University of Oxford, Oxford, Oxfordshire OX3 9DU, UK
| | - Peter Donnelly
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, Oxfordshire OX3 7BN, UK.,Department of Statistics, University of Oxford, Oxford, Oxfordshire OX1 3LB, UK
| | - Jenny C Taylor
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, Oxfordshire OX3 7BN, UK.,National Institute for Health Research Oxford Biomedical Research Centre (NIHR Oxford BRC), Oxford, Oxfordshire OX3 7LE, UK
| | - Edward Blair
- Department of Clinical Genetics, Oxford University Hospitals NHS Trust, Oxford, Oxfordshire OX3 7HE, UK
| | - David Nutt
- Division of Brain Sciences, Department of Medicine, Centre for Neuropsychopharmacology, Imperial College London, London W12 0NN, UK
| | - A Radu Aricescu
- Medical Research Council (MRC) Laboratory of Molecular Biology, Neurobiology Division, Cambridge, Cambridgeshire CB2 0QH, UK
| | - Ingo H Greger
- Medical Research Council (MRC) Laboratory of Molecular Biology, Neurobiology Division, Cambridge, Cambridgeshire CB2 0QH, UK
| | - Stuart N Peirson
- Nuffield Department of Clinical Neurosciences, Sleep and Circadian Neuroscience Institute, University of Oxford, Oxford, Oxfordshire OX3 9DU, UK
| | - Jonathan Flint
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California-Los Angeles, CA 90095, USA
| | - Hilary C Martin
- Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
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22
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Pfeffer M, Korf HW, Wicht H. Synchronizing effects of melatonin on diurnal and circadian rhythms. Gen Comp Endocrinol 2018; 258:215-221. [PMID: 28533170 DOI: 10.1016/j.ygcen.2017.05.013] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Revised: 04/27/2017] [Accepted: 05/16/2017] [Indexed: 01/02/2023]
Abstract
In mammals, the rhythmic secretion of melatonin from the pineal gland is driven by the circadian clock in the suprachiasmatic nucleus (SCN) of the hypothalamus. The robust nightly peak of melatonin secretion is an output signal of the circadian clock and is supposed to deliver the circadian message to the whole of the organism. Since the circadian system regulates many behavioral and physiological processes, its disruption by external (shift-work, jet-lag) or internal desynchronization (blindness, aging) causes many different health problems. Externally applied melatonin is used in humans as a chronobiotic drug to treat desynchronization and circadian disorders, and the success of these treatments does, at first glance, underline the supposed pivotal role of melatonin in the synchronization of the circadian system. On the other hand, pinealectomy in experimental animals and humans does not abolish their rhythms of rest and activity. Furthermore, mice with deficient melatoninergic systems neither display overt defects in their rhythmic behavior nor do they show obvious signs of disease susceptibility, let alone premature mortality. During the last years, our laboratory has investigated several mouse stains with intact or compromised internal melatonin signaling systems in order to better understand the physiological role of the melatoninergic system. These and other investigations which will be reviewed in the present contribution confirm the synchronizing effect of endogenous melatonin and the melatoninergic system. However, these effects are subtle. Thus melatonin does not appear as the master of internal synchronization, but as one component in a cocktail of synchronizing agents.
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Affiliation(s)
- Martina Pfeffer
- Dr. Senckenbergische Anatomie II, Fachbereich Medizin, Goethe-Universität Frankfurt, Theodor-Stern-Kai 7, D-60590 Frankfurt am Main, Germany; Dr. Senckenbergisches Chronomedizinisches Institut, Goethe-Universität Frankfurt, Theodor-Stern-Kai 7, D-60590 Frankfurt am Main, Germany.
| | - Horst-Werner Korf
- Dr. Senckenbergische Anatomie II, Fachbereich Medizin, Goethe-Universität Frankfurt, Theodor-Stern-Kai 7, D-60590 Frankfurt am Main, Germany; Dr. Senckenbergisches Chronomedizinisches Institut, Goethe-Universität Frankfurt, Theodor-Stern-Kai 7, D-60590 Frankfurt am Main, Germany
| | - Helmut Wicht
- Dr. Senckenbergische Anatomie II, Fachbereich Medizin, Goethe-Universität Frankfurt, Theodor-Stern-Kai 7, D-60590 Frankfurt am Main, Germany
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23
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Detection of Epistasis for Flowering Time Using Bayesian Multilocus Estimation in a Barley MAGIC Population. Genetics 2017; 208:525-536. [PMID: 29254994 PMCID: PMC5788519 DOI: 10.1534/genetics.117.300546] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 12/12/2017] [Indexed: 12/16/2022] Open
Abstract
Gene-by-gene interactions, also known as epistasis, regulate many complex traits in different species. With the availability of low-cost genotyping it is now possible to study epistasis on a genome-wide scale. However, identifying genome-wide epistasis is a high-dimensional multiple regression problem and needs the application of dimensionality reduction techniques. Flowering Time (FT) in crops is a complex trait that is known to be influenced by many interacting genes and pathways in various crops. In this study, we successfully apply Sure Independence Screening (SIS) for dimensionality reduction to identify two-way and three-way epistasis for the FT trait in a Multiparent Advanced Generation Inter-Cross (MAGIC) barley population using the Bayesian multilocus model. The MAGIC barley population was generated from intercrossing among eight parental lines and thus, offered greater genetic diversity to detect higher-order epistatic interactions. Our results suggest that SIS is an efficient dimensionality reduction approach to detect high-order interactions in a Bayesian multilocus model. We also observe that many of our findings (genomic regions with main or higher-order epistatic effects) overlap with known candidate genes that have been already reported in barley and closely related species for the FT trait.
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24
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Koritala BSC, Lee K. Natural Variation of the Circadian Clock in Neurospora. ADVANCES IN GENETICS 2017; 99:1-37. [PMID: 29050553 DOI: 10.1016/bs.adgen.2017.09.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Most living organisms on earth experience daily and expected changes from the rotation of the earth. For an organism, the ability to predict and prepare for incoming stresses or resources is a very important skill for survival. This cellular process of measuring daily time of the day is collectively called the circadian clock. Because of its fundamental role in survival in nature, there is a great interest in studying the natural variation of the circadian clock. However, characterizing the genetic and molecular mechanisms underlying natural variation of circadian clocks remains a challenging task. In this chapter, we will summarize the progress in studying natural variation of the circadian clock in the successful eukaryotic model Neurospora, which led to discovering many design principles of the molecular mechanisms of the eukaryotic circadian clock. Despite the success of the system in revealing the molecular mechanisms of the circadian clock, Neurospora has not been utilized to extensively study natural variation. We will review the challenges that hindered the natural variation studies in Neurospora, and how they were overcome. We will also review the advantages of Neurospora for natural variation studies. Since Neurospora is the model fungal species for circadian study, it represents over 5 million species of fungi on earth. These fungi play important roles in ecosystems on earth, and as such Neurospora could serve as an important model for understanding the ecological role of natural variation in fungal circadian clocks.
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Affiliation(s)
- Bala S C Koritala
- Department of Biology, Rutgers, The State University of New Jersey, Camden, NJ, United States; Center for Computational and Integrative Biology, Rutgers, The State University of New Jersey, Camden, NJ, United States
| | - Kwangwon Lee
- Department of Biology, Rutgers, The State University of New Jersey, Camden, NJ, United States; Center for Computational and Integrative Biology, Rutgers, The State University of New Jersey, Camden, NJ, United States.
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25
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Peirson SN, Brown LA, Pothecary CA, Benson LA, Fisk AS. Light and the laboratory mouse. J Neurosci Methods 2017; 300:26-36. [PMID: 28414048 PMCID: PMC5909038 DOI: 10.1016/j.jneumeth.2017.04.007] [Citation(s) in RCA: 117] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Revised: 04/10/2017] [Accepted: 04/11/2017] [Indexed: 02/06/2023]
Abstract
Light exerts widespread effects on physiology and behaviour. As well as the widely-appreciated role of light in vision, light also plays a critical role in many non-visual responses, including regulating circadian rhythms, sleep, pupil constriction, heart rate, hormone release and learning and memory. In mammals, responses to light are all mediated via retinal photoreceptors, including the classical rods and cones involved in vision as well as the recently identified melanopsin-expressing photoreceptive retinal ganglion cells (pRGCs). Understanding the effects of light on the laboratory mouse therefore depends upon an appreciation of the physiology of these retinal photoreceptors, including their differing sens itivities to absolute light levels and wavelengths. The signals from these photoreceptors are often integrated, with different responses involving distinct retinal projections, making generalisations challenging. Furthermore, many commonly used laboratory mouse strains carry mutations that affect visual or non-visual physiology, ranging from inherited retinal degeneration to genetic differences in sleep and circadian rhythms. Here we provide an overview of the visual and non-visual systems before discussing practical considerations for the use of light for researchers and animal facility staff working with laboratory mice.
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Affiliation(s)
- Stuart N Peirson
- Sleep and Circadian Neuroscience Institute (SCNi), Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford Molecular Pathology Institute, Dunn School of Pathology, South Parks Road, Oxford, United Kingdom.
| | - Laurence A Brown
- Sleep and Circadian Neuroscience Institute (SCNi), Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford Molecular Pathology Institute, Dunn School of Pathology, South Parks Road, Oxford, United Kingdom
| | - Carina A Pothecary
- Sleep and Circadian Neuroscience Institute (SCNi), Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford Molecular Pathology Institute, Dunn School of Pathology, South Parks Road, Oxford, United Kingdom
| | - Lindsay A Benson
- Sleep and Circadian Neuroscience Institute (SCNi), Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford Molecular Pathology Institute, Dunn School of Pathology, South Parks Road, Oxford, United Kingdom
| | - Angus S Fisk
- Sleep and Circadian Neuroscience Institute (SCNi), Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford Molecular Pathology Institute, Dunn School of Pathology, South Parks Road, Oxford, United Kingdom
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26
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Hastings MH, Herzog ED. Clock Genes, Oscillators, and Cellular Networks in the Suprachiasmatic Nuclei. J Biol Rhythms 2016; 19:400-13. [PMID: 15534320 DOI: 10.1177/0748730404268786] [Citation(s) in RCA: 186] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The mammalian SCN contains a biological clock that drives remarkably precise circadian rhythms in vivo and in vitro. Recent advances have revealed molecular and cellular mechanisms required for the generation of these daily rhythms and their synchronization between SCN neurons and to the environmental light cycle. This review of the evidence for a cell-autonomous circadian pacemaker within specialized neurons of the SCN focuses on 6 genes implicated within the pace making mechanism, an additional 4 genes implicated in pathways from the pacemaker, and the intercellular and intracellular mechanisms that synchronize SCN neurons to each other and to solar time.
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Affiliation(s)
- Michael H Hastings
- MRC Laboratory of Molecular Biology, Division of Neurobiology, Cambridge, UK.
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27
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Hofstetter JR, Trofatter JA, Kernek KL, Nurnberger JI, Mayeda AR. New Quantitative Trait Loci for the Genetic Variance in Circadian Period of Locomotor Activity between Inbred Strains of Mice. J Biol Rhythms 2016; 18:450-62. [PMID: 14667146 DOI: 10.1177/0748730403259468] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Provisional quantitativetrait loci (QTL) for circadian locomotor period and wheel-running period have been identified in recombinant inbred (RI) mouse strains. To confirm thoseQTLand identify newones, the geneticcomponent of variance of the circadian period was partitionedamongan F2 intercross of RI mouse strains (BXD19 and CXB07). First, a genomic survey using 108 SSLP markers with an average spacing of 15 cM was carried out in a population of 259 (BXD19 · CXB07)F2 animals. The genome-wide survey identified two significant QTLfor period of locomotor activity measured by infrared photobeam crossings on mousechromosomes 1 (lod score5.66) and 14 (lod score4.33). TheQTL on distal chromosome 1 confirmed a previous report based on congenic B6.D2-Mtv7a/ Ty mice. Lod scores greater than 2.0 were found on chromosomes 1, 2, 6, 12, 13, and 14. In a targeted extension study, additional genotyping was performed on these chromosomes in the full sample of 341 F2 progeny. The 6 chromosome-wide surveys identified 3 additional QTL on mouse chromosomes 6, 12, and 13. The QTLon chromosome 12 overlaps with circadian period QTLidentified in several prior studies. For wheel-running period, the chromosome-wide surveys identified QTLon chromosomes 2 and 13 and one highly suggestive QTLon proximal chromosome 1. The results are compared to other published studies of QTL of circadian period.
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Affiliation(s)
- J R Hofstetter
- Department of Veterans Affairs, Richard L. Roudebush Medical Center, Indianapolis, IN 46202, USA
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Abstract
The circadian system in higher organisms temporally orchestrates rhythmic changes in a vast number of genes and gene products in different organs. Complex interactions between these components, both within and among cells, ultimately lead to rhythmic behavior and physiology. Identifying the plethora of circadian targets and mapping their interactions with one another is therefore essential to comprehend the molecular mechanisms of circadian regulation. The emergence of new technology for unbiased identification of biomolecules and for mapping interactions at the genome-wide scale is offering powerful tools to decipher the regulatory networks underpinning circadian rhythms. In this review, the authors discuss the potential application of these genome-wide approaches in the study of circadian rhythms.
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Affiliation(s)
- Luciano De Haro
- The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
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Abstract
The mouse has joined the fruit fly, bread mold, and cyanobacteria as a tractable genetic system for studying mechanisms of circadian rhythms. The circadian rhythms of “knock-out” mice for specific clock genes, however, have demonstrated significant variability between laboratories. In this brief review, the authors discuss possible sources of this variability, focusing particularly on questions of modifier loci of circadian rhythms that vary between inbred mouse strains. They conclude with a short list of recommendations for researchers working on circadian rhythms in mixed-strain mice.
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Affiliation(s)
- Russell N Van Gelder
- Department of Ophthalmology and Visual Sciences, Washington University Medical School, St. Louis, MO 63110, USA.
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Laermans J, Depoortere I. Chronobesity: role of the circadian system in the obesity epidemic. Obes Rev 2016; 17:108-25. [PMID: 26693661 DOI: 10.1111/obr.12351] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Revised: 09/25/2015] [Accepted: 10/01/2015] [Indexed: 01/17/2023]
Abstract
Although obesity is considered to result from an imbalance between energy uptake and energy expenditure, the strategy of dietary changes and physical exercise has failed to tackle the global obesity epidemic. In search of alternative and more adequate treatment options, research has aimed at further unravelling the mechanisms underlying this excessive weight gain. While numerous studies are focusing on the neuroendocrine alterations that occur after bariatric Roux-en-Y gastric bypass surgery, an increasing amount of chronobiological studies have started to raise awareness concerning the pivotal role of the circadian system in the development and exacerbation of obesity. This internal timekeeping mechanism rhythmically regulates metabolic and physiological processes in order to meet the fluctuating demands in energy use and supply throughout the 24-h day. This review elaborates on the extensive bidirectional interaction between the circadian system and metabolism and explains how disruption of body clocks by means of shift work, frequent time zone travelling or non-stop consumption of calorie-dense foods can evoke detrimental metabolic alterations that contribute to obesity. Altering the body's circadian rhythms by means of time-related dietary approaches (chrononutrition) or pharmacological substances (chronobiotics) may therefore represent a novel and interesting way to prevent or treat obesity and associated comorbidities.
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Affiliation(s)
- J Laermans
- Gut Peptide Research Lab, Translational Research Center for Gastrointestinal Disorders (TARGID), University of Leuven, Leuven, Belgium
| | - I Depoortere
- Gut Peptide Research Lab, Translational Research Center for Gastrointestinal Disorders (TARGID), University of Leuven, Leuven, Belgium
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Nikhil KL, Abhilash L, Sharma VK. Molecular Correlates of Circadian Clocks in Fruit Fly Drosophila melanogaster Populations Exhibiting early and late Emergence Chronotypes. J Biol Rhythms 2016; 31:125-41. [PMID: 26833082 DOI: 10.1177/0748730415627933] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Although association of circadian clock properties with the timing of rhythmic behaviors (chronotype) has been extensively documented over several decades, recent studies on mice and Drosophila have failed to observe such associations. In addition, studies on human populations that examined effects of clock gene mutations/polymorphisms on chronotypes have revealed disparate and often contradictory results, thereby highlighting the need for a suitable model organism to study circadian clocks' role in chronotype regulation, the lack of which has hindered exploration of the underlying molecular-genetic bases. We used a laboratory selection approach to raise populations of Drosophila melanogaster that emerge in the morning (early) or in the evening (late), and over 14 years of continued selection, we report clear divergence of their circadian phenotypes. We also assessed the molecular correlates of early and late emergence chronotypes and report significant divergence in transcriptional regulation, including the mean phase, amplitude and levels of period (per), timeless (tim), clock (clk) and vrille (vri) messenger RNA (mRNA) expression. Corroborating some of the previously reported light-sensitivity and oscillator network coupling differences between the early and the late populations, we also report differences in mRNA expression of the circadian photoreceptor cryptochrome (cry) and in the mean phase, amplitude and levels of the neuropeptide pigment-dispersing factor (PDF). These results provide the first-ever direct evidence for divergent evolution of molecular circadian clocks in response to selection imposed on an overt rhythmic behavior and highlight early and late populations as potential models for chronotype studies by providing a preliminary groundwork for further exploration of molecular-genetic correlates underlying circadian clock-chronotype association.
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Affiliation(s)
| | - Lakshman Abhilash
- Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, India
| | - Vijay Kumar Sharma
- Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, India /
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Genetic contributions to circadian activity rhythm and sleep pattern phenotypes in pedigrees segregating for severe bipolar disorder. Proc Natl Acad Sci U S A 2015; 113:E754-61. [PMID: 26712028 DOI: 10.1073/pnas.1513525113] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Abnormalities in sleep and circadian rhythms are central features of bipolar disorder (BP), often persisting between episodes. We report here, to our knowledge, the first systematic analysis of circadian rhythm activity in pedigrees segregating severe BP (BP-I). By analyzing actigraphy data obtained from members of 26 Costa Rican and Colombian pedigrees [136 euthymic (i.e., interepisode) BP-I individuals and 422 non-BP-I relatives], we delineated 73 phenotypes, of which 49 demonstrated significant heritability and 13 showed significant trait-like association with BP-I. All BP-I-associated traits related to activity level, with BP-I individuals consistently demonstrating lower activity levels than their non-BP-I relatives. We analyzed all 49 heritable phenotypes using genetic linkage analysis, with special emphasis on phenotypes judged to have the strongest impact on the biology underlying BP. We identified a locus for interdaily stability of activity, at a threshold exceeding genome-wide significance, on chromosome 12pter, a region that also showed pleiotropic linkage to two additional activity phenotypes.
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Pfeffer M, Wicht H, von Gall C, Korf HW. Owls and larks in mice. Front Neurol 2015; 6:101. [PMID: 26029157 PMCID: PMC4432671 DOI: 10.3389/fneur.2015.00101] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Accepted: 04/24/2015] [Indexed: 11/13/2022] Open
Abstract
Humans come in different chronotypes and, particularly, the late chronotype (the so-called owl) has been shown to be associated with several health risks. A number of studies show that laboratory mice also display various chronotypes. In mice as well as in humans, the chronotype shows correlations with the period length and rhythm stability. In addition, some mouse models for human diseases show alterations in their chronotypic behavior, which are comparable to those humans. Thus, analysis of the behavior of mice is a powerful tool to unravel the molecular and genetic background of the chronotype and the prevalence of risks and diseases that are associated with it. In this review, we summarize the correlation of chronotype with free-running period length and rhythm stability in inbred mouse strains, in mice with a compromised molecular clockwork, and in a mouse model for neurodegeneration.
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Affiliation(s)
- Martina Pfeffer
- Dr. Senckenbergische Anatomie II, Fachbereich Medizin der Goethe-Universität , Frankfurt am Main , Germany ; Dr. Senckenbergisches Chronomedizinisches Institut, Fachbereich Medizin der Goethe-Universität , Frankfurt am Main , Germany
| | - Helmut Wicht
- Dr. Senckenbergische Anatomie II, Fachbereich Medizin der Goethe-Universität , Frankfurt am Main , Germany ; Dr. Senckenbergisches Chronomedizinisches Institut, Fachbereich Medizin der Goethe-Universität , Frankfurt am Main , Germany
| | - Charlotte von Gall
- Institut für Anatomie II, Fachbereich Medizin, Heinrich Heine Universität , Düsseldorf , Germany
| | - Horst-Werner Korf
- Dr. Senckenbergische Anatomie II, Fachbereich Medizin der Goethe-Universität , Frankfurt am Main , Germany ; Dr. Senckenbergisches Chronomedizinisches Institut, Fachbereich Medizin der Goethe-Universität , Frankfurt am Main , Germany
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Monnahan PJ, Kelly JK. Epistasis Is a Major Determinant of the Additive Genetic Variance in Mimulus guttatus. PLoS Genet 2015; 11:e1005201. [PMID: 25946702 PMCID: PMC4422649 DOI: 10.1371/journal.pgen.1005201] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Accepted: 04/08/2015] [Indexed: 11/21/2022] Open
Abstract
The influence of genetic interactions (epistasis) on the genetic variance of quantitative traits is a major unresolved problem relevant to medical, agricultural, and evolutionary genetics. The additive genetic component is typically a high proportion of the total genetic variance in quantitative traits, despite that underlying genes must interact to determine phenotype. This study estimates direct and interaction effects for 11 pairs of Quantitative Trait Loci (QTLs) affecting floral traits within a single population of Mimulus guttatus. With estimates of all 9 genotypes for each QTL pair, we are able to map from QTL effects to variance components as a function of population allele frequencies, and thus predict changes in variance components as allele frequencies change. This mapping requires an analytical framework that properly accounts for bias introduced by estimation errors. We find that even with abundant interactions between QTLs, most of the genetic variance is likely to be additive. However, the strong dependency of allelic average effects on genetic background implies that epistasis is a major determinant of the additive genetic variance, and thus, the population’s ability to respond to selection. Complex traits are influenced not only by the effects of individual genes but also by the myriad ways that these genes interact with one another, commonly referred to as epistasis. Theory suggests that epistasis could have important population-level implications in terms of the genetic variance components that govern evolution in response to natural or artificial selection. Unfortunately, empirical examples extending from observed interactions between genes to genetic variances are scant, particularly for natural populations. Here, we characterize epistasis between naturally segregating polymorphisms in M. guttatus and determine the cumulative effect of epistasis on population genetic variance components. To do this, we first elaborate the necessary statistical theory to accommodate estimation error in genetic effects, as failing to do so will upwardly bias variance predictions. We find that gene interactions have a net positive effect on both the total and additive genetic variance for most traits; however, the contribution of individual loci to the additive variance depends heavily on the genotype frequencies at other loci. Therefore, the effect of epistasis extends beyond the individual’s phenotype to influence how both populations and their component alleles respond to selection.
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Affiliation(s)
- Patrick J. Monnahan
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Lawrence, Kansas, United States of America
- * E-mail:
| | - John K. Kelly
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Lawrence, Kansas, United States of America
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Musameh MD, Wang WYS, Nelson CP, Lluís-Ganella C, Debiec R, Subirana I, Elosua R, Balmforth AJ, Ball SG, Hall AS, Kathiresan S, Thompson JR, Lucas G, Samani NJ, Tomaszewski M. Analysis of gene-gene interactions among common variants in candidate cardiovascular genes in coronary artery disease. PLoS One 2015; 10:e0117684. [PMID: 25658981 PMCID: PMC4320092 DOI: 10.1371/journal.pone.0117684] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2013] [Accepted: 12/30/2014] [Indexed: 11/19/2022] Open
Abstract
Objective Only a small fraction of coronary artery disease (CAD) heritability has been explained by common variants identified to date. Interactions between genes of importance to cardiovascular regulation may account for some of the missing heritability of CAD. This study aimed to investigate the role of gene-gene interactions in common variants in candidate cardiovascular genes in CAD. Approach and Results 2,101 patients with CAD from the British Heart Foundation Family Heart Study and 2,426 CAD-free controls were included in the discovery cohort. All subjects were genotyped with the Illumina HumanCVD BeadChip enriched for genes and pathways relevant to the cardiovascular system and disease. The primary analysis in the discovery cohort examined pairwise interactions among 913 common (minor allele frequency >0.1) independent single nucleotide polymorphisms (SNPs) with at least nominal association with CAD in single locus analysis. A secondary exploratory interaction analysis was performed among all 11,332 independent common SNPs surviving quality control criteria. Replication analyses were conducted in 2,967 patients and 3,075 controls from the Myocardial Infarction Genetics Consortium. None of the interactions amongst 913 SNPs analysed in the primary analysis was statistically significant after correction for multiple testing (required P<1.2x10-7). Similarly, none of the pairwise gene-gene interactions in the secondary analysis reached statistical significance after correction for multiple testing (required P = 7.8x10-10). None of 36 suggestive interactions from the primary analysis or 31 interactions from the secondary analysis was significant in the replication cohort. Our study had 80% power to detect odds ratios > 1.7 for common variants in the primary analysis. Conclusions Moderately large additive interactions between common SNPs in genes relevant to cardiovascular disease do not appear to play a major role in genetic predisposition to CAD. The role of genetic interactions amongst less common SNPs and with medium and small magnitude effects remain to be investigated.
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Affiliation(s)
- Muntaser D. Musameh
- Department of Cardiovascular Sciences, University of Leicester, Glenfield Hospital, Leicester, United Kingdom
- NIHR Leicester Cardiovascular Biomedical Research Unit, Glenfield Hospital, Leicester, United Kingdom
- * E-mail:
| | - William Y. S. Wang
- School of Medicine, University of Queensland, Brisbane, Queensland, Australia
| | - Christopher P. Nelson
- Department of Cardiovascular Sciences, University of Leicester, Glenfield Hospital, Leicester, United Kingdom
- NIHR Leicester Cardiovascular Biomedical Research Unit, Glenfield Hospital, Leicester, United Kingdom
| | | | - Radoslaw Debiec
- Department of Cardiovascular Sciences, University of Leicester, Glenfield Hospital, Leicester, United Kingdom
- NIHR Leicester Cardiovascular Biomedical Research Unit, Glenfield Hospital, Leicester, United Kingdom
| | - Isaac Subirana
- Cardiovascular Epidemiology and Genetics, IMIM, Barcelona, Spain
- Epidemiology and Public Health Network (CIBERESP), Barcelona, Spain
| | - Roberto Elosua
- Cardiovascular Epidemiology and Genetics, IMIM, Barcelona, Spain
| | - Anthony J. Balmforth
- Division of Epidemiology, LIGHT, School of Medicine, University of Leeds, Leeds, United Kingdom
| | - Stephen G. Ball
- University of Leeds, MCRC, Leeds Institute of Genetics, Health and Therapeutics, Leeds, United Kingdom
| | - Alistair S. Hall
- Division of Epidemiology, LIGHT, School of Medicine, University of Leeds, Leeds, United Kingdom
| | - Sekar Kathiresan
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - John R. Thompson
- Department of Cardiovascular Sciences, University of Leicester, Glenfield Hospital, Leicester, United Kingdom
| | - Gavin Lucas
- Cardiovascular Epidemiology and Genetics, IMIM, Barcelona, Spain
| | - Nilesh J. Samani
- Department of Cardiovascular Sciences, University of Leicester, Glenfield Hospital, Leicester, United Kingdom
- NIHR Leicester Cardiovascular Biomedical Research Unit, Glenfield Hospital, Leicester, United Kingdom
| | - Maciej Tomaszewski
- Department of Cardiovascular Sciences, University of Leicester, Glenfield Hospital, Leicester, United Kingdom
- NIHR Leicester Cardiovascular Biomedical Research Unit, Glenfield Hospital, Leicester, United Kingdom
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Ma L, Keinan A, Clark AG. Biological knowledge-driven analysis of epistasis in human GWAS with application to lipid traits. Methods Mol Biol 2015; 1253:35-45. [PMID: 25403526 DOI: 10.1007/978-1-4939-2155-3_3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
While the importance of epistasis is well established, specific gene-gene interactions have rarely been identified in human genome-wide association studies (GWAS), mainly due to low power associated with such interaction tests. In this chapter, we integrate biological knowledge and human GWAS data to reveal epistatic interactions underlying quantitative lipid traits, which are major risk factors for coronary artery disease. To increase power to detect interactions, we only tested pairs of SNPs filtered by prior biological knowledge, including GWAS results, protein-protein interactions (PPIs), and pathway information. Using published GWAS and 9,713 European Americans (EA) from the Atherosclerosis Risk in Communities (ARIC) study, we identified an interaction between HMGCR and LIPC affecting high-density lipoprotein cholesterol (HDL-C) levels. We then validated this interaction in additional multiethnic cohorts from ARIC, the Framingham Heart Study, and the Multi-Ethnic Study of Atherosclerosis. Both HMGCR and LIPC are involved in the metabolism of lipids and lipoproteins, and LIPC itself has been marginally associated with HDL-C. Furthermore, no significant interaction was detected using PPI and pathway information, mainly due to the stringent significance level required after correcting for the large number of tests conducted. These results suggest the potential of biological knowledge-driven approaches to detect epistatic interactions in human GWAS, which may hold the key to exploring the role gene-gene interactions play in connecting genotypes and complex phenotypes in future GWAS.
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Affiliation(s)
- Li Ma
- Department of Animal and Avian Sciences, University of Maryland, Bldg 142, College Park, MD, 20742, USA,
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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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Izumo M, Pejchal M, Schook AC, Lange RP, Walisser JA, Sato TR, Wang X, Bradfield CA, Takahashi JS. Differential effects of light and feeding on circadian organization of peripheral clocks in a forebrain Bmal1 mutant. eLife 2014; 3:e04617. [PMID: 25525750 PMCID: PMC4298698 DOI: 10.7554/elife.04617] [Citation(s) in RCA: 128] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Accepted: 12/18/2014] [Indexed: 12/14/2022] Open
Abstract
In order to assess the contribution of a central clock in the hypothalamic suprachiasmatic nucleus (SCN) to circadian behavior and the organization of peripheral clocks, we generated forebrain/SCN-specific Bmal1 knockout mice by using floxed Bmal1 and pan-neuronal Cre lines. The forebrain knockout mice showed >90% deletion of BMAL1 in the SCN and exhibited an immediate and complete loss of circadian behavior in constant conditions. Circadian rhythms in peripheral tissues persisted but became desynchronized and damped in constant darkness. The loss of synchrony was rescued by light/dark cycles and partially by restricted feeding (only in the liver and kidney but not in the other tissues) in a distinct manner. These results suggest that the forebrain/SCN is essential for internal temporal order of robust circadian programs in peripheral clocks, and that individual peripheral clocks are affected differently by light and feeding in the absence of a functional oscillator in the forebrain.
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Affiliation(s)
- Mariko Izumo
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, United States
| | - Martina Pejchal
- Department of Neurobiology, Northwestern University, Evanston, United States
| | - Andrew C Schook
- Department of Neurobiology, Northwestern University, Evanston, United States
- Howard Hughes Medical Institute, Northwestern University, Evanston, United States
| | - Ryan P Lange
- Department of Neurobiology, Northwestern University, Evanston, United States
| | - Jacqueline A Walisser
- McArdle Laboratory for Cancer Research, University of Wisconsin, Madison, United States
| | - Takashi R Sato
- Werner Reichardt Centre for Integrative Neuroscience, University of Tübingen, Tübingen, Germany
- JST, PRESTO, University of Tübingen, Tübingen, Germany
| | - Xiaozhong Wang
- Department of Molecular Biosciences, Northwestern University, Evanston, United States
| | | | - Joseph S Takahashi
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, United States
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, United States
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Hepatocyte circadian clock controls acetaminophen bioactivation through NADPH-cytochrome P450 oxidoreductase. Proc Natl Acad Sci U S A 2014; 111:18757-62. [PMID: 25512522 DOI: 10.1073/pnas.1421708111] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The diurnal variation in acetaminophen (APAP) hepatotoxicity (chronotoxicity) reportedly is driven by oscillations in metabolism that are influenced by the circadian phases of feeding and fasting. To determine the relative contributions of the central clock and the hepatocyte circadian clock in modulating the chronotoxicity of APAP, we used a conditional null allele of brain and muscle Arnt-like 1 (Bmal1, aka Mop3 or Arntl) allowing deletion of the clock from hepatocytes while keeping the central and other peripheral clocks (e.g., the clocks controlling food intake) intact. We show that deletion of the hepatocyte clock dramatically reduces APAP bioactivation and toxicity in vivo and in vitro because of a reduction in NADPH-cytochrome P450 oxidoreductase gene expression, protein, and activity.
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40
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Logan RW, Williams WP, McClung CA. Circadian rhythms and addiction: mechanistic insights and future directions. Behav Neurosci 2014; 128:387-412. [PMID: 24731209 DOI: 10.1037/a0036268] [Citation(s) in RCA: 94] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Circadian rhythms are prominent in many physiological and behavioral functions. Circadian disruptions either by environmental or molecular perturbation can have profound health consequences, including the development and progression of addiction. Both animal and humans studies indicate extensive bidirectional relationships between the circadian system and drugs of abuse. Addicted individuals display disrupted rhythms, and chronic disruption or particular chronotypes may increase the risk for substance abuse and relapse. Moreover, polymorphisms in circadian genes and an evening chronotype have been linked to mood and addiction disorders, and recent efforts suggest an association with the function of reward neurocircuitry. Animal studies are beginning to determine how altered circadian gene function results in drug-induced neuroplasticity and behaviors. Many studies suggest a critical role for circadian rhythms in reward-related pathways in the brain and indicate that drugs of abuse directly affect the central circadian pacemaker. In this review, we highlight key findings demonstrating the importance of circadian rhythms in addiction and how future studies will reveal important mechanistic insights into the involvement of circadian rhythms in drug addiction.
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Affiliation(s)
- Ryan W Logan
- Department of Psychiatry, University of Pittsburgh School of Medicine
| | - Wilbur P Williams
- Department of Psychiatry, University of Pittsburgh School of Medicine
| | - Colleen A McClung
- Department of Psychiatry, University of Pittsburgh School of Medicine
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Zhou L, Bryant CD, Loudon A, Palmer AA, Vitaterna MH, Turek FW. The circadian clock gene Csnk1e regulates rapid eye movement sleep amount, and nonrapid eye movement sleep architecture in mice. Sleep 2014; 37:785-93, 793A-793C. [PMID: 24744456 DOI: 10.5665/sleep.3590] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
STUDY OBJECTIVES Efforts to identify the genetic basis of mammalian sleep have included quantitative trait locus (QTL) mapping and gene targeting of known core circadian clock genes. We combined three different genetic approaches to identify and test a positional candidate sleep gene - the circadian gene casein kinase 1 epsilon (Csnk1e), which is located in a QTL we identified for rapid eye movement (REM) sleep on chromosome 15. MEASUREMENTS AND RESULTS Using electroencephalographic (EEG) and electromyographic (EMG) recordings, baseline sleep was examined in a 12-h light:12-h dark (LD 12:12) cycle in mice of seven genotypes, including Csnk1e(tau/tau) and Csnk1e(-/-) mutant mice, Csnk1e (B6.D2) and Csnk1e (D2.B6) congenic mice, and their respective wild-type littermate control mice. Additionally, Csnk1e(tau/tau) and wild-type mice were examined in constant darkness (DD). Csnk1e(tau/tau) mutant mice and both Csnk1e (B6.D2) and Csnk1e (D2.B6) congenic mice showed significantly higher proportion of sleep time spent in REM sleep during the dark period than wild-type controls - the original phenotype for which the QTL on chromosome 15 was identified. This phenotype persisted in Csnk1e(tau/tau) mice while under free-running DD conditions. Other sleep phenotypes observed in Csnk1e(tau/tau) mice and congenics included a decreased number of bouts of nonrapid eye movement (NREM) sleep and an increased average NREM sleep bout duration. CONCLUSIONS These results demonstrate a role for Csnk1e in regulating not only the timing of sleep, but also the REM sleep amount and NREM sleep architecture, and support Csnk1e as a causal gene in the sleep QTL on chromosome 15.
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Affiliation(s)
- Lili Zhou
- Center for Sleep and Circadian Biology, Northwestern University, Evanston, IL ; Department of Neurobiology, Northwestern University, Evanston, IL
| | - Camron D Bryant
- Departments of Pharmacology and Experimental Therapeutics and Psychiatry, Boston University School of Medicine, Boston, MA
| | - Andrew Loudon
- Faculty of Life Sciences, University of Manchester, Manchester, UK
| | - Abraham A Palmer
- Department of Human Genetics, University of Chicago, Chicago, IL ; Department of Psychiatry and Behavioral Neuroscience, University of Chicago, Chicago, IL
| | - Martha Hotz Vitaterna
- Center for Sleep and Circadian Biology, Northwestern University, Evanston, IL ; Department of Neurobiology, Northwestern University, Evanston, IL
| | - Fred W Turek
- Center for Sleep and Circadian Biology, Northwestern University, Evanston, IL ; Department of Neurobiology, Northwestern University, Evanston, IL
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Rogala AR, Morgan AP, Christensen AM, Gooch TJ, Bell TA, Miller DR, Godfrey VL, de Villena FPM. The Collaborative Cross as a resource for modeling human disease: CC011/Unc, a new mouse model for spontaneous colitis. Mamm Genome 2014; 25:95-108. [PMID: 24487921 PMCID: PMC3960486 DOI: 10.1007/s00335-013-9499-2] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2013] [Accepted: 12/09/2013] [Indexed: 02/07/2023]
Abstract
Inflammatory bowel disease (IBD) is an immune-mediated condition driven by improper responses to intestinal microflora in the context of environmental and genetic background. GWAS in humans have identified many loci associated with IBD, but animal models are valuable for dissecting the underlying molecular mechanisms, characterizing environmental and genetic contributions and developing treatments. Mouse models rely on interventions such as chemical treatment or introduction of an infectious agent to induce disease. Here, we describe a new model for IBD in which the disease develops spontaneously in 20-week-old mice in the absence of known murine pathogens. The model is part of the Collaborative Cross and came to our attention due to a high incidence of rectal prolapse in an incompletely inbred line. Necropsies revealed a profound proliferative colitis with variable degrees of ulceration and vasculitis, splenomegaly and enlarged mesenteric lymph nodes with no discernible anomalies of other organ systems. Phenotypic characterization of the CC011/Unc mice with homozygosity ranging from 94.1 to 99.8% suggested that the trait was fixed and acted recessively in crosses to the colitis-resistant C57BL/6J inbred strain. Using a QTL approach, we identified four loci, Ccc1, Ccc2, Ccc3 and Ccc4 on chromosomes 12, 14, 1 and 8 that collectively explain 27.7% of the phenotypic variation. Surprisingly, we also found that minute levels of residual heterozygosity in CC011/Unc have significant impact on the phenotype. This work demonstrates the utility of the CC as a source of models of human disease that arises through new combinations of alleles at susceptibility loci.
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Affiliation(s)
- Allison R. Rogala
- Division of Laboratory Animal Medicine, University of North Carolina, Chapel Hill, NC USA
| | - Andrew P. Morgan
- Department of Genetics, Lineberger Comprehensive Cancer Center, and Carolina Center for Genome Sciences, University of North Carolina, Chapel Hill, NC USA
| | - Alexis M. Christensen
- Division of Laboratory Animal Medicine, University of North Carolina, Chapel Hill, NC USA
| | - Terry J. Gooch
- Department of Genetics, Lineberger Comprehensive Cancer Center, and Carolina Center for Genome Sciences, University of North Carolina, Chapel Hill, NC USA
| | - Timothy A. Bell
- Department of Genetics, Lineberger Comprehensive Cancer Center, and Carolina Center for Genome Sciences, University of North Carolina, Chapel Hill, NC USA
| | - Darla R. Miller
- Department of Genetics, Lineberger Comprehensive Cancer Center, and Carolina Center for Genome Sciences, University of North Carolina, Chapel Hill, NC USA
| | - Virginia L. Godfrey
- Division of Laboratory Animal Medicine, University of North Carolina, Chapel Hill, NC USA
| | - Fernando Pardo-Manuel de Villena
- Department of Genetics, University of North Carolina, Chapel Hill, NC USA
- Department of Genetics, Lineberger Comprehensive Cancer Center, and Carolina Center for Genome Sciences, University of North Carolina, Chapel Hill, NC USA
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43
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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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44
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Paladino N, Mul Fedele ML, Duhart JM, Marpegan L, Golombek DA. Modulation of mammalian circadian rhythms by tumor necrosis factor-α. Chronobiol Int 2014; 31:668-79. [PMID: 24527954 DOI: 10.3109/07420528.2014.886588] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
UNLABELLED Systemic low doses of the endotoxin lipopolysaccharide (LPS, 100 µg/kg) administered during the early night induce phase-delays of locomotor activity rhythms in mice. Our aim was to evaluate the role of tumor necrosis factor (Tnf)-alpha and its receptor 1/p55 (Tnfr1) in the modulation of LPS-induced circadian effects on the suprachiasmatic nucleus (SCN). We observed that Tnfr1-defective mice (Tnfr1 KO), although exhibiting similar circadian behavior and light response to that of control mice, did not show LPS-induced phase-delays of locomotor activity rhythms, nor LPS-induced cFos and Per2 expression in the SCN and Per1 expression in the paraventricular hypothalamic nucleus (PVN) as compared to wild-type (WT) mice. We also analyzed Tnfr1 expression in the SCN of WT mice, peaking during the early night, when LPS has a circadian effect. Peripheral inoculation of LPS induced an increase in cytokine/chemokine levels (Tnf, Il-6 and Ccl2) in the SCN and in the PVN. In conclusion, in this study, we show that LPS-induced circadian responses are mediated by Tnf. Our results also suggest that this cytokine stimulates the SCN after LPS peripheral inoculation; and the time-related effect of LPS (i.e. phase shifts elicited only at early night) might depend on the increased levels of Tnfr1 expression. We also confirmed that LPS modulates clock gene expression in the SCN and PVN in WT but not in Tnfr1 KO mice. HIGHLIGHTS We demonstrate a fundamental role for Tnf and its receptor in circadian modulation by immune stimuli at the level of the SCN biological clock.
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Affiliation(s)
- Natalia Paladino
- Laboratorio de Cronobiología, Universidad Nacional de Quilmes , Buenos Aires , Argentina
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45
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Kostrzewa E, Kas MJ. The use of mouse models to unravel genetic architecture of physical activity: a review. GENES BRAIN AND BEHAVIOR 2013; 13:87-103. [DOI: 10.1111/gbb.12091] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2013] [Revised: 08/15/2013] [Accepted: 10/01/2013] [Indexed: 12/26/2022]
Affiliation(s)
- E. Kostrzewa
- Department of Translational Neuroscience, Brain Center Rudolf Magnus; University Medical Center Utrecht; Utrecht the Netherlands
| | - M. J. Kas
- Department of Translational Neuroscience, Brain Center Rudolf Magnus; University Medical Center Utrecht; Utrecht the Netherlands
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46
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Vaze KM, Nikhil KL, Sharma VK. Genetic architecture underlying morning and evening circadian phenotypes in fruit flies Drosophila melanogaster. Heredity (Edinb) 2013; 111:265-74. [PMID: 23612693 PMCID: PMC3807266 DOI: 10.1038/hdy.2013.28] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2012] [Revised: 02/12/2013] [Accepted: 03/06/2013] [Indexed: 11/08/2022] Open
Abstract
Circadian rhythms are perhaps among the genetically best characterized behaviours. Several mutations with drastic effects on circadian processes have been identified and models developed to explain how clock genes and their products generate self-sustained oscillations. Although natural variations in circadian phenotypes have been studied extensively, the genetic basis of such adaptive variations remains largely unknown. Here we report the results of a preliminary genetic analysis of adaptive divergence of circadian phenotypes in populations of fruit flies Drosophila melanogaster. Two sets of populations, 'early' and 'late', were created in a long-term laboratory selection for morning and evening emergence, with four independent replicates each. Over the course of ∼55 generations, the early flies evolved increased morning emergence and a shorter circadian period, whereas late flies evolved increased evening emergence and longer period. To examine the genetic basis of circadian phenotypes, we set up crosses between early and late flies, and monitored emergence and activity/rest rhythms in the F1, backcrossed and F2 progeny. Our analysis suggests that the genetic basis of divergent circadian phenotypes in early and late stocks is primarily autosomal. Line-cross analysis revealed that additive and non-additive genetic effects contribute to the divergence of circadian phenotypes in early and late flies.
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Affiliation(s)
- K M Vaze
- Chronobiology Laboratory, Evolutionary and
Organismal Biology Unit, Jawaharlal Nehru Centre for Advanced Scientific Research,
Bangalore, India
| | - K L Nikhil
- Chronobiology Laboratory, Evolutionary and
Organismal Biology Unit, Jawaharlal Nehru Centre for Advanced Scientific Research,
Bangalore, India
| | - V K Sharma
- Chronobiology Laboratory, Evolutionary and
Organismal Biology Unit, Jawaharlal Nehru Centre for Advanced Scientific Research,
Bangalore, India
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47
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Bookout AL, de Groot MHM, Owen BM, Lee S, Gautron L, Lawrence HL, Ding X, Elmquist JK, Takahashi JS, Mangelsdorf DJ, Kliewer SA. FGF21 regulates metabolism and circadian behavior by acting on the nervous system. Nat Med 2013; 19:1147-52. [PMID: 23933984 PMCID: PMC3769420 DOI: 10.1038/nm.3249] [Citation(s) in RCA: 399] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2013] [Accepted: 05/29/2013] [Indexed: 12/11/2022]
Abstract
Fibroblast growth factor 21 (FGF21) is a hepatokine that acts as a global starvation signal to modulate fuel partitioning and metabolism and repress growth; however, the site of action of these diverse effects remains unclear. FGF21 signals through a heteromeric cell-surface receptor composed of one of three FGF receptors (FGFR1c, FGFR2c or FGFR3c) in complex with β-Klotho, a single-pass transmembrane protein that is enriched in metabolic tissues. Here we show that in addition to its known effects on peripheral metabolism, FGF21 increases systemic glucocorticoid levels, suppresses physical activity and alters circadian behavior, which are all features of the adaptive starvation response. These effects are mediated through β-Klotho expression in the suprachiasmatic nucleus of the hypothalamus and the dorsal vagal complex of the hindbrain. Mice lacking the gene encoding β-Klotho (Klb) in these regions are refractory to these effects, as well as those on metabolism, insulin and growth. These findings demonstrate a crucial role for the nervous system in mediating the diverse physiologic and pharmacologic actions of FGF21.
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Affiliation(s)
- Angie L Bookout
- 1] Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, Texas, USA. [2] Division of Hypothalamic Research, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, USA
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48
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McCulley WD, Ascheid S, Crabbe JC, Rosenwasser AM. Selective breeding for ethanol-related traits alters circadian phenotype. Alcohol 2013; 47:187-94. [PMID: 23414725 DOI: 10.1016/j.alcohol.2013.01.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2012] [Revised: 01/10/2013] [Accepted: 01/12/2013] [Indexed: 10/27/2022]
Abstract
Previous studies in mice and rats have shown that selective breeding for high and low ethanol preference results in divergence of circadian phenotype in the selected lines. These results indicate that some alleles influencing ethanol preference also contribute to circadian rhythm regulation. Selective breeding has also been used to produce lines of mice differing in a number of other ethanol-related traits, while studies of phenotypic and genetic correlation indicate that diverse ethanol-related traits are influenced by both shared and unshared genetics. In the present study, we examined several features of circadian activity rhythms in a mouse line selected for binge-like drinking and in mouse lines selected for high and low severity of ethanol withdrawal convulsions. Specifically, Experiment 1 compared High Drinking in the Dark (HDID-1) mice to their genetically heterogeneous progenitor line (HS/Npt), and Experiment 2 compared Withdrawal Seizure-Prone (WSP-2) and Withdrawal Seizure-Resistant (WSR-2) mice. Both line pairs displayed differences in their daily activity patterns under light-dark conditions. In addition, HDID-1 mice showed shorter free-running periods in constant light and less coherent activity rhythms across lighting conditions relative to HS/Npt controls, while WSP-2 mice showed longer free-running periods in constant darkness relative to WSR-2 mice. These results strengthen the evidence for genetic linkages between responsiveness to ethanol and circadian regulation, and extend this evidence to include ethanol-related phenotypes other than preference drinking. However, the present results also indicate that the nature of genetic correlations between and within phenotypic domains is highly complex.
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49
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Abstract
Using a clever combination of genetic and biochemical tools researchers have shown that a transcription factor called USF1 has a central role in determining how mutations of the Clock gene manifest themselves in the behaviour of different mouse strains.
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Affiliation(s)
- Maud Demarque
- Maud Demarque is at the Department of Molecular Biology, University of Geneva, Geneva, Switzerland
| | - Ueli Schibler
- Ueli Schibler is at the Department of Molecular Biology, University of Geneva, Geneva, Switzerland
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50
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Shimomura K, Kumar V, Koike N, Kim TK, Chong J, Buhr ED, Whiteley AR, Low SS, Omura C, Fenner D, Owens JR, Richards M, Yoo SH, Hong HK, Vitaterna MH, Bass J, Pletcher MT, Wiltshire T, Hogenesch J, Lowrey PL, Takahashi JS. Usf1, a suppressor of the circadian Clock mutant, reveals the nature of the DNA-binding of the CLOCK:BMAL1 complex in mice. eLife 2013; 2:e00426. [PMID: 23580255 PMCID: PMC3622178 DOI: 10.7554/elife.00426] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Accepted: 02/12/2013] [Indexed: 11/13/2022] Open
Abstract
Genetic and molecular approaches have been critical for elucidating the mechanism of the mammalian circadian clock. Here, we demonstrate that the ClockΔ19 mutant behavioral phenotype is significantly modified by mouse strain genetic background. We map a suppressor of the ClockΔ19 mutation to a ∼900 kb interval on mouse chromosome 1 and identify the transcription factor, Usf1, as the responsible gene. A SNP in the promoter of Usf1 causes elevation of its transcript and protein in strains that suppress the Clock mutant phenotype. USF1 competes with the CLOCK:BMAL1 complex for binding to E-box sites in target genes. Saturation binding experiments demonstrate reduced affinity of the CLOCKΔ19:BMAL1 complex for E-box sites, thereby permitting increased USF1 occupancy on a genome-wide basis. We propose that USF1 is an important modulator of molecular and behavioral circadian rhythms in mammals. DOI:http://dx.doi.org/10.7554/eLife.00426.001.
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Affiliation(s)
- Kazuhiro Shimomura
- Center for Functional Genomics, Department of Neurobiology, Center for Sleep and Circadian Biology, Northwestern University, Evanston, United States
| | - Vivek Kumar
- Department of Neuroscience, Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, United States
| | - Nobuya Koike
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, United States
| | - Tae-Kyung Kim
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, United States
| | - Jason Chong
- Department of Neurobiology, Northwestern University, Evanston, United States
| | - Ethan D Buhr
- Department of Neurobiology, Northwestern University, Evanston, United States
| | - Andrew R Whiteley
- Department of Neurobiology, Northwestern University, Evanston, United States
| | - Sharon S Low
- Department of Neurobiology, Northwestern University, Evanston, United States
| | - Chiaki Omura
- Department of Neurobiology, Center for Functional Genomics, Northwestern University, Evanston, United States
| | - Deborah Fenner
- Department of Neurobiology, Center for Functional Genomics, Northwestern University, Evanston, United States
| | - Joseph R Owens
- Department of Neurobiology, Center for Sleep and Circadian Biology, Northwestern University, Evanston, United States
| | - Marc Richards
- Department of Neurobiology, Northwestern University, Evanston, United States
| | - Seung-Hee Yoo
- Department of Neuroscience, Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, United States
| | - Hee-Kyung Hong
- Department of Neurobiology, Center for Functional Genomics, Northwestern University, Evanston, United States
| | - Martha H Vitaterna
- Center for Functional Genomics, Department of Neurobiology, Center for Sleep and Circadian Biology, Northwestern University, Evanston, United States
| | - Joseph Bass
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, United States
| | - Mathew T Pletcher
- Department of Genomics, Genomics Institute of the Novartis Research Foundation, San Diego, United States
| | - Tim Wiltshire
- Department of Genomics, Genomics Institute of the Novartis Research Foundation, San Diego, United States
| | - John Hogenesch
- Department of Pharmacology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
| | - Phillip L Lowrey
- Department of Neurobiology, Northwestern University, Evanston, United States
| | - Joseph S Takahashi
- Department of Neuroscience, Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, United States
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