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Yin D, Zhang B, Chong Y, Ren W, Xu S, Yang G. Adaptive changes in BMAL2 with increased locomotion associated with the evolution of unihemispheric slow-wave sleep in mammals. Sleep 2024; 47:zsae018. [PMID: 38289699 PMCID: PMC11009019 DOI: 10.1093/sleep/zsae018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 01/11/2024] [Indexed: 02/01/2024] Open
Abstract
Marine mammals, especially cetaceans, have evolved a very special form of sleep characterized by unihemispheric slow-wave sleep (USWS) and a negligible amount or complete absence of rapid-eye-movement sleep; however, the underlying genetic mechanisms remain unclear. Here, we detected unique, significant selection signatures in basic helix-loop-helix ARNT like 2 (BMAL2; also called ARNTL2), a key circadian regulator, in marine mammal lineages, and identified two nonsynonymous amino acid substitutions (K204E and K346Q) in the important PER-ARNT-SIM domain of cetacean BMAL2 via sequence comparison with other mammals. In vitro assays revealed that these cetacean-specific mutations specifically enhanced the response to E-box-like enhancer and consequently promoted the transcriptional activation of PER2, which is closely linked to sleep regulation. The increased PER2 expression, which was further confirmed both in vitro and in vivo, is beneficial for allowing cetaceans to maintain continuous movement and alertness during sleep. Concordantly, the locomotor activities of zebrafish overexpressing the cetacean-specific mutant bmal2 were significantly higher than the zebrafish overexpressing the wild-type gene. Subsequently, transcriptome analyses revealed that cetacean-specific mutations caused the upregulation of arousal-related genes and the downregulation of several sleep-promoting genes, which is consistent with the need to maintain hemispheric arousal during USWS. Our findings suggest a potential close relationship between adaptive changes in BMAL2 and the remarkable adaptation of USWS and may provide novel insights into the genetic basis of the evolution of animal sleep.
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Affiliation(s)
- Daiqing Yin
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, Guangdong 511458, China
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Biao Zhang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Yujie Chong
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Wenhua Ren
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Shixia Xu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Guang Yang
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, Guangdong 511458, China
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
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2
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Stabilization of hypoxia-inducible factor-1α alleviates osteoarthritis via interacting with Per2 and resetting the circadian clock. Tissue Cell 2022; 79:101942. [DOI: 10.1016/j.tice.2022.101942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 09/19/2022] [Accepted: 09/19/2022] [Indexed: 11/20/2022]
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3
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Hariri H, Pellicelli M, St-Arnaud R. Nfil3, a target of the NACA transcriptional coregulator, affects osteoblast and osteocyte gene expression differentially. Bone 2020; 141:115624. [PMID: 32877713 DOI: 10.1016/j.bone.2020.115624] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 08/25/2020] [Accepted: 08/28/2020] [Indexed: 10/25/2022]
Abstract
Intermittent administration of PTH(1-34) has a profound osteoanabolic effect on the skeleton. At the cellular level, osteoblasts and osteocytes are two crucial cell types that respond to PTH stimulation in bone. The transcriptional cofactor Nascent polypeptide Associated Complex and coregulator alpha (NACA) is a downstream target of the PTH-Gαs-PKA axis in osteoblasts. NACA functions as a transcriptional cofactor affecting bZIP factor-mediated transcription of target promoters in osteoblasts, such as Osteocalcin (Bglap2). Here, we used RNA-Seq and ChIP-Seq against NACA in PTH-treated MC3T3-E1 osteoblastic cells to identify novel targets of the PTH-activated NACA. Our approach identified Nuclear factor interleukin-3-regulated (Nfil3) as a target promoter of this pathway. Knockdown of Naca reduced the response of Nfil3 to PTH(1-34) stimulation. In silico analysis of the Nfil3 promoter revealed potential binding sites for NACA (located within the ChIP fragment) and CREB. We show that following PTH stimulation, phosphorylated-CREB binds the proximal promoter of Nfil3 in osteoblasts. The activity of the Nfil3 promoter (-818/+182 bp) is regulated by CREB and this activation relies on the presence of NACA. In addition, we show that knockdown of Nfil3 enhances the expression of osteoblastic differentiation markers in MC3T3-E1 cells while it represses osteocytic marker gene expression in IDG-SW3 cells. These results show that the PTH-induced NACA axis regulates Nfil3 expression and suggest that NFIL3 acts as a transcriptional repressor in osteoblasts while it exhibits differential activity as an activator in osteocytes.
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Affiliation(s)
- Hadla Hariri
- Research Centre, Shriners Hospital for Children - Canada, Montreal, Quebec H4A 0A9, Canada; Department of Human Genetics, McGill University, Montreal, Quebec H3A 0C7, Canada
| | - Martin Pellicelli
- Research Centre, Shriners Hospital for Children - Canada, Montreal, Quebec H4A 0A9, Canada
| | - René St-Arnaud
- Research Centre, Shriners Hospital for Children - Canada, Montreal, Quebec H4A 0A9, Canada; Department of Human Genetics, McGill University, Montreal, Quebec H3A 0C7, Canada; Department of Surgery, McGill University, Montreal, Quebec H3G 1A4, Canada; Department of Medicine, McGill University, Montreal, Quebec H4A 3J1, Canada.
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4
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Cheng AH, Bouchard-Cannon P, Hegazi S, Lowden C, Fung SW, Chiang CK, Ness RW, Cheng HYM. SOX2-Dependent Transcription in Clock Neurons Promotes the Robustness of the Central Circadian Pacemaker. Cell Rep 2020; 26:3191-3202.e8. [PMID: 30893593 DOI: 10.1016/j.celrep.2019.02.068] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 12/08/2018] [Accepted: 02/19/2019] [Indexed: 11/20/2022] Open
Abstract
Clock neurons within the mammalian suprachiasmatic nuclei (SCN) encode circadian time using interlocked transcription-translation feedback loops (TTFLs) that drive rhythmic gene expression. However, the contributions of other transcription factors outside of the circadian TTFLs to the functionality of the SCN remain obscure. Here, we report that the stem and progenitor cell transcription factor, sex-determining region Y-box 2 (SOX2), is expressed in adult SCN neurons and positively regulates transcription of the core clock gene, Period2. Mice lacking SOX2 selectively in SCN neurons display imprecise, poorly consolidated behavioral rhythms that do not entrain efficiently to environmental light cycles and that are highly susceptible to constant light-induced arrhythmicity. RNA sequencing revealed that Sox2 deficiency alters the SCN transcriptome, reducing the expression of core clock genes and neuropeptide-receptor systems. By defining the transcriptional landscape within SCN neurons, SOX2 enables the generation of robust, entrainable circadian rhythms that accurately reflect environmental time.
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Affiliation(s)
- Arthur H Cheng
- Department of Biology, University of Toronto Mississauga, Mississauga, ON L5L 1C6, Canada; Department of Cell & Systems Biology, University of Toronto, Toronto, ON M5S 3G5, Canada
| | - Pascale Bouchard-Cannon
- Department of Biology, University of Toronto Mississauga, Mississauga, ON L5L 1C6, Canada; Department of Cell & Systems Biology, University of Toronto, Toronto, ON M5S 3G5, Canada
| | - Sara Hegazi
- Department of Biology, University of Toronto Mississauga, Mississauga, ON L5L 1C6, Canada; Department of Cell & Systems Biology, University of Toronto, Toronto, ON M5S 3G5, Canada
| | - Christopher Lowden
- Department of Biology, University of Toronto Mississauga, Mississauga, ON L5L 1C6, Canada; Department of Cell & Systems Biology, University of Toronto, Toronto, ON M5S 3G5, Canada
| | - Samuel W Fung
- Department of Biology, University of Toronto Mississauga, Mississauga, ON L5L 1C6, Canada
| | - Cheng-Kang Chiang
- Department of Chemistry, National Dong Hwa University, Shoufeng, Hualien 97401, Taiwan, ROC
| | - Rob W Ness
- Department of Biology, University of Toronto Mississauga, Mississauga, ON L5L 1C6, Canada; Department of Ecology & Evolutionary Biology, University of Toronto, Toronto, ON M5S 3B2, Canada
| | - Hai-Ying Mary Cheng
- Department of Biology, University of Toronto Mississauga, Mississauga, ON L5L 1C6, Canada; Department of Cell & Systems Biology, University of Toronto, Toronto, ON M5S 3G5, Canada.
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5
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Doi M, Shimatani H, Atobe Y, Murai I, Hayashi H, Takahashi Y, Fustin JM, Yamaguchi Y, Kiyonari H, Koike N, Yagita K, Lee C, Abe M, Sakimura K, Okamura H. Non-coding cis-element of Period2 is essential for maintaining organismal circadian behaviour and body temperature rhythmicity. Nat Commun 2019; 10:2563. [PMID: 31189882 PMCID: PMC6561950 DOI: 10.1038/s41467-019-10532-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2018] [Accepted: 05/16/2019] [Indexed: 12/22/2022] Open
Abstract
Non-coding cis-regulatory elements are essential determinants of development, but their exact impacts on behavior and physiology in adults remain elusive. Cis-element-based transcriptional regulation is believed to be crucial for generating circadian rhythms in behavior and physiology. However, genetic evidence supporting this model is based on mutations in the protein-coding sequences of clock genes. Here, we report generation of mutant mice carrying a mutation only at the E'-box cis-element in the promoter region of the core clock gene Per2. The Per2 E'-box mutation abolishes sustainable molecular clock oscillations and renders circadian locomotor activity and body temperature rhythms unstable. Without the E'-box, Per2 messenger RNA and protein expression remain at mid-to-high levels. Our work delineates the Per2 E'-box as a critical nodal element for keeping sustainable cell-autonomous circadian oscillation and reveals the extent of the impact of the non-coding cis-element in daily maintenance of animal locomotor activity and body temperature rhythmicity.
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Affiliation(s)
- Masao Doi
- Department of Systems Biology, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyō-ku, Kyoto, 606-8501, Japan.
| | - Hiroyuki Shimatani
- Department of Systems Biology, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyō-ku, Kyoto, 606-8501, Japan
| | - Yuta Atobe
- Department of Systems Biology, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyō-ku, Kyoto, 606-8501, Japan
| | - Iori Murai
- Department of Systems Biology, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyō-ku, Kyoto, 606-8501, Japan.,Laboratory of Molecular Brain Science, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyō-ku, Kyoto, 606-8501, Japan
| | - Hida Hayashi
- Department of Systems Biology, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyō-ku, Kyoto, 606-8501, Japan
| | - Yukari Takahashi
- Department of Systems Biology, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyō-ku, Kyoto, 606-8501, Japan
| | - Jean-Michel Fustin
- Department of Systems Biology, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyō-ku, Kyoto, 606-8501, Japan
| | - Yoshiaki Yamaguchi
- Department of Systems Biology, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyō-ku, Kyoto, 606-8501, Japan
| | - Hiroshi Kiyonari
- Laboratories for Animal Resource Development and Genetic Engineering, RIKEN Center for Biosystems Dynamics Research, Kobe, 650-0047, Japan
| | - Nobuya Koike
- Department of Physiology and Systems Bioscience, Kyoto Prefectural University of Medicine, Kyoto, 602-8566, Japan
| | - Kazuhiro Yagita
- Department of Physiology and Systems Bioscience, Kyoto Prefectural University of Medicine, Kyoto, 602-8566, Japan
| | - Choogon Lee
- Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, FL 32306, USA
| | - Manabu Abe
- Department of Cellular Neurobiology, Brain Research Institute, Niigata University, Niigata, 951-8585, Japan
| | - Kenji Sakimura
- Department of Cellular Neurobiology, Brain Research Institute, Niigata University, Niigata, 951-8585, Japan
| | - Hitoshi Okamura
- Department of Systems Biology, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyō-ku, Kyoto, 606-8501, Japan. .,Laboratory of Molecular Brain Science, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyō-ku, Kyoto, 606-8501, Japan.
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6
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Shimizu T, Watanabe K, Anayama N, Miyazaki K. Effect of lipopolysaccharide on circadian clock genes Per2 and Bmal1 in mouse ovary. J Physiol Sci 2017; 67:623-628. [PMID: 28213822 PMCID: PMC10717690 DOI: 10.1007/s12576-017-0532-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 02/12/2017] [Indexed: 12/12/2022]
Abstract
In mammals, circadian rhythms are associated with multiple physiological events. The aim of the present study was to examine the effect of lipopolysaccharide (LPS) on circadian systems in the ovary. Immature female mice were received an intra-peritoneal injection of equine chorionic gonadotropin (eCG) and LPS. Total RNA was collected from the ovary at 6-h intervals throughout a 48 h of experimental period. The expression of the circadian genes period 2 (Per2) and brain and muscle ARNT-like 1 (Bmal1) such as circadian genes was measured by quantitative PCR. Although expression of Per2 and Bmal1 in the ovary did not display clear diurnal oscillation, LPS suppressed the amplitude of Per2 expression. Additionally, LPS inhibited the expression of cytochrome P450 aromatase (CYP19) and luteinizing hormone receptor (LHr) genes in the ovary of eCG-treated mice. Our data suggest that Per2 may be associated with the inhibition of CYP19 and LHr expression by LPS in the ovaries of immature mice.
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Affiliation(s)
- Takashi Shimizu
- Graduate School of Animal and Food Hygiene, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, 0808555, Japan.
| | - Kaya Watanabe
- Graduate School of Animal and Food Hygiene, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, 0808555, Japan
| | - Nozomi Anayama
- Graduate School of Animal and Food Hygiene, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, 0808555, Japan
| | - Koyomi Miyazaki
- Biomedical Research Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki, 3058568, Japan
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7
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Tokuda IT, Okamoto A, Matsumura R, Takumi T, Akashi M. Potential contribution of tandem circadian enhancers to nonlinear oscillations in clock gene expression. Mol Biol Cell 2017; 28:2333-2342. [PMID: 28637769 PMCID: PMC5555660 DOI: 10.1091/mbc.e17-02-0129] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Revised: 06/12/2017] [Accepted: 06/14/2017] [Indexed: 01/14/2023] Open
Abstract
Limit-cycle oscillations require the presence of nonlinear processes. Although mathematical studies have long suggested that multiple nonlinear processes are required for autonomous circadian oscillation in clock gene expression, the underlying mechanism remains controversial. Here we show experimentally that cell-autonomous circadian transcription of a mammalian clock gene requires a functionally interdependent tandem E-box motif; the lack of either of the two E-boxes results in arrhythmic transcription. Although previous studies indicated the role of the tandem motifs in increasing circadian amplitude, enhancing amplitude does not explain the mechanism for limit-cycle oscillations in transcription. In this study, mathematical analysis suggests that the interdependent behavior of enhancer elements including not only E-boxes but also ROR response elements might contribute to limit-cycle oscillations by increasing transcriptional nonlinearity. As expected, introduction of the interdependence of circadian enhancer elements into mathematical models resulted in autonomous transcriptional oscillation with low Hill coefficients. Together these findings suggest that interdependent tandem enhancer motifs on multiple clock genes might cooperatively enhance nonlinearity in the whole circadian feedback system, which would lead to limit-cycle oscillations in clock gene expression.
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Affiliation(s)
- Isao T Tokuda
- Department of Mechanical Engineering, Ritsumeikan University, Kusatsu 525-8577, Japan
| | - Akihiko Okamoto
- Research Institute for Time Studies, Yamaguchi University, Yamaguchi 753-8511, Japan
| | - Ritsuko Matsumura
- Research Institute for Time Studies, Yamaguchi University, Yamaguchi 753-8511, Japan
| | - Toru Takumi
- RIKEN Brain Science Institute, Wako 351-0198, Japan
| | - Makoto Akashi
- Research Institute for Time Studies, Yamaguchi University, Yamaguchi 753-8511, Japan
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8
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Matsumura R, Akashi M. Multiple circadian transcriptional elements cooperatively regulate cell-autonomous transcriptional oscillation of Period3, a mammalian clock gene. J Biol Chem 2017; 292:16081-16092. [PMID: 28821614 DOI: 10.1074/jbc.m117.806836] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 08/07/2017] [Indexed: 11/06/2022] Open
Abstract
Cell-autonomous oscillation in clock gene expression drives circadian rhythms. The development of comprehensive analytical techniques, such as bioinformatics and ChIP-sequencing, has enabled the genome-wide identification of potential circadian transcriptional elements that regulate the transcriptional oscillation of clock genes. However, detailed analyses using traditional biochemical and molecular-biological approaches, such as binding and reporter assays, are still necessary to determine whether these potential circadian transcriptional elements are actually functional and how significantly they contribute to driving transcriptional oscillation. Here, we focused on the molecular mechanism of transcriptional oscillations in the mammalian clock gene Period3 (Per3). The PER3 protein is essential for robust peripheral clocks and is a key component in circadian output processes. We found three E box-like elements located upstream of human Per3 transcription start sites that additively contributed to cell-autonomous transcriptional oscillation. However, we also found that Per3 is still expressed in a circadian manner when all three E box-like elements are functionally impaired. We noted that Per3 transcription was activated by the synergistic actions of two D box-like elements and the three E box-like elements, leading to a drastic increase in circadian amplitude. Interestingly, circadian expression of Per3 was completely disrupted only when all five transcriptional elements were functionally impaired. These results indicate that three E box-like and two D box-like elements cooperatively and redundantly regulate cell-autonomous transcriptional oscillation of Per3.
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Affiliation(s)
- Ritsuko Matsumura
- From the Research Institute for Time Studies, Yamaguchi University, 1677-1 Yoshida, Yamaguchi 753-8511, Japan
| | - Makoto Akashi
- From the Research Institute for Time Studies, Yamaguchi University, 1677-1 Yoshida, Yamaguchi 753-8511, Japan
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9
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A simple method using ex vivo culture of hair follicle tissue to investigate intrinsic circadian characteristics in humans. Sci Rep 2017; 7:6824. [PMID: 28755004 PMCID: PMC5533706 DOI: 10.1038/s41598-017-07268-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 06/23/2017] [Indexed: 12/03/2022] Open
Abstract
Almost all organisms maintain a circadian clock from birth to death to synchronize their own physiology and behavior with the earth’s rotation. Because the in vivo evaluation of human circadian characteristics is labor-intensive, in vitro or ex vivo approaches could provide advantages. In this study, to enable the simple and non-invasive evaluation of autonomous circadian oscillation, we established a method for monitoring clock gene expression by performing ex vivo culture of whole hair root tissue. This method is extremely simple and imposes little burden on subjects. Results obtained using Cryptochrome-deficient mice support that circadian period length in hair tissue correlates with intrinsic period length observed in physiology and behavior. We then applied this method to old-old subjects with severe dementia, who showed abnormal circadian behavior, and found that their peripheral clocks autonomously oscillated in a manner similar to those of healthy or younger subjects, indicating that the effect of cellular senescence on the autonomous clock oscillator is limited at least in some cell types. Although further validation may be required, the hair tissue-based culture assay would be a tool to investigate intrinsic circadian characteristics in humans.
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10
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Xing L, An Y, Shi G, Yan J, Xie P, Qu Z, Zhang Z, Liu Z, Pan D, Xu Y. Correlated evolution between CK1δ Protein and the Serine-rich Motif Contributes to Regulating the Mammalian Circadian Clock. J Biol Chem 2016; 292:161-171. [PMID: 27879317 DOI: 10.1074/jbc.m116.751214] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 11/21/2016] [Indexed: 11/06/2022] Open
Abstract
Understanding the mechanism underlying the physiological divergence of species is a long-standing issue in evolutionary biology. The circadian clock is a highly conserved system existing in almost all organisms that regulates a wide range of physiological and behavioral events to adapt to the day-night cycle. Here, the interactions between hCK1ϵ/δ/DBT (Drosophila ortholog of CK1δ/ϵ) and serine-rich (SR) motifs from hPER2 (ortholog of Drosophila per) were reconstructed in a Drosophila circadian system. The results indicated that in Drosophila, the SR mutant form hPER2S662G does not recapitulate the mouse or human mutant phenotype. However, introducing hCK1δ (but not DBT) shortened the circadian period and restored the SR motif function. We found that hCK1δ is catalytically more efficient than DBT in phosphorylating the SR motif, which demonstrates that the evolution of CK1δ activity is required for SR motif modulation. Moreover, an abundance of phosphorylatable SR motifs and the striking emergence of putative SR motifs in vertebrate proteins were observed, which provides further evidence that the correlated evolution between kinase activity and its substrates set the stage for functional diversity in vertebrates. It is possible that such correlated evolution may serve as a biomarker associated with the adaptive benefits of diverse organisms. These results also provide a concrete example of how functional synthesis can be achieved through introducing evolutionary partners in vivo.
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Affiliation(s)
- Lijuan Xing
- From the Cambridge-Suda Genomic Resource Center, Soochow University, 199 Renai Road, Suzhou 215123 and
| | - Yang An
- the MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Nanjing University, 12 Xuefu Road, Pukou District, Nanjing 210061, China
| | - Guangsen Shi
- From the Cambridge-Suda Genomic Resource Center, Soochow University, 199 Renai Road, Suzhou 215123 and
| | - Jie Yan
- From the Cambridge-Suda Genomic Resource Center, Soochow University, 199 Renai Road, Suzhou 215123 and
| | - Pancheng Xie
- the MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Nanjing University, 12 Xuefu Road, Pukou District, Nanjing 210061, China
| | - Zhipeng Qu
- the MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Nanjing University, 12 Xuefu Road, Pukou District, Nanjing 210061, China
| | - Zhihui Zhang
- the MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Nanjing University, 12 Xuefu Road, Pukou District, Nanjing 210061, China
| | - Zhiwei Liu
- From the Cambridge-Suda Genomic Resource Center, Soochow University, 199 Renai Road, Suzhou 215123 and
| | - Dejing Pan
- From the Cambridge-Suda Genomic Resource Center, Soochow University, 199 Renai Road, Suzhou 215123 and
| | - Ying Xu
- From the Cambridge-Suda Genomic Resource Center, Soochow University, 199 Renai Road, Suzhou 215123 and .,the MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Nanjing University, 12 Xuefu Road, Pukou District, Nanjing 210061, China
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11
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Lück S, Westermark PO. Circadian mRNA expression: insights from modeling and transcriptomics. Cell Mol Life Sci 2016; 73:497-521. [PMID: 26496725 PMCID: PMC11108398 DOI: 10.1007/s00018-015-2072-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 10/13/2015] [Accepted: 10/14/2015] [Indexed: 01/08/2023]
Abstract
Circadian clocks synchronize organisms to the 24 h rhythms of the environment. These clocks persist under constant conditions, have their origin at the cellular level, and produce an output of rhythmic mRNA expression affecting thousands of transcripts in many mammalian cell types. Here, we review the charting of circadian output rhythms in mRNA expression, focusing on mammals. We emphasize the challenges in statistics, interpretation, and quantitative descriptions that such investigations have faced and continue to face, and outline remaining outstanding questions.
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Affiliation(s)
- Sarah Lück
- Institute for Theoretical Biology, Charité - Universitätsmedizin Berlin, Invalidenstrasse 43, 10115, Berlin, Germany
| | - Pål O Westermark
- Institute for Theoretical Biology, Charité - Universitätsmedizin Berlin, Invalidenstrasse 43, 10115, Berlin, Germany.
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12
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Tanoue S, Fujimoto K, Myung J, Hatanaka F, Kato Y, Takumi T. DEC2-E4BP4 Heterodimer Represses the Transcriptional Enhancer Activity of the EE Element in the Per2 Promoter. Front Neurol 2015; 6:166. [PMID: 26257703 PMCID: PMC4512152 DOI: 10.3389/fneur.2015.00166] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Accepted: 07/09/2015] [Indexed: 01/12/2023] Open
Abstract
The circadian oscillation of clock gene expression in mammals is based on the interconnected transcriptional/translational feedback loops of Period (Per) and Bmal1. The Per feedback loop initiates transcription through direct binding of the BMAL1–CLOCK (NPAS2) heterodimer to the E-box of the Per2 promoter region. Negative feedback of PER protein on this promoter subsequently represses transcription. Other circadian transcription regulators, particularly E4BP4 and DEC2, regulate the amplitude and phase of Per2 expression rhythms. Moreover, a direct repeat of E-box-like (EE) elements in the Per2 promoter is required for its cell-autonomous circadian rhythm. However, the detailed mechanism for repression of the two core sequences of the EE element in the Per2 promoter region is unknown. Here, we show that E4BP4 binds to the Per2 EE element with DEC2 to repress transcription and identify the DEC2–E4BP4 heterodimer as a key repressor of the tightly interlocked Per2 feedback loop in the mammalian circadian oscillator. Our results suggest an additional modulatory mechanism for tuning of the phase of cell-autonomous Per2 gene expression cycling.
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Affiliation(s)
- Shintaro Tanoue
- Graduate School of Biomedical Sciences, Hiroshima University , Hiroshima , Japan
| | - Katsumi Fujimoto
- Graduate School of Biomedical Sciences, Hiroshima University , Hiroshima , Japan
| | - Jihwan Myung
- Graduate School of Biomedical Sciences, Hiroshima University , Hiroshima , Japan ; RIKEN Brain Science Institute , Wako, Saitama , Japan
| | - Fumiyuki Hatanaka
- Graduate School of Biomedical Sciences, Hiroshima University , Hiroshima , Japan ; RIKEN Brain Science Institute , Wako, Saitama , Japan
| | - Yukio Kato
- Graduate School of Biomedical Sciences, Hiroshima University , Hiroshima , Japan
| | - Toru Takumi
- Graduate School of Biomedical Sciences, Hiroshima University , Hiroshima , Japan ; RIKEN Brain Science Institute , Wako, Saitama , Japan ; CREST, Japan Science and Technology Agency , Tokyo , Japan
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13
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Isayama K, Zhao L, Chen H, Yamauchi N, Shigeyoshi Y, Hashimoto S, Hattori MA. Removal of Rev-erbα inhibition contributes to the prostaglandin G/H synthase 2 expression in rat endometrial stromal cells. Am J Physiol Endocrinol Metab 2015; 308:E650-61. [PMID: 25648833 DOI: 10.1152/ajpendo.00533.2014] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Accepted: 01/28/2015] [Indexed: 12/23/2022]
Abstract
The rhythmic expression of clock genes in the uterus is attenuated during decidualization. This study focused on Ptgs2, which is essential for decidualization, as a putative clock-controlled gene, and aimed to reveal the functions of clock genes in relation to Ptgs2 during decidualization. We compared the transcript levels of clock genes in the rat uterus on days 4.5 (D4.5) and 6.5 of pregnancy. The transcript levels of clock genes (Per2, Bmal1, Rorα, and Rev-erbα) had decreased at implantation sites on day 6.5 (D6.5e) compared with those on D4.5, whereas Ptgs2 transcripts had increased on D6.5e. Similar observations of Rev-erbα and Ptgs2 were also obtained in the endometrium on D6.5e by immunohistochemistry. In the decidual cells induced by medroxyprogesterone and 2-O-dibutyryl-cAMP, the rhythmic expression levels of clock genes were attenuated, whereas Ptgs2 transcription was induced. These results indicate that decidualization causes the attenuation of clock genes and the induction of Ptgs2. Furthermore, in the experiment of Bmal1 siRNA, the rhythmic expression of clock genes and Ptgs2 was attenuated by the siRNA. Transcript levels of Ptgs2 and prostaglandin (PG)E₂ production were increased by treatment with the Rev-erbα antagonist, suggesting the contribution of the nuclear receptor Rev-erbα to Ptgs2 expression. Moreover, Rev-erbα knockdown enhanced the induction of Ptgs2 transcription and PGE₂ production by forskolin. Chromatin immunoprecipitation-PCR analysis revealed that Rev-erbα could directly bind to a proximal RORE site of Ptgs2. Collectively, this study demonstrates that the attenuation of the circadian clock, especially its core component Rev-erbα, contributes to the induction of Ptgs2 during decidualization.
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MESH Headings
- 5' Untranslated Regions
- ARNTL Transcription Factors/antagonists & inhibitors
- ARNTL Transcription Factors/genetics
- ARNTL Transcription Factors/metabolism
- Animals
- Cells, Cultured
- Circadian Clocks
- Cyclooxygenase 2/genetics
- Cyclooxygenase 2/metabolism
- Endometrium/cytology
- Endometrium/enzymology
- Endometrium/metabolism
- Female
- Gene Expression Regulation, Enzymologic
- Nuclear Receptor Subfamily 1, Group D, Member 1/antagonists & inhibitors
- Nuclear Receptor Subfamily 1, Group D, Member 1/genetics
- Nuclear Receptor Subfamily 1, Group D, Member 1/metabolism
- Nuclear Receptor Subfamily 1, Group F, Member 1/genetics
- Nuclear Receptor Subfamily 1, Group F, Member 1/metabolism
- Placentation
- Pregnancy
- Prolactin/analogs & derivatives
- Prolactin/genetics
- Prolactin/metabolism
- RNA Interference
- RNA, Small Interfering
- Rats
- Rats, Transgenic
- Response Elements
- Stromal Cells/cytology
- Stromal Cells/enzymology
- Stromal Cells/metabolism
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Affiliation(s)
- Keishiro Isayama
- Department of Animal and Marine Bioresource Sciences, Graduate School of Agriculture, Kyushu University, Fukuoka, Japan
| | - Lijia Zhao
- Department of Animal and Marine Bioresource Sciences, Graduate School of Agriculture, Kyushu University, Fukuoka, Japan
| | - Huatao Chen
- Department of Animal and Marine Bioresource Sciences, Graduate School of Agriculture, Kyushu University, Fukuoka, Japan
| | - Nobuhiko Yamauchi
- Department of Animal and Marine Bioresource Sciences, Graduate School of Agriculture, Kyushu University, Fukuoka, Japan
| | - Yasufumi Shigeyoshi
- Department of Anatomy and Neurobiology, Kinki University School of Medicine, Osaka, Japan; and
| | | | - Masa-aki Hattori
- Department of Animal and Marine Bioresource Sciences, Graduate School of Agriculture, Kyushu University, Fukuoka, Japan;
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14
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Tasaki H, Zhao L, Isayama K, Chen H, Yamauchi N, Shigeyoshi Y, Hashimoto S, Hattori MA. Inhibitory role of REV-ERBα in the expression of bone morphogenetic protein gene family in rat uterus endometrium stromal cells. Am J Physiol Cell Physiol 2015; 308:C528-38. [DOI: 10.1152/ajpcell.00220.2014] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Accepted: 01/05/2015] [Indexed: 11/22/2022]
Abstract
Uterus circadian rhythms have been implicated in the gestation processes of mammals through entraining of the clock proteins to numerous downstream genes. Bone morphogenetic proteins (BMPs), having clock-controlled regulatory sites in their gene promoters, are expressed in the uterus during decidualization, but the regulation of the Bmp gene expression is poorly understood. The present study was designed to dissect the physiological roles of the uterus oscillators in the Bmp expression using the uterus endometrial stromal cells (UESCs) isolated from Per2-dLuc transgenic rats on day 4.5 of gestation. The in vitro decidualization of UESCs was induced by medroxyprogesterone acetate and 2-O-dibutyryl cAMP. A significant decline of Per2-dLuc bioluminescence activity was induced in decidual cells, and concomitantly, the expression of canonical clock genes was downregulated. Conversely, the expression of the core Bmp genes Bmp2, Bmp4, Bmp6, and Bmp7 was upregulated. In UESCs transfected with Bmal1-specific siRNA, in which Rev-erbα expression was downregulated, Bmp genes, such as Bmp2, Bmp4, and Bmp6 were upregulated. However, Bmp1, Bmp7, and Bmp8a were not significantly affected by Bmal1 silencing. The expression of all Bmp genes was enhanced after treatment with the REV-ERBα antagonist (SR8278), although their rhythmic profiles were differed from each other. The binding of REV-ERBα to the proximal regions of the Bmp2 and Bmp4 promoters was revealed by chromatin immunoprecipitation-PCR analysis. Collectively, these results indicate that the Bmp genes are upregulated by the attenuation of the cellular circadian clock; in particular, its core component REV-ERBα functions as a transcriptional silencer in the Bmp gene family.
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Affiliation(s)
- Hirotaka Tasaki
- Department of Animal and Marine Bioresource Sciences, Graduate School of Agriculture, Kyushu University, Fukuoka, Japan
| | - Lijia Zhao
- Department of Animal and Marine Bioresource Sciences, Graduate School of Agriculture, Kyushu University, Fukuoka, Japan
| | - Keishiro Isayama
- Department of Animal and Marine Bioresource Sciences, Graduate School of Agriculture, Kyushu University, Fukuoka, Japan
| | - Huatao Chen
- Department of Animal and Marine Bioresource Sciences, Graduate School of Agriculture, Kyushu University, Fukuoka, Japan
| | - Nobuhiko Yamauchi
- Department of Animal and Marine Bioresource Sciences, Graduate School of Agriculture, Kyushu University, Fukuoka, Japan
| | - Yasufumi Shigeyoshi
- Department of Anatomy and Neurobiology, Kinki University School of Medicine, Osaka, Japan; and
| | | | - Masa-aki Hattori
- Department of Animal and Marine Bioresource Sciences, Graduate School of Agriculture, Kyushu University, Fukuoka, Japan
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15
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Matsumura R, Tsuchiya Y, Tokuda I, Matsuo T, Sato M, Node K, Nishida E, Akashi M. The mammalian circadian clock protein period counteracts cryptochrome in phosphorylation dynamics of circadian locomotor output cycles kaput (CLOCK). J Biol Chem 2014; 289:32064-32072. [PMID: 25271155 PMCID: PMC4231683 DOI: 10.1074/jbc.m114.578278] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Revised: 09/30/2014] [Indexed: 11/06/2022] Open
Abstract
The circadian transcription factor CLOCK exhibits a circadian oscillation in its phosphorylation levels. Although it remains unclear whether this phosphorylation contributes to circadian rhythm generation, it has been suggested to be involved in transcriptional activity, intracellular localization, and degradative turnover of CLOCK. Here, we obtained direct evidence that CLOCK phosphorylation may be essential for autonomous circadian oscillation in clock gene expression. Importantly, we found that the circadian transcriptional repressors Cryptochrome (CRY) and Period (PER) showed an opposite effect on CLOCK phosphorylation; CRY impaired BMAL1-dependent CLOCK phosphorylation, whereas PER protected the phosphorylation against CRY. Interestingly, unlike PER1 and PER2, PER3 did not exert a protective action, which correlates with the phenotypic differences among mice lacking the Per genes. Further studies on the regulatory mechanism of CLOCK phosphorylation would thus lead to elucidation of the mechanism of CRY-mediated transcriptional repression and an understanding of the true role of PER in the negative feedback system.
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Affiliation(s)
- Ritsuko Matsumura
- Research Institute for Time Studies, Yamaguchi University, 1677-1 Yoshida, Yamaguchi 753-8511, Japan
| | - Yoshiki Tsuchiya
- Department of Cell and Developmental Biology, Graduate School of Biostudies, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Isao Tokuda
- Department of Mechanical Engineering, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu 525-8577, Japan, and
| | - Takahiro Matsuo
- Research Institute for Time Studies, Yamaguchi University, 1677-1 Yoshida, Yamaguchi 753-8511, Japan
| | - Miho Sato
- Research Institute for Time Studies, Yamaguchi University, 1677-1 Yoshida, Yamaguchi 753-8511, Japan
| | - Koichi Node
- Department of Cardiovascular Medicine, Saga University, 5-1-1 Nabeshima, Saga 849-8501, Japan
| | - Eisuke Nishida
- Department of Cell and Developmental Biology, Graduate School of Biostudies, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Makoto Akashi
- Research Institute for Time Studies, Yamaguchi University, 1677-1 Yoshida, Yamaguchi 753-8511, Japan,.
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16
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Okabe T, Kumagai M, Nakajima Y, Shirotake S, Kodaira K, Oyama M, Ueno M, Ikeda M. The impact of HIF1α on the Per2 circadian rhythm in renal cancer cell lines. PLoS One 2014; 9:e109693. [PMID: 25333958 PMCID: PMC4204850 DOI: 10.1371/journal.pone.0109693] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Accepted: 09/12/2014] [Indexed: 11/25/2022] Open
Abstract
In mammals, the circadian rhythm central generator consists of interactions among clock genes, including Per1/2/3, Cry1/2, Bmal1, and Clock. Circadian rhythm disruption may lead to increased risk of cancer in humans, and deregulation of clock genes has been implicated in many types of cancers. Among these genes, Per2 is reported to have tumor suppressor properties, but little is known about the correlation between Per2 and HIF, which is the main target of renal cell carcinoma (RCC) therapy. In this study, the rhythmic expression of the Per2 gene was not detectable in renal cancer cell lines, with the exception of Caki-2 cells. In Caki-2 cells, HIF1α increased the amplitude of Per2 oscillation by directly binding to the HIF-binding site located on the Per2 promoter. These results indicate that HIF1α may enhance the amplitude of the Per2 circadian rhythm.
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Affiliation(s)
- Takashi Okabe
- Department of Uro-oncology, Saitama Medical University International Medical Center, Saitama, Japan
| | - Megumi Kumagai
- Department of Physiology, Saitama Medical University, Saitama, Japan
- Molecular Clock Project, Project Research Division, Research Center for Genomic Medicine, Saitama Medical University, Saitama, Japan
| | - Yoshihiro Nakajima
- Health Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Kagawa, Japan
| | - Suguru Shirotake
- Department of Uro-oncology, Saitama Medical University International Medical Center, Saitama, Japan
| | - Kiichiro Kodaira
- Department of Uro-oncology, Saitama Medical University International Medical Center, Saitama, Japan
| | - Masafumi Oyama
- Department of Uro-oncology, Saitama Medical University International Medical Center, Saitama, Japan
| | - Munehisa Ueno
- Department of Uro-oncology, Saitama Medical University International Medical Center, Saitama, Japan
| | - Masaaki Ikeda
- Department of Physiology, Saitama Medical University, Saitama, Japan
- Molecular Clock Project, Project Research Division, Research Center for Genomic Medicine, Saitama Medical University, Saitama, Japan
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17
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Hirai T, Tanaka K, Togari A. β-adrenergic receptor signaling regulates Ptgs2 by driving circadian gene expression in osteoblasts. J Cell Sci 2014; 127:3711-9. [PMID: 24994935 DOI: 10.1242/jcs.148148] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The sympathetic nervous system modulates bone remodeling and mediates the expression of core clock genes in part through the β-adrenergic receptor (β-AR) in osteoblasts. In this study, we show that in MC3T3-E1 osteoblastic cells that isoproterenol (Iso), a non-selective β-AR agonist, upregulated the transcriptional factor Nfil3, and induced rhythmic mRNA expression of prostaglandin-endoperoxide synthase 2 (Ptgs2, also known as Cox2). The rhythmic effects of Iso on Ptgs2 expression were mediated by interplay between the Per2 and Bmal1 clock genes in osteoblasts. In addition, Ptgs2 was significantly decreased in bone after continuous Iso treatment. Overexpression of Nfil3 decreased Ptgs2 expression in MC3T3-E1 cells. Knockdown of Nfil3 upregulated the expression of Ptgs2 in MC3TC-E1 cells, indicating that Nfil3 negatively regulated Ptgs2 in osteoblasts. Furthermore, Iso acutely induced the expression Nfil3 and increased the binding of Nfil3 to the Ptgs2 promoter in MC3T3-E1 cells. These results suggest that Iso-mediated induction of Nfil3 in osteoblasts regulates the expression of Ptgs2 by driving the expression of circadian clock genes. These findings provide new evidence for a physiological role of circadian clockwork in bone metabolism.
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Affiliation(s)
- Takao Hirai
- Department of Pharmacology, School of Dentistry, Aichi-Gakuin University, Nagoya 464-8650, Japan
| | - Kenjiro Tanaka
- Department of Pharmacology, School of Dentistry, Aichi-Gakuin University, Nagoya 464-8650, Japan
| | - Akifumi Togari
- Department of Pharmacology, School of Dentistry, Aichi-Gakuin University, Nagoya 464-8650, Japan
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18
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Akashi M, Okamoto A, Tsuchiya Y, Todo T, Nishida E, Node K. A positive role for PERIOD in mammalian circadian gene expression. Cell Rep 2014; 7:1056-64. [PMID: 24794436 DOI: 10.1016/j.celrep.2014.03.072] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2013] [Revised: 02/05/2014] [Accepted: 03/28/2014] [Indexed: 12/29/2022] Open
Abstract
In the current model of the mammalian circadian clock, PERIOD (PER) represses the activity of the circadian transcription factors BMAL1 and CLOCK, either independently or together with CRYPTOCHROME (CRY). Here, we provide evidence that PER has an entirely different function from that reported previously, namely, that PER inhibits CRY-mediated transcriptional repression through interference with CRY recruitment into the BMAL1-CLOCK complex. This indirect positive function of PER is consistent with previous data from genetic analyses using Per-deficient or mutant mice. Overall, our results support the hypothesis that PER plays different roles in different circadian phases: an early phase in which it suppresses CRY activity, and a later phase in which it acts as a transcriptional repressor with CRY. This buffering effect of PER on CRY might help to prolong the period of rhythmic gene expression. Additional studies are required to carefully examine the promoter- and phase-specific roles of PER.
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Affiliation(s)
- Makoto Akashi
- The Research Institute for Time Studies, Yamaguchi University, Yamaguchi 753-8511, Japan.
| | - Akihiko Okamoto
- The Research Institute for Time Studies, Yamaguchi University, Yamaguchi 753-8511, Japan
| | - Yoshiki Tsuchiya
- Department of Cell and Developmental Biology, Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Takeshi Todo
- Department of Radiation Biology and Medical Genetics, Graduate School of Medicine, Osaka University, Osaka 565-0871, Japan
| | - Eisuke Nishida
- Department of Cell and Developmental Biology, Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Koichi Node
- Department of Cardiovascular Medicine, Saga University, Saga 849-8501, Japan
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19
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Mori K, Iijima N, Higo S, Aikawa S, Matsuo I, Takumi K, Sakamoto A, Ozawa H. Epigenetic suppression of mouse Per2 expression in the suprachiasmatic nucleus by the inhalational anesthetic, sevoflurane. PLoS One 2014; 9:e87319. [PMID: 24498074 PMCID: PMC3909093 DOI: 10.1371/journal.pone.0087319] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2013] [Accepted: 12/20/2013] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND We previously reported that sevoflurane anesthesia reversibly suppresses the expression of the clock gene, Period2 (Per2), in the mouse suprachiasmatic nucleus (SCN). However, the molecular mechanisms underlying this suppression remain unclear. In this study, we examined the possibility that sevoflurane suppresses Per2 expression via epigenetic modification of the Per2 promoter. METHODS Mice were anesthetized with a gas mixture of 2.5% sevoflurane/40% oxygen at a 6 L/min flow for 1 or 4 h. After termination, brains were removed and samples of SCN tissue were derived from frozen brain sections. Chromatin immunoprecipitation (ChIP) assays using anti-acetylated-histone antibodies were performed to investigate the effects of sevoflurane on histone acetylation of the Per2 promoter. Interaction between the E'-box (a cis-element in the Per2 promoter) and CLOCK (the Clock gene product) was also assessed by a ChIP assay using an anti-CLOCK antibody. The SCN concentration of nicotinamide adenine dinucleotide (NAD(+)), a CLOCK regulator, was assessed by liquid chromatography-mass spectrometry. RESULTS Acetylation of histone H4 in the proximal region of the Per2 promoter was significantly reduced by sevoflurane. This change in the epigenetic profile of the Per2 gene was observed prior to suppression of Per2 expression. Simultaneously, a reduction in the CLOCK-E'-box interaction in the Per2 promoter was observed. Sevoflurane treatment did not affect the concentration of NAD(+) in the SCN. CONCLUSIONS Independent of NAD(+) concentration in the SCN, sevoflurane decreases CLOCK binding to the Per2 promoter E'-box motif, reducing histone acetylation and leading to suppression of Per2 expression.
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Affiliation(s)
- Keisuke Mori
- Department of Anatomy and Neurobiology, Graduate School of Medicine, Nippon Medical School, Tokyo, Japan
- Department of Anesthesiology and Pain Medicine, Graduate School of Medicine, Nippon Medical School, Tokyo, Japan
| | - Norio Iijima
- Department of Anatomy and Neurobiology, Graduate School of Medicine, Nippon Medical School, Tokyo, Japan
| | - Shimpei Higo
- Department of Anatomy and Neurobiology, Graduate School of Medicine, Nippon Medical School, Tokyo, Japan
| | - Satoko Aikawa
- Department of Anatomy and Neurobiology, Graduate School of Medicine, Nippon Medical School, Tokyo, Japan
| | - Izumi Matsuo
- Department of Anatomy and Neurobiology, Graduate School of Medicine, Nippon Medical School, Tokyo, Japan
- Department of Anesthesiology and Pain Medicine, Graduate School of Medicine, Nippon Medical School, Tokyo, Japan
| | - Ken Takumi
- Department of Anatomy and Neurobiology, Graduate School of Medicine, Nippon Medical School, Tokyo, Japan
| | - Atsuhiro Sakamoto
- Department of Anesthesiology and Pain Medicine, Graduate School of Medicine, Nippon Medical School, Tokyo, Japan
| | - Hitoshi Ozawa
- Department of Anatomy and Neurobiology, Graduate School of Medicine, Nippon Medical School, Tokyo, Japan
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20
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Cheon S, Park N, Cho S, Kim K. Glucocorticoid-mediated Period2 induction delays the phase of circadian rhythm. Nucleic Acids Res 2013; 41:6161-74. [PMID: 23620290 PMCID: PMC3695510 DOI: 10.1093/nar/gkt307] [Citation(s) in RCA: 82] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2012] [Revised: 04/02/2013] [Accepted: 04/03/2013] [Indexed: 11/21/2022] Open
Abstract
Glucocorticoid (GC) signaling synchronizes the circadian rhythm of individual peripheral cells and induces the expression of circadian genes, including Period1 (Per1) and Period2 (Per2). However, no GC response element (GRE) has been reported in the Per2 promoter region. Here we report the molecular mechanisms of Per2 induction by GC signaling and its relevance to the regulation of circadian timing. We found that GC prominently induced Per2 expression and delayed the circadian phase. The overlapping GRE and E-box (GE2) region in the proximal Per2 promoter was responsible for GC-mediated Per2 induction. The GRE in the Per2 promoter was unique in that brain and muscle ARNT-like protein-1 (BMAL1) was essential for GC-induced Per2 expression, whereas other GRE-containing promoters, such as Per1 and mouse mammary tumor virus, responded to dexamethasone in the absence of BMAL1. This specialized regulatory mechanism was mediated by BMAL1-dependent binding of the GC receptor to GRE in Per2 promoter. When Per2 induction was abrogated by the mutation of the GRE or E-box, the circadian oscillation phase failed to be delayed compared with that of the wild-type. Therefore, the current study demonstrates that the rapid Per2 induction mediated by GC is crucial for delaying the circadian rhythm.
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Affiliation(s)
- Solmi Cheon
- Interdisciplinary Program in Neuroscience, Seoul National University, Seoul 151-742, Korea, Brain Research Center for the 21st Century Frontier R&D Program in Neuroscience, Seoul 151-742, Korea, Department of Biological Sciences, Seoul National University, Seoul 151-742, Korea and Department of Physiology, Neurodegeneration Control Research Center, Kyung Hee University School of Medicine, Seoul 130-701, Korea
| | - Noheon Park
- Interdisciplinary Program in Neuroscience, Seoul National University, Seoul 151-742, Korea, Brain Research Center for the 21st Century Frontier R&D Program in Neuroscience, Seoul 151-742, Korea, Department of Biological Sciences, Seoul National University, Seoul 151-742, Korea and Department of Physiology, Neurodegeneration Control Research Center, Kyung Hee University School of Medicine, Seoul 130-701, Korea
| | - Sehyung Cho
- Interdisciplinary Program in Neuroscience, Seoul National University, Seoul 151-742, Korea, Brain Research Center for the 21st Century Frontier R&D Program in Neuroscience, Seoul 151-742, Korea, Department of Biological Sciences, Seoul National University, Seoul 151-742, Korea and Department of Physiology, Neurodegeneration Control Research Center, Kyung Hee University School of Medicine, Seoul 130-701, Korea
| | - Kyungjin Kim
- Interdisciplinary Program in Neuroscience, Seoul National University, Seoul 151-742, Korea, Brain Research Center for the 21st Century Frontier R&D Program in Neuroscience, Seoul 151-742, Korea, Department of Biological Sciences, Seoul National University, Seoul 151-742, Korea and Department of Physiology, Neurodegeneration Control Research Center, Kyung Hee University School of Medicine, Seoul 130-701, Korea
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21
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Kadomatsu T, Uragami S, Akashi M, Tsuchiya Y, Nakajima H, Nakashima Y, Endo M, Miyata K, Terada K, Todo T, Node K, Oike Y. A molecular clock regulates angiopoietin-like protein 2 expression. PLoS One 2013; 8:e57921. [PMID: 23469106 PMCID: PMC3585275 DOI: 10.1371/journal.pone.0057921] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2012] [Accepted: 01/27/2013] [Indexed: 11/18/2022] Open
Abstract
Various physiological and behavioral processes exhibit circadian rhythmicity. These rhythms are usually maintained by negative feedback loops of core clock genes, namely, CLOCK, BMAL, PER, and CRY. Recently, dysfunction in the circadian clock has been recognized as an important foundation for the pathophysiology of lifestyle-related diseases, such as obesity, cardiovascular disease, and some cancers. We have reported that angiopoietin-like protein 2 (ANGPTL2) contributes to the pathogenesis of these lifestyle-related diseases by inducing chronic inflammation. However, molecular mechanisms underlying regulation of ANGPTL2 expression are poorly understood. Here, we assess circadian rhythmicity of ANGPTL2 expression in various mouse tissues. We observed that ANGPTL2 rhythmicity was similar to that of the PER2 gene, which is regulated by the CLOCK/BMAL1 complex. Promoter activity of the human ANGPTL2 gene was significantly induced by CLOCK and BMAL1, an induction markedly attenuated by CRY co-expression. We also identified functional E-boxes in the ANGPTL2 promoter and observed occupancy of these sites by endogenous CLOCK in human osteosarcoma cells. Furthermore, Cry-deficient mice exhibited arrhythmic Angptl2 expression. Taken together, these data suggest that periodic expression of ANGPTL2 is regulated by a molecular clock.
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Affiliation(s)
- Tsuyoshi Kadomatsu
- Department of Molecular Genetics, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
- * E-mail: (TK); (YO)
| | - Shota Uragami
- Department of Molecular Genetics, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Makoto Akashi
- Research Institute for Time Studies, Yamaguchi University, Yamaguchi, Japan
| | - Yoshiki Tsuchiya
- Department of Neuroscience and Cell Biology, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Hiroo Nakajima
- Department of Radiation Biology and Medical Genetics, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Yukiko Nakashima
- Department of Molecular Genetics, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Motoyoshi Endo
- Department of Molecular Genetics, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Keishi Miyata
- Department of Molecular Genetics, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Kazutoyo Terada
- Department of Molecular Genetics, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Takeshi Todo
- Department of Radiation Biology and Medical Genetics, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Koichi Node
- Department of Cardiovascular and Renal Medicine, Faculty of Medicine, Saga University, Saga, Japan
| | - Yuichi Oike
- Department of Molecular Genetics, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
- * E-mail: (TK); (YO)
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22
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Miki T, Matsumoto T, Zhao Z, Lee CC. p53 regulates Period2 expression and the circadian clock. Nat Commun 2013; 4:2444. [PMID: 24051492 PMCID: PMC3798035 DOI: 10.1038/ncomms3444] [Citation(s) in RCA: 116] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2013] [Accepted: 08/15/2013] [Indexed: 02/06/2023] Open
Abstract
The mechanistic interconnectivity between circadian regulation and the genotoxic stress response remains poorly understood. Here we show that the expression of Period 2 (Per2), a circadian regulator, is directly regulated by p53 binding to a response element in the Per2 promoter. This p53 response element is evolutionarily conserved and overlaps with the E-Box element critical for BMAL1/CLOCK binding and its transcriptional activation of Per2 expression. Our studies reveal that p53 blocks BMAL1/CLOCK binding to the Per2 promoter, leading to repression of Per2 expression. In the suprachiasmatic nucleus (SCN), p53 expression and its binding to the Per2 promoter are under circadian control. Per2 expression in the SCN is altered by p53 deficiency or stabilization of p53 by Nutlin-3. Behaviourally, p53⁻/⁻ mice have a shorter period length that lacks stability, and they exhibit impaired photo-entrainment to a light pulse under a free-running state. Our studies demonstrate that p53 modulates mouse circadian behaviour.
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Affiliation(s)
- Takao Miki
- Department of Biochemistry and Molecular Biology, Medical School, University of Texas Health Science Center-Houston, Houston, Texas 77030
| | - Tomoko Matsumoto
- Department of Biochemistry and Molecular Biology, Medical School, University of Texas Health Science Center-Houston, Houston, Texas 77030
| | - Zhaoyang Zhao
- Department of Biochemistry and Molecular Biology, Medical School, University of Texas Health Science Center-Houston, Houston, Texas 77030
| | - Cheng Chi Lee
- Department of Biochemistry and Molecular Biology, Medical School, University of Texas Health Science Center-Houston, Houston, Texas 77030
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23
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Intermolecular recognition revealed by the complex structure of human CLOCK-BMAL1 basic helix-loop-helix domains with E-box DNA. Cell Res 2012; 23:213-24. [PMID: 23229515 DOI: 10.1038/cr.2012.170] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
CLOCK (circadian locomotor output cycles kaput) and BMAL1 (brain and muscle ARNT-like 1) are both transcription factors of the circadian core loop in mammals. Recently published mouse CLOCK-BMAL1 bHLH (basic helix-loop-helix)-PAS (period-ARNT-single-minded) complex structure sheds light on the mechanism for heterodimer formation, but the structural details of the protein-DNA recognition mechanisms remain elusive. Here we have elucidated the crystal structure of human CLOCK-BMAL1 bHLH domains bound to a canonical E-box DNA. We demonstrate that CLOCK and BMAL1 bHLH domains can be mutually selected, and that hydrogen-bonding networks mediate their E-box recognition. We identified a hydrophobic contact between BMAL1 Ile80 and a flanking thymine nucleotide, suggesting that CLOCK-BMAL1 actually reads 7-bp DNA and not the previously believed 6-bp DNA. To find potential non-canonical E-boxes that could be recognized by CLOCK-BMAL1, we constructed systematic single-nucleotide mutations on the E-box and measured their relevant affinities. We defined two non-canonical E-box patterns with high affinities, AACGTGA and CATGTGA, in which the flanking A7-T7' base pair is indispensable for recognition. These results will help us to identify functional CLOCK-BMAL1-binding sites in vivo and to search for clock-controlled genes. Furthermore, we assessed the inhibitory role of potential phosphorylation sites in bHLH regions. We found that the phospho-mimicking mutation on BMAL1 Ser78 could efficiently block DNA binding as well as abolish normal circadian oscillation in cells. We propose that BMAL1 Ser78 should be a key residue mediating input signal-regulated transcriptional inhibition for external cues to entrain the circadian clock by kinase cascade.
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Ramanathan C, Khan SK, Kathale ND, Xu H, Liu AC. Monitoring cell-autonomous circadian clock rhythms of gene expression using luciferase bioluminescence reporters. J Vis Exp 2012:4234. [PMID: 23052244 DOI: 10.3791/4234] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
In mammals, many aspects of behavior and physiology such as sleep-wake cycles and liver metabolism are regulated by endogenous circadian clocks (reviewed). The circadian time-keeping system is a hierarchical multi-oscillator network, with the central clock located in the suprachiasmatic nucleus (SCN) synchronizing and coordinating extra-SCN and peripheral clocks elsewhere. Individual cells are the functional units for generation and maintenance of circadian rhythms, and these oscillators of different tissue types in the organism share a remarkably similar biochemical negative feedback mechanism. However, due to interactions at the neuronal network level in the SCN and through rhythmic, systemic cues at the organismal level, circadian rhythms at the organismal level are not necessarily cell-autonomous. Compared to traditional studies of locomotor activity in vivo and SCN explants ex vivo, cell-based in vitro assays allow for discovery of cell-autonomous circadian defects. Strategically, cell-based models are more experimentally tractable for phenotypic characterization and rapid discovery of basic clock mechanisms. Because circadian rhythms are dynamic, longitudinal measurements with high temporal resolution are needed to assess clock function. In recent years, real-time bioluminescence recording using firefly luciferase as a reporter has become a common technique for studying circadian rhythms in mammals, as it allows for examination of the persistence and dynamics of molecular rhythms. To monitor cell-autonomous circadian rhythms of gene expression, luciferase reporters can be introduced into cells via transient transfection or stable transduction. Here we describe a stable transduction protocol using lentivirus-mediated gene delivery. The lentiviral vector system is superior to traditional methods such as transient transfection and germline transmission because of its efficiency and versatility: it permits efficient delivery and stable integration into the host genome of both dividing and non-dividing cells. Once a reporter cell line is established, the dynamics of clock function can be examined through bioluminescence recording. We first describe the generation of P(Per2)-dLuc reporter lines, and then present data from this and other circadian reporters. In these assays, 3T3 mouse fibroblasts and U2OS human osteosarcoma cells are used as cellular models. We also discuss various ways of using these clock models in circadian studies. Methods described here can be applied to a great variety of cell types to study the cellular and molecular basis of circadian clocks, and may prove useful in tackling problems in other biological systems.
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Ozaki N, Noshiro M, Kawamoto T, Nakashima A, Honda K, Fukuzaki-Dohi U, Honma S, Fujimoto K, Tanimoto K, Tanne K, Kato Y. Regulation of basic helix-loop-helix transcription factors Dec1 and Dec2 by RORα and their roles in adipogenesis. Genes Cells 2012; 17:109-21. [PMID: 22244086 DOI: 10.1111/j.1365-2443.2011.01574.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
DEC1 and DEC2, members of the basic helix-loop-helix superfamily, are involved in various biological phenomena including clock systems, cell differentiation and metabolism. In clock systems, Dec1 and Dec2 expression are up-regulated by the CLOCK:BMAL1 heterodimer via E-box (CACGTG), exhibiting a circadian rhythm in the suprachiasmatic nucleus (SCN), the central circadian pacemaker and other peripheral tissues. In this study, using assays of luciferase reporters, electrophoretic mobility shift and chromatin immunoprecipitation, we identified novel nuclear receptor response elements, ROR response elements (RORE), in Dec1 and Dec2 promoters. These ROREs responded to the transcriptional activator RORα, but not to the repressor REVERBα, although the Bmal1 promoter responded to both RORα and REVERBα. Therefore, RORα, but not REVERBα, is involved in the regulation of Dec1 and Dec2 expression without significantly affecting their rhythmicity. Since RORα, DEC1 and DEC2 reportedly suppressed adipogenic differentiation, we examined expression of Rorα, Dec1, Dec2 and other clock-controlled genes in differentiating 3T3-L1 adipocytes. The results suggested that RORα suppresses adipogenic differentiation at a later stage of differentiation by RORE-mediated stimulation of Dec1 and Dec2 expression.
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Affiliation(s)
- Noritsugu Ozaki
- Department of Orthodontics and Craniofacial Developmental Biology, Hiroshima University Graduate School of Biomedical Sciences, Hiroshima 734-8553, Japan
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Zhang X, Patel SP, McCarthy JJ, Rabchevsky AG, Goldhamer DJ, Esser KA. A non-canonical E-box within the MyoD core enhancer is necessary for circadian expression in skeletal muscle. Nucleic Acids Res 2011; 40:3419-30. [PMID: 22210883 PMCID: PMC3333858 DOI: 10.1093/nar/gkr1297] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The myogenic differentiation 1 (MyoD) gene is a master regulator of myogenesis. We previously reported that the expression of MyoD mRNA oscillates over 24 h in skeletal muscle and that the circadian clock transcription factors, BMAL1 (brain and muscle ARNT-like 1) and CLOCK (circadian locomotor output cycles kaput), were bound to the core enhancer (CE) of the MyoD gene in vivo. In this study, we provide in vivo and in vitro evidence that the CE is necessary for circadian expression of MyoD in adult muscle. Gel shift assays identified a conserved non-canonical E-box within the CE that is bound by CLOCK and BMAL1. Functional analysis revealed that this E-box was required for full activation by BMAL1/CLOCK and for in vitro circadian oscillation. Expression profiling of muscle of CE(loxP/loxP) mice found approximately 1300 genes mis-expressed relative to wild-type. Based on the informatics results, we analyzed the respiratory function of mitochondria isolated from wild-type and CE(loxP/loxP) mice. These assays determined that State 5 respiration was significantly reduced in CE(loxP/loxP) muscle. The results of this work identify a novel element in the MyoD enhancer that confers circadian regulation to MyoD in skeletal muscle and suggest that loss of circadian regulation leads to changes in myogenic expression and downstream mitochondrial function.
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Affiliation(s)
- Xiping Zhang
- Center for Muscle Biology, Department of Physiology, University of Kentucky, Lexington, KY 40536, USA
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Scoma HD, Humby M, Yadav G, Zhang Q, Fogerty J, Besharse JC. The de-ubiquitinylating enzyme, USP2, is associated with the circadian clockwork and regulates its sensitivity to light. PLoS One 2011; 6:e25382. [PMID: 21966515 PMCID: PMC3179520 DOI: 10.1371/journal.pone.0025382] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2011] [Accepted: 09/02/2011] [Indexed: 11/18/2022] Open
Abstract
We have identified a novel component of the circadian clock that regulates its sensitivity to light at the evening light to dark transition. USP2 (Ubiquitin Specific Protease 2), which de-ubiquitinylates and stabilizes target proteins, is rhythmically expressed in multiple tissues including the SCN. We have developed a knockout model of USP2 and found that exposure to low irradiance light at ZT12 increases phase delays of USP2(-/-) mice compared to wildtype. We additionally show that USP2b is in a complex with several clock components and regulates the stability and turnover of BMAL1, which in turn alters the expression of several CLOCK/BMAL1 controlled genes. Rhythmic expression of USP2 in the SCN and other tissues offers a new level of control of the clock machinery through de-ubiqutinylation and suggests a role for USP2 during circadian adaptation to environmental day length changes.
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Affiliation(s)
- Heather Dehlin Scoma
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
| | - Monica Humby
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
| | - Geetha Yadav
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
| | - Qingjiong Zhang
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
| | - Joseph Fogerty
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
| | - Joseph C. Besharse
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
- * E-mail:
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Circadian regulation of intracellular G-protein signalling mediates intercellular synchrony and rhythmicity in the suprachiasmatic nucleus. Nat Commun 2011; 2:327. [PMID: 21610730 PMCID: PMC3112533 DOI: 10.1038/ncomms1316] [Citation(s) in RCA: 105] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2010] [Accepted: 04/18/2011] [Indexed: 12/14/2022] Open
Abstract
Synchronous oscillations of thousands of cellular clocks in the suprachiasmatic nucleus (SCN), the circadian centre, are coordinated by precisely timed cell–cell communication, the principle of which is largely unknown. Here we show that the amount of RGS16 (regulator of G protein signalling 16), a protein known to inactivate Gαi, increases at a selective circadian time to allow time-dependent activation of intracellular cyclic AMP signalling in the SCN. Gene ablation of Rgs16 leads to the loss of circadian production of cAMP and as a result lengthens circadian period of behavioural rhythm. The temporally precise regulation of the cAMP signal by clock-controlled RGS16 is needed for the dorsomedial SCN to maintain a normal phase-relationship to the ventrolateral SCN. Thus, RGS16-dependent temporal regulation of intracellular G protein signalling coordinates the intercellular synchrony of SCN pacemaker neurons and thereby defines the 24 h rhythm in behaviour. Circadian rhythm is controlled by the suprachiasmatic nucleus and the mechanisms that control the rhythm are largely undiscovered. In this study, a G protein regulator, RGS16, is shown to be involved in the production of cyclic AMP that is required for the suprachiasmatic nucleus to maintain rhythm
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Yamajuku D, Shibata Y, Kitazawa M, Katakura T, Urata H, Kojima T, Takayasu S, Nakata O, Hashimoto S. Cellular DBP and E4BP4 proteins are critical for determining the period length of the circadian oscillator. FEBS Lett 2011; 585:2217-22. [DOI: 10.1016/j.febslet.2011.05.038] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2011] [Revised: 05/04/2011] [Accepted: 05/09/2011] [Indexed: 10/18/2022]
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Kashiwada M, Cassel SL, Colgan JD, Rothman PB. NFIL3/E4BP4 controls type 2 T helper cell cytokine expression. EMBO J 2011; 30:2071-82. [PMID: 21499227 DOI: 10.1038/emboj.2011.111] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2010] [Accepted: 03/17/2011] [Indexed: 12/21/2022] Open
Abstract
Type 2 T helper (T(H)2) cells are critical for the development of allergic immune responses; however, the molecular mechanism controlling their effector function is still largely unclear. Here, we report that the transcription factor NFIL3/E4BP4 regulates cytokine production and effector function by T(H)2 cells. NFIL3 is highly expressed in T(H)2 cells but much less in T(H)1 cells. Production of interleukin (IL)-13 and IL-5 is significantly increased in Nfil3(-/-) T(H)2 cells and is decreased by expression of NFIL3 in wild-type T(H)2 cells. NFIL3 directly binds to and negatively regulates the Il13 gene. In contrast, IL-4 production is decreased in Nfil3(-/-) T(H)2 cells. Increased IL-13 and IL-5 together with decreased IL-4 production by antigen-stimulated splenocytes from the immunized Nfil3(-/-) mice was also observed. The ability of NFIL3 to alter T(H)2 cytokine production is a T-cell intrinsic effect. Taken together, these data indicate that NFIL3 is a key regulator of T(H)2 responses.
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Affiliation(s)
- Masaki Kashiwada
- Department of Internal Medicine, University of Iowa, Iowa City, IA, USA
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Szántóová K, Zeman M, Veselá A, Herichová I. Effect of phase delay lighting rotation schedule on daily expression of per2, bmal1, rev-erbα, pparα, and pdk4 genes in the heart and liver of Wistar rats. Mol Cell Biochem 2010; 348:53-60. [DOI: 10.1007/s11010-010-0636-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2010] [Accepted: 10/28/2010] [Indexed: 01/21/2023]
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Genome-wide profiling of the core clock protein BMAL1 targets reveals a strict relationship with metabolism. Mol Cell Biol 2010; 30:5636-48. [PMID: 20937769 DOI: 10.1128/mcb.00781-10] [Citation(s) in RCA: 115] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Circadian rhythms are common to most organisms and govern much of homeostasis and physiology. Since a significant fraction of the mammalian genome is controlled by the clock machinery, understanding the genome-wide signaling and epigenetic basis of circadian gene expression is essential. BMAL1 is a critical circadian transcription factor that regulates genes via E-box elements in their promoters. We used multiple high-throughput approaches, including chromatin immunoprecipitation-based systematic analyses and DNA microarrays combined with bioinformatics, to generate genome-wide profiles of BMAL1 target genes. We reveal that, in addition to E-boxes, the CCAATG element contributes to elicit robust circadian expression. BMAL1 occupancy is found in more than 150 sites, including all known clock genes. Importantly, a significant proportion of BMAL1 targets include genes that encode central regulators of metabolic processes. The database generated in this study constitutes a useful resource to decipher the network of circadian gene control and its intimate links with several fundamental physiological functions.
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Noguchi T, Michihata T, Nakamura W, Takumi T, Shimizu R, Yamamoto M, Ikeda M, Ohmiya Y, Nakajima Y. Dual-Color Luciferase Mouse Directly Demonstrates Coupled Expression of Two Clock Genes. Biochemistry 2010; 49:8053-61. [DOI: 10.1021/bi100545h] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Takako Noguchi
- National Institute of Advanced Industrial Science and Technology (AIST), 1-8-31 Midorigaoka, Ikeda, Osaka 563-8577, Japan
| | - Tomoko Michihata
- National Institute of Advanced Industrial Science and Technology (AIST), 1-8-31 Midorigaoka, Ikeda, Osaka 563-8577, Japan
| | - Wataru Nakamura
- Osaka University Graduate School of Dentistry, 1-8 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Toru Takumi
- Graduate School of Biomedical Sciences, Hiroshima University, 1-2-3 Kasumi, Minamiku, Hiroshima 734-8553, Japan
- Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, Saitama 332-0012, Japan
| | | | | | - Masaaki Ikeda
- Department of Physiology, Saitama Medical University, 38 Morohongo, Moroyama, Iruma-gun, Saitama 350-0495, Japan
- Molecular Clock Project, Project Research Division, Research Center for Genomic Medicine, Saitama Medical University, 1397-1 Yamane, Hidaka, Saitama 350-1241, Japan
| | - Yoshihiro Ohmiya
- National Institute of Advanced Industrial Science and Technology (AIST), 1-8-31 Midorigaoka, Ikeda, Osaka 563-8577, Japan
| | - Yoshihiro Nakajima
- National Institute of Advanced Industrial Science and Technology (AIST), 1-8-31 Midorigaoka, Ikeda, Osaka 563-8577, Japan
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Yamajuku D, Shibata Y, Kitazawa M, Katakura T, Urata H, Kojima T, Nakata O, Hashimoto S. Identification of functional clock-controlled elements involved in differential timing of Per1 and Per2 transcription. Nucleic Acids Res 2010; 38:7964-73. [PMID: 20693532 PMCID: PMC3001056 DOI: 10.1093/nar/gkq678] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
It has been proposed that robust rhythmic gene expression requires clock-controlled elements (CCEs). Transcription of Per1 was reported to be regulated by the E-box and D-box in conventional reporter assays. However, such experiments are inconclusive in terms of how the CCEs and their combinations determine the phase of the Per1 gene. Whereas the phase of Per2 oscillation was found to be the most delayed among the three Period genes, the phase-delaying regions of the Per2 promoter remain to be determined. We therefore investigated the regulatory mechanism of circadian Per1 and Per2 transcription using an in vitro rhythm oscillation-monitoring system. We found that the copy number of the E-box might play an important role in determining the phase of Per1 oscillation. Based on real-time bioluminescence assays with various promoter constructs, we provide evidence that the non-canonical E-box is involved in the phase delay of Per2 oscillation. Transfection experiments confirmed that the non-canonical E-box could be activated by CLOCK/BMAL1. We also show that the D-box in the third conserved segment of the Per2 promoter generated high amplitude. Our experiments demonstrate that the copy number and various combinations of functional CCEs ultimately led to different circadian phases and amplitudes.
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Affiliation(s)
- Daisuke Yamajuku
- Pharmacology Research Laboratories, Astellas Pharma, Inc., 21 Miyukigaoka, Tsukuba, Ibaraki 305-8585, Japan.
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Olex AL, Hiltbold EM, Leng X, Fetrow JS. Dynamics of dendritic cell maturation are identified through a novel filtering strategy applied to biological time-course microarray replicates. BMC Immunol 2010; 11:41. [PMID: 20682054 PMCID: PMC2928180 DOI: 10.1186/1471-2172-11-41] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2009] [Accepted: 08/03/2010] [Indexed: 01/04/2023] Open
Abstract
Background Dendritic cells (DC) play a central role in primary immune responses and become potent stimulators of the adaptive immune response after undergoing the critical process of maturation. Understanding the dynamics of DC maturation would provide key insights into this important process. Time course microarray experiments can provide unique insights into DC maturation dynamics. Replicate experiments are necessary to address the issues of experimental and biological variability. Statistical methods and averaging are often used to identify significant signals. Here a novel strategy for filtering of replicate time course microarray data, which identifies consistent signals between the replicates, is presented and applied to a DC time course microarray experiment. Results The temporal dynamics of DC maturation were studied by stimulating DC with poly(I:C) and following gene expression at 5 time points from 1 to 24 hours. The novel filtering strategy uses standard statistical and fold change techniques, along with the consistency of replicate temporal profiles, to identify those differentially expressed genes that were consistent in two biological replicate experiments. To address the issue of cluster reproducibility a consensus clustering method, which identifies clusters of genes whose expression varies consistently between replicates, was also developed and applied. Analysis of the resulting clusters revealed many known and novel characteristics of DC maturation, such as the up-regulation of specific immune response pathways. Intriguingly, more genes were down-regulated than up-regulated. Results identify a more comprehensive program of down-regulation, including many genes involved in protein synthesis, metabolism, and housekeeping needed for maintenance of cellular integrity and metabolism. Conclusions The new filtering strategy emphasizes the importance of consistent and reproducible results when analyzing microarray data and utilizes consistency between replicate experiments as a criterion in both feature selection and clustering, without averaging or otherwise combining replicate data. Observation of a significant down-regulation program during DC maturation indicates that DC are preparing for cell death and provides a path to better understand the process. This new filtering strategy can be adapted for use in analyzing other large-scale time course data sets with replicates.
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Affiliation(s)
- Amy L Olex
- Department of Computer Science, Wake Forest University, Winston-Salem, NC 27109, USA
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Stratmann M, Stadler F, Tamanini F, van der Horst GT, Ripperger JA. Flexible phase adjustment of circadian albumin D site-binding protein (DBP) gene expression by CRYPTOCHROME1. Genes Dev 2010; 24:1317-28. [PMID: 20551177 PMCID: PMC2885666 DOI: 10.1101/gad.578810] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2010] [Accepted: 04/20/2010] [Indexed: 11/25/2022]
Abstract
The albumin D site-binding protein (DBP) governs circadian transcription of a number of hepatic detoxification and metabolic enzymes prior to the activity phase and subsequent food intake of mice. However, the behavior of mice is drastically affected by the photoperiod. Therefore, continuous adjustment of the phase of circadian Dbp expression is required in the liver. Here we describe a direct impact of CRYPTOCHROME1 (CRY1) on the phase of Dbp expression. Dbp and the nuclear receptor Rev-Erbalpha are circadian target genes of BMAL1 and CLOCK. Surprisingly, dynamic CRY1 binding to the Dbp promoter region delayed BMAL1 and CLOCK-mediated transcription of Dbp compared with Rev-Erbalpha. Extended presence of CRY1 in the nucleus enabled continuous uncoupling of the phase of Dbp from Rev-Erbalpha expression upon change from short to longer photoperiods. CRY1 thus maintained the peak of DBP accumulation close to the activity phase. In contrast, Rev-Erbalpha expression was phase-locked to the circadian oscillator and shaped by accumulation of its own gene product. Our data indicate that fine-tuning of circadian transcription in the liver is even more sophisticated than expected.
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Affiliation(s)
- Markus Stratmann
- Department of Molecular Biology, University of Geneva, 1211 Geneva 4, Switzerland
| | - Frédéric Stadler
- Department of Medicine, Unit of Biochemistry, University of Fribourg, 1700 Fribourg, Switzerland
| | - Filippo Tamanini
- Department of Genetics, Erasmus University Medical Center, 3000 CA Rotterdam, The Netherlands
| | | | - Jürgen A. Ripperger
- Department of Medicine, Unit of Biochemistry, University of Fribourg, 1700 Fribourg, Switzerland
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Niwa K, Nakajima Y, Ohmiya Y. Applications of luciferin biosynthesis: Bioluminescence assays for l-cysteine and luciferase. Anal Biochem 2010; 396:316-8. [DOI: 10.1016/j.ab.2009.09.014] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2009] [Revised: 09/07/2009] [Accepted: 09/09/2009] [Indexed: 11/16/2022]
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Rothman PB. The transcriptional regulator NFIL3 controls IgE production. TRANSACTIONS OF THE AMERICAN CLINICAL AND CLIMATOLOGICAL ASSOCIATION 2010; 121:156-171. [PMID: 20697558 PMCID: PMC2917151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Cytokines are essential modulators of the immune response that underlies the inflammatory component of atopic asthma and other allergic diseases, lnterleukin-4 is an important cytokine for the regulation of allergic immune responses. However, the molecular mechanisms that regulate the response of cells to IL-4 are still not completely defined. IL-4 plays an important role in B cell biology. It can regulate B cell differentiation. For example, IL-4 induces immunoglobulin heavy chain class switching to IgE by inducing germline immunoglobulin heavy chain transcription. It also induces expression of CD23 and MHC class II. Further understanding of the mechanisms by which IL-4 mediates these biologic responses may lead to novel mechanisms for therapeutic intervention and control of allergy. To define how different signaling pathways activated by IL-4 regulate gene transcription, we identified many differentially expressed genes by IL-4 stimulation by microarray analysis. NFIL3 (nuclear factor, interleukin 3 regulated) is the most strongly induced transcription factor by IL-4 stimulation in a STAT6-dependent manner. To analyze the role of NFIL3 in the immune system, we have generated NFIL3-deficient mice. NFIL3-deficient mice showed greatly impaired IgE production in response to antigen. NFIL3-deficient B cells fail to produce IgE in response to LPS plus IL-4. These defects may be due to the reduced production of immunoglobulin heavy chain germline epsilon transcripts in the absence of NFIL3. Moreover, NFIL3 KO mice sensitized and challenged with ovalbumin showed reduced airway hyper-responsiveness when compared to wild-type mice. Therefore, we hypothesize that NFIL3 is a critical regulator for IgE production and airway hyper-responsiveness.
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Affiliation(s)
- Paul B Rothman
- Roy J. and Lucille A. Carver College of Medicine, University of Iowa, 212 CMAB, 451 Newton Road, Iowa City, Iowa 52242, USA.
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IL-4-induced transcription factor NFIL3/E4BP4 controls IgE class switching. Proc Natl Acad Sci U S A 2009; 107:821-6. [PMID: 20080759 DOI: 10.1073/pnas.0909235107] [Citation(s) in RCA: 128] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
IL-4 signaling promotes IgE class switching through STAT6 activation and the induction of Ig germ-line epsilon (GLepsilon) transcription. Previously, we and others identified a transcription factor, Nfil3, as a gene induced by IL-4 stimulation in B cells. However, the precise roles of nuclear factor, IL-3-regulated (NFIL3) in IL-4 signaling are unknown. Here, we report that NFIL3 is important for IgE class switching. NFIL3-deficient mice show impaired IgE class switching, and this defect is B-cell intrinsic. The induction of GLepsilon transcripts after LPS and IL-4 stimulation is significantly reduced in NFIL3-deficient B cells. Expression of NFIL3 in NFIL3-deficient B cells restores the impairment of IgE production, and overexpression of NFIL3 in the presence of cycloheximide induces GLepsilon transcripts. Moreover, NFIL3 binds to Iepsilon promoter in vivo. Together, these results identify NFIL3 as a key regulator of IL-4-induced GLepsilon transcription in response to IL-4 and subsequent IgE class switching.
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Up-regulation of circadian clock gene Period 2 in the prostate mesenchymal cells during flutamide-induced apoptosis. Mol Cell Biochem 2009; 335:37-45. [PMID: 19714448 DOI: 10.1007/s11010-009-0238-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2009] [Accepted: 08/13/2009] [Indexed: 10/20/2022]
Abstract
Androgen regulates the proper development and physiological function of the prostate. Here, we investigated the modulation of androgen and androgen receptor (AR) antagonist on circadian oscillations of a clock core gene Period 2 (Per2) in rat prostate mesenchymal cells (PMCs). Circadian oscillations were analyzed with the real-time monitoring system of gene expression using transgenic rats introduced with mouse Per2 promoter fused to a destabilized luciferase (Per2-dLuc) reporter gene. Analyses of circadian oscillations, immunofluorescence, and androgen response element (ARE)-luciferase reporter assay revealed that circadian clocks are operative and the AR protein is functional in PMCs in vitro. Androgen such as testosterone (T) and dihydrotestosterone (DHT) did not cause any changes in circadian Per2-dLuc oscillations of confluent cells. Conversely, flutamide (FL) up-regulated the amplitude of circadian Per2-dLuc oscillations in a dose-dependent manner, whereas T antagonized the action of FL. The PER2 protein was markedly accumulated by FL treatment and localized in both the nucleus and cytoplasm during the first peak period of circadian Per2-dLuc oscillations. Simultaneously, FL treatment increased apoptotic cell death. Collectively, the present study demonstrates that a clock gene Per2 is up-regulated in PMCs during FL-induced apoptotic cell death. Thus, circadian oscillations of Per2 gene expression may be closely linked to the cellular states of PMCs such as apoptotic cell death.
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41
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Fustin JM, O'Neill JS, Hastings MH, Hazlerigg DG, Dardente H. Cry1 circadian phase in vitro: wrapped up with an E-box. J Biol Rhythms 2009; 24:16-24. [PMID: 19150926 DOI: 10.1177/0748730408329267] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The circadian timing of gene expression is determined by transcriptional regulation through upstream response elements present throughout the genome. Central to this regulation are the actions of a core group of transcriptional activators and repressors, which act through, and are themselves regulated by, a small set of canonical circadian response elements. Among these, the E-box (CACGTG) is crucial for daytime transcriptional activity. The mammalian Period (Per1-3) and Cryptochrome (Cry1-2) genes are E-box-regulated genes, but in peripheral tissues peak Cry1 mRNA expression is delayed by several hours relative to that of Per. It has been proposed that this delay originates from interactions between the proximal E-box and retinoic acid-related orphan receptor response elements (RORE) present in the Cry1 promoter. By using real-time luciferase reporter assays in NIH3T3 cells the authors show here that a proximal 47-bp E-box containing region of the Cry1 promoter is both necessary and sufficient to drive circadian Cry1 transcription with an appropriate phase delay (around 4 h) relative to Per2. The results therefore suggest that, at least in this in vitro model of the clock, RORE are not necessary for the appropriate circadian regulation of Cry1 expression and rather suggest that sequences surrounding the proximal E-boxes confer gene-specific circadian phasing.
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Affiliation(s)
- J M Fustin
- Aberdeen University, School of Biological Sciences, Aberdeen, UK
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42
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Rueda C, Fernández MA, Peddada SD. Estimation of Parameters Subject to Order Restrictions on a Circle With Application to Estimation of Phase Angles of Cell Cycle Genes. J Am Stat Assoc 2009; 104:338-347. [PMID: 19750145 DOI: 10.1198/jasa.2009.0120] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Motivated by a problem encountered in the analysis of cell cycle gene expression data, this article deals with the estimation of parameters subject to order restrictions on a unit circle. A normal eukaryotic cell cycle has four major phases during cell division, and a cell cycle gene has its peak expression (phase angle) during the phase that may correspond to its biological function. Because the phases are ordered along a circle, the phase angles of cell cycle genes are ordered unknown parameters on a unit circle. The problem of interest is to estimate the phase angles using the information regarding the order among them. We address this problem by developing a circular version of the well-known isotonic regression for Euclidean data. Because of the underlying geometry, the standard pool adjacent violator algorithm (PAVA) cannot be used for deriving the circular isotonic regression estimator (CIRE). However, PAVA can be modified to obtain a computationally efficient algorithm for deriving the CIRE. We illustrate the CIRE by estimating the phase angles of some of well-known cell cycle genes using the unrestricted estimators obtained in the literature.
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Affiliation(s)
- Cristina Rueda
- Department of Statistics and Operations Research, University of Valladolid, Valladolid, Spain
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43
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Hara Y, Onishi Y, Oishi K, Miyazaki K, Fukamizu A, Ishida N. Molecular characterization of Mybbp1a as a co-repressor on the Period2 promoter. Nucleic Acids Res 2009; 37:1115-26. [PMID: 19129230 PMCID: PMC2651808 DOI: 10.1093/nar/gkn1013] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The circadian clock comprises transcriptional feedback loops of clock genes. Cryptochromes are essential components of the negative feedback loop in mammals as they inhibit CLOCK-BMAL1-mediated transcription. We purified mouse CRY1 (mCRY1) protein complexes from Sarcoma 180 cells to determine their roles in circadian gene expression and discovered that Myb-binding protein 1a (Mybbp1a) interacts with mCRY1. Mybbp1a regulates various transcription factors, but its role in circadian gene expression is unknown. We found that Mybbp1a functions as a co-repressor of Per2 expression and repressed Per2 promoter activity in reporter assays. Chromatin immunoprecipitation (ChIP) assays revealed endogenous Mybbp1a binding to the Per2 promoter that temporally matched that of mCRY1. Furthermore, Mybbp1a binding to the Per2 promoter correlated with the start of the down-regulation of Per2 expression and with the dimethylation of histone H3 Lys9, to which it could also bind. These findings suggest that Mybbp1a and mCRY1 can form complexes on the Per2 promoter that function as negative regulators of Per2 expression.
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Affiliation(s)
- Yasuhiro Hara
- Clock Cell Biology, Institute for Biological Resources and Functions, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
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Hirata M, He PJ, Shibuya N, Uchikawa M, Yamauchi N, Hashimoto S, Hattori MA. Progesterone, but not estradiol, synchronizes circadian oscillator in the uterus endometrial stromal cells. Mol Cell Biochem 2008; 324:31-8. [DOI: 10.1007/s11010-008-9981-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2008] [Accepted: 11/28/2008] [Indexed: 11/29/2022]
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Woo KC, Kim TD, Lee KH, Kim DY, Kim W, Lee KY, Kim KT. Mouse period 2 mRNA circadian oscillation is modulated by PTB-mediated rhythmic mRNA degradation. Nucleic Acids Res 2008; 37:26-37. [PMID: 19010962 PMCID: PMC2615616 DOI: 10.1093/nar/gkn893] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Circadian mRNA oscillations are the main feature of core clock genes. Among them, period 2 is a key component in negative-feedback regulation, showing robust diurnal oscillations. Moreover, period 2 has been found to have a physiological role in the cell cycle or the tumor suppression. The present study reports that 3′-untranslated region (UTR)-dependent mRNA decay is involved in the regulation of circadian oscillation of period 2 mRNA. Within the mper2 3′UTR, both the CU-rich region and polypyrimidine tract-binding protein (PTB) are more responsible for mRNA stability and degradation kinetics than are other factors. Depletion of PTB with RNAi results in mper2 mRNA stabilization. During the circadian oscillations of mper2, cytoplasmic PTB showed a reciprocal expression profile compared with mper2 mRNA and its peak amplitude was increased when PTB was depleted. This report on the regulation of mper2 proposes that post-transcriptional mRNA decay mediated by PTB is a fine-tuned regulatory mechanism that includes dampening-down effects during circadian mRNA oscillations.
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Affiliation(s)
- Kyung-Chul Woo
- Department of Life Science, Division of Molecular and Life Science, Pohang University of Science and Technology, Pohang, South Korea
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Albrecht U, Bordon A, Schmutz I, Ripperger J. The multiple facets of Per2. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2008; 72:95-104. [PMID: 18419266 DOI: 10.1101/sqb.2007.72.001] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The Period 2 (Per2) gene is an important component of the circadian system. It appears to be not only part of the core oscillator mechanism, but also part of the input and output pathways of the clock. Because of its involvement at multiple levels of the circadian system, Per2 needs to meet a variety of different demands. We discuss how Per2 might be able to fulfill multiple functions by reviewing known facts and combine this with speculations based on these facts. This might provide new views about Per2 function and help to better understand diseases that are rooted in the circadian system.
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Affiliation(s)
- U Albrecht
- Department of Medicine, University of Fribourg, 1700 Fribourg, Switzerland
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Nakashima A, Kawamoto T, Honda KK, Ueshima T, Noshiro M, Iwata T, Fujimoto K, Kubo H, Honma S, Yorioka N, Kohno N, Kato Y. DEC1 modulates the circadian phase of clock gene expression. Mol Cell Biol 2008; 28:4080-92. [PMID: 18411297 PMCID: PMC2423136 DOI: 10.1128/mcb.02168-07] [Citation(s) in RCA: 124] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2007] [Revised: 01/01/2008] [Accepted: 04/05/2008] [Indexed: 12/20/2022] Open
Abstract
DEC1 suppresses CLOCK/BMAL1-enhanced promoter activity, but its role in the circadian system of mammals remains unclear. Here we examined the effect of Dec1 overexpression or deficiency on circadian gene expression triggered with 50% serum. Overexpression of Dec1 delayed the phase of clock genes such as Dec1, Dec2, Per1, and Dbp that contain E boxes in their regulatory regions, whereas it had little effect on the circadian phase of Per2 and Cry1 carrying CACGTT E' boxes. In contrast, Dec1 deficiency advanced the phase of the E-box-containing clock genes but not that of the E'-box-containing clock genes. Accordingly, DEC1 showed strong binding and transrepression on the E box, but not on the E' box, in chromatin immunoprecipitation, electrophoretic mobility shift, and luciferase reporter assays. Dec1-/- mice showed behavioral rhythms with slightly but significantly longer circadian periods under conditions of constant darkness and faster reentrainment to a 6-h phase-advanced shift of a light-dark cycle. Knockdown of Dec2 with small interfering RNA advanced the phase of Dec1 and Dbp expression, and double knockdown of Dec1 and Dec2 had much stronger effects on the expression of the E-box-containing clock genes. These findings suggest that DEC1, along with DEC2, plays a role in the finer regulation and robustness of the molecular clock.
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Affiliation(s)
- Ayumu Nakashima
- Department of Dental and Medical Biochemistry, Hiroshima University Graduate School of Biomedical Sciences, Hiroshima 734-8553, Japan
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Wilkins AK, Barton PI, Tidor B. The Per2 negative feedback loop sets the period in the mammalian circadian clock mechanism. PLoS Comput Biol 2008; 3:e242. [PMID: 18085817 PMCID: PMC2134962 DOI: 10.1371/journal.pcbi.0030242] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2007] [Accepted: 10/19/2007] [Indexed: 11/21/2022] Open
Abstract
Processes that repeat in time, such as the cell cycle, the circadian rhythm, and seasonal variations, are prevalent in biology. Mathematical models can represent our knowledge of the underlying mechanisms, and numerical methods can then facilitate analysis, which forms the foundation for a more integrated understanding as well as for design and intervention. Here, the intracellular molecular network responsible for the mammalian circadian clock system was studied. A new formulation of detailed sensitivity analysis is introduced and applied to elucidate the influence of individual rate processes, represented through their parameters, on network functional characteristics. One of four negative feedback loops in the model, the Per2 loop, was uniquely identified as most responsible for setting the period of oscillation; none of the other feedback loops were found to play as substantial a role. The analysis further suggested that the activity of the kinases CK1δ and CK1ɛ were well placed within the network such that they could be instrumental in implementing short-term adjustments to the period in the circadian clock system. The numerical results reported here are supported by previously published experimental data. Network models of biological systems are appearing at an increasing rate. By encapsulating mechanistic detail of chemical and physical processes, mathematical models can successfully simulate and predict emergent network properties. However, methods are needed for analyzing the role played by individual biochemical steps in producing context-dependent system behavior, thereby linking individual molecular knowledge with network properties. Here, we apply sensitivity analysis to analyze mammalian circadian rhythms and find that a contiguous series of reactions in one of the four negative feedback loops carries primary responsibility for determining the intrinsic length of day. The key reactions, all involving the gene per2 and its products, include Per2 mRNA export and degradation, and PER2 phosphorylation, transcription, and translation. Interestingly, mutations affecting PER2 phosphorylation have previously been linked to circadian disorders. The method may be generally applicable to probe structure–function relationships in biological networks.
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Affiliation(s)
- A. Katharina Wilkins
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Paul I Barton
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Bruce Tidor
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- * To whom correspondence should be addressed. E-mail:
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Nakahata Y, Yoshida M, Takano A, Soma H, Yamamoto T, Yasuda A, Nakatsu T, Takumi T. A direct repeat of E-box-like elements is required for cell-autonomous circadian rhythm of clock genes. BMC Mol Biol 2008; 9:1. [PMID: 18177499 PMCID: PMC2254435 DOI: 10.1186/1471-2199-9-1] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2007] [Accepted: 01/04/2008] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The circadian expression of the mammalian clock genes is based on transcriptional feedback loops. Two basic helix-loop-helix (bHLH) PAS (for Period-Arnt-Sim) domain-containing transcriptional activators, CLOCK and BMAL1, are known to regulate gene expression by interacting with a promoter element termed the E-box (CACGTG). The non-canonical E-boxes or E-box-like sequences have also been reported to be necessary for circadian oscillation. RESULTS We report a new cis-element required for cell-autonomous circadian transcription of clock genes. This new element consists of a canonical E-box or a non-canonical E-box and an E-box-like sequence in tandem with the latter with a short interval, 6 base pairs, between them. We demonstrate that both E-box or E-box-like sequences are needed to generate cell-autonomous oscillation. We also verify that the spacing nucleotides with constant length between these 2 E-elements are crucial for robust oscillation. Furthermore, by in silico analysis we conclude that several clock and clock-controlled genes possess a direct repeat of the E-box-like elements in their promoter region. CONCLUSION We propose a novel possible mechanism regulated by double E-box-like elements, not to a single E-box, for circadian transcriptional oscillation. The direct repeat of the E-box-like elements identified in this study is the minimal required element for the generation of cell-autonomous transcriptional oscillation of clock and clock-controlled genes.
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Affiliation(s)
| | - Mayumi Yoshida
- Osaka Bioscience Institute, Suita, Osaka 565-0874, Japan
- Kyoto University Graduate School of Biostudies, Sakyo, Kyoto 606-8501, Japan
| | - Atsuko Takano
- Osaka Bioscience Institute, Suita, Osaka 565-0874, Japan
| | - Haruhiko Soma
- Life Science Laboratory, Material Laboratories, Sony Corporation, Shinagawa, Tokyo 144-0001, Japan
| | - Takuro Yamamoto
- Life Science Laboratory, Material Laboratories, Sony Corporation, Shinagawa, Tokyo 144-0001, Japan
| | - Akio Yasuda
- Life Science Laboratory, Material Laboratories, Sony Corporation, Shinagawa, Tokyo 144-0001, Japan
| | - Toru Nakatsu
- Department of Structural Biology, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo, Kyoto 606-8501, Japan
| | - Toru Takumi
- Osaka Bioscience Institute, Suita, Osaka 565-0874, Japan
- Department of Molecular Neuroscience, Kyoto University Graduate School of Medicine, Sakyo, Kyoto 606-8501, Japan
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Gómez-Abellán P, Hernández-Morante JJ, Luján JA, Madrid JA, Garaulet M. Clock genes are implicated in the human metabolic syndrome. Int J Obes (Lond) 2008; 32:121-8. [PMID: 17653067 DOI: 10.1038/sj.ijo.0803689] [Citation(s) in RCA: 121] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
BACKGROUND Clock genes play a role in adipose tissue (AT) in animal experimental models. However, it remains to be elucidated whether these genes are expressed in human AT. OBJECTIVE We investigated the expression of several clock genes, Bmal1, Per2 and Cry1, in human AT from visceral and subcutaneous abdominal depots. A second objective was to elucidate whether these clock genes expressions were related to the metabolic syndrome features. METHODS Visceral and subcutaneous AT samples were obtained from morbid obese men (n=8), age: 42+/-13 years and body mass index>/=40 kg/m(2), undergoing laparoscopic surgery due to obesity. Biopsies were taken as paired samples at the beginning of the surgical process (1100 hour). Metabolic syndrome features such as waist circumference, plasma glucose, triglycerides, total cholesterol, high-density lipoprotein cholesterol and low-density lipoprotein (LDL) cholesterol were also studied. Homeostasis model assessment index of insulin resistance was also calculated. The expression of the different clock genes, hBmal1, hPer2 and hCry1, was determined by quantitative real-time PCR. RESULTS Clock genes were expressed in both human AT depots. hBmal1 expression was significantly lower than hPer2 and hCry1 in both AT (P<0.001). All genes were highly correlated to one another in the subcutaneous fat, while no correlation was found between Bmal1 and Per2 in the visceral AT. Clock genes AT expression was associated with the metabolic syndrome parameters: hPer2 expression level from visceral depot was inversely correlated to waist circumference (P<0.01), while the three clock genes studied were significantly and negatively correlated to total cholesterol and LDL cholesterol (P<0.01). CONCLUSION We have demonstrated for the first time in humans that clock genes are expressed in both subcutaneous and visceral fat. Their association with abdominal fat content and cardiovascular risk factors may be an indicator of the potential role of these clock genes in the metabolic syndrome disturbances.
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Affiliation(s)
- P Gómez-Abellán
- Department of Physiology, University of Murcia, Murcia, Spain
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