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Shu F, Liu H, Chen X, Liu Y, Zhou J, Tang L, Cao W, Yang S, Long Y, Li R, Wang H, Wang H, Jiang G. m6A Modification Promotes EMT and Metastasis of Castration-Resistant Prostate Cancer by Upregulating NFIB. Cancer Res 2024; 84:1947-1962. [PMID: 38536119 DOI: 10.1158/0008-5472.can-23-1954] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 12/04/2023] [Accepted: 03/21/2024] [Indexed: 06/15/2024]
Abstract
The widespread use of androgen receptor (AR) signaling inhibitors has led to an increased incidence of AR-negative castration-resistant prostate cancer (CRPC), limiting effective treatment and patient survival. A more comprehensive understanding of the molecular mechanisms supporting AR-negative CRPC could reveal therapeutic vulnerabilities to improve treatment. This study showed that the transcription factor nuclear factor I/B (NFIB) was upregulated in patient with AR-negative CRPC tumors and cell lines and was positively associated with an epithelial-to-mesenchymal transition (EMT) phenotype. Loss of NFIB inhibited EMT and reduced migration of CRPC cells. NFIB directly bound to gene promoters and regulated the transcription of EMT-related factors E-cadherin (CDH1) and vimentin (VIM), independent of other typical EMT-related transcriptional factors. In vivo data further supported the positive role of NFIB in the metastasis of AR-negative CRPC cells. Moreover, N6-methyladenosine (m6A) modification induced NFIB upregulation in AR-negative CRPC. Mechanistically, the m6A levels of mRNA, including NFIB and its E3 ubiquitin ligase TRIM8, were increased in AR-negative CRPC cells. Elevated m6A methylation of NFIB mRNA recruited YTHDF2 to increase mRNA stability and protein expression. Inversely, the m6A modification of TRIM8 mRNA, induced by ALKBH5 downregulation, decreased its translation and expression, which further promoted NFIB protein stability. Overall, this study reveals that upregulation of NFIB, mediated by m6A modification, triggers EMT and metastasis in AR-negative CRPC. Targeting the m6A/NFIB axis is a potential prevention and treatment strategy for AR-negative CRPC metastasis. SIGNIFICANCE NFIB upregulation mediated by increased m6A levels in AR-negative castration-resistant prostate cancer regulates transcription of EMT-related factors to promote metastasis, providing a potential therapeutic target to improve prostate cancer treatment.
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Affiliation(s)
- Feng Shu
- Department of Clinical Laboratory, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, Guangdong, China
| | - Hao Liu
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Xiaohui Chen
- Department of Clinical Laboratory, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, Guangdong, China
| | - Ye Liu
- Department of Pathology, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, Guangdong, China
| | - Jiangli Zhou
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Lei Tang
- Department of Pathology, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, Guangdong, China
| | - Wanwei Cao
- Department of Pathology, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, Guangdong, China
| | - Shanshan Yang
- Department of Clinical Laboratory, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, Guangdong, China
| | - Yili Long
- Department of Clinical Laboratory, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, Guangdong, China
| | - Rongna Li
- Department of Clinical Laboratory, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, Guangdong, China
| | - Hao Wang
- Department of Clinical Laboratory, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Hongsheng Wang
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Guanmin Jiang
- Department of Clinical Laboratory, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, Guangdong, China
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Štefánik P, Morová M, Herichová I. Impact of Long-Lasting Environmental Factors on Regulation Mediated by the miR-34 Family. Biomedicines 2024; 12:424. [PMID: 38398026 PMCID: PMC10887245 DOI: 10.3390/biomedicines12020424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 02/04/2024] [Accepted: 02/06/2024] [Indexed: 02/25/2024] Open
Abstract
The present review focuses on the interactions of newly emerging environmental factors with miRNA-mediated regulation. In particular, we draw attention to the effects of phthalates, electromagnetic fields (EMFs) and a disrupted light/dark cycle. miRNAs are small non-coding RNA molecules with a tremendous regulatory impact, which is usually executed via gene expression inhibition. To address the capacity of environmental factors to influence miRNA-mediated regulation, the miR-34 family was selected for its well-described oncostatic and neuro-modulatory properties. The expression of miR-34 is in a tissue-dependent manner to some extent under the control of the circadian system. There is experimental evidence implicating that phthalates, EMFs and the circadian system interact with the miR-34 family, in both lines of its physiological functioning. The inhibition of miR-34 expression in response to phthalates, EMFs and light contamination has been described in cancer tissue and cell lines and was associated with a decline in oncostatic miR-34a signalling (decrease in p21 expression) and a promotion of tumorigenesis (increases in Noth1, cyclin D1 and cry1 expressions). The effects of miR-34 on neural functions have also been influenced by phthalates, EMFs and a disrupted light/dark cycle. Environmental factors shifted the effects of miR-34 from beneficial to the promotion of neurodegeneration and decreased cognition. Moreover, the apoptogenic capacity of miR-34 induced via phthalate administration in the testes has been shown to negatively influence germ cell proliferation. To conclude, as the oncostatic and positive neuromodulatory functions of the miR-34 family can be strongly influenced by environmental factors, their interactions should be taken into consideration in translational medicine.
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Affiliation(s)
- Peter Štefánik
- Department of Animal Physiology and Ethology, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, 84215 Bratislava, Slovakia
| | - Martina Morová
- Department of Animal Physiology and Ethology, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, 84215 Bratislava, Slovakia
| | - Iveta Herichová
- Department of Animal Physiology and Ethology, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, 84215 Bratislava, Slovakia
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Han C, Lim JY, Koike N, Kim SY, Ono K, Tran CK, Mangutov E, Kim E, Zhang Y, Li L, Pradhan AA, Yagita K, Chen Z, Yoo SH, Burish MJ. Regulation of headache response and transcriptomic network by the trigeminal ganglion clock. Headache 2024; 64:195-210. [PMID: 38288634 PMCID: PMC10961824 DOI: 10.1111/head.14670] [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: 07/02/2023] [Revised: 12/06/2023] [Accepted: 12/20/2023] [Indexed: 02/17/2024]
Abstract
OBJECTIVE To characterize the circadian features of the trigeminal ganglion in a mouse model of headache. BACKGROUND Several headache disorders, such as migraine and cluster headache, are known to exhibit distinct circadian rhythms of attacks. The circadian basis for these rhythmic pain responses, however, remains poorly understood. METHODS We examined trigeminal ganglion ex vivo and single-cell cultures from Per2::LucSV reporter mice and performed immunohistochemistry. Circadian behavior and transcriptomics were investigated using a novel combination of trigeminovascular and circadian models: a nitroglycerin mouse headache model with mechanical thresholds measured every 6 h, and trigeminal ganglion RNA sequencing measured every 4 h for 24 h. Finally, we performed pharmacogenomic analysis of gene targets for migraine, cluster headache, and trigeminal neuralgia treatments as well as trigeminal ganglion neuropeptides; this information was cross-referenced with our cycling genes from RNA sequencing data to identify potential targets for chronotherapy. RESULTS The trigeminal ganglion demonstrates strong circadian rhythms in both ex vivo and single-cell cultures, with core circadian proteins found in both neuronal and non-neuronal cells. Using our novel behavioral model, we showed that nitroglycerin-treated mice display circadian rhythms of pain sensitivity which were abolished in arrhythmic Per1/2 double knockout mice. Furthermore, RNA-sequencing analysis of the trigeminal ganglion revealed 466 genes that displayed circadian oscillations in the control group, including core clock genes and clock-regulated pain neurotransmitters. In the nitroglycerin group, we observed a profound circadian reprogramming of gene expression, as 331 of circadian genes in the control group lost rhythm and another 584 genes gained rhythm. Finally, pharmacogenetics analysis identified 10 genes in our trigeminal ganglion circadian transcriptome that encode target proteins of current medications used to treat migraine, cluster headache, or trigeminal neuralgia. CONCLUSION Our study unveiled robust circadian rhythms in the trigeminal ganglion at the behavioral, transcriptomic, and pharmacogenetic levels. These results support a fundamental role of the clock in pain pathophysiology. PLAIN LANGUAGE SUMMARY Several headache diseases, such as migraine and cluster headache, have headaches that occur at the same time each day. We learned that the trigeminal ganglion, an important pain structure in several headache diseases, has a 24-hour cycle that might be related to this daily cycle of headaches. Our genetic analysis suggests that some medications may be more effective in treating migraine and cluster headache when taken at specific times of the day.
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Affiliation(s)
- Chorong Han
- Department of Biochemistry and Molecular Biology, UTHealth Houston, Houston, Texas, USA
| | - Ji Ye Lim
- Department of Biochemistry and Molecular Biology, UTHealth Houston, Houston, Texas, USA
| | - Nobuya Koike
- Department of Physiology and Systems Bioscience, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Sun Young Kim
- Department of Biochemistry and Molecular Biology, UTHealth Houston, Houston, Texas, USA
| | - Kaori Ono
- Department of Biochemistry and Molecular Biology, UTHealth Houston, Houston, Texas, USA
| | - Celia K. Tran
- Department of Biochemistry and Molecular Biology, UTHealth Houston, Houston, Texas, USA
| | - Elizaveta Mangutov
- Center for Clinical Pharmacology, Department of Anesthesiology, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
| | - Eunju Kim
- Department of Biochemistry and Molecular Biology, UTHealth Houston, Houston, Texas, USA
| | - Yanping Zhang
- Center for Clinical Pharmacology, Department of Anesthesiology, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
| | - Lingyong Li
- Division of Molecular and Translational Biomedicine, Department of Anesthesiology and Perioperative Medicine, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Amynah A. Pradhan
- Center for Clinical Pharmacology, Department of Anesthesiology, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
| | - Kazuhiro Yagita
- Department of Physiology and Systems Bioscience, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Zheng Chen
- Department of Biochemistry and Molecular Biology, UTHealth Houston, Houston, Texas, USA
| | - Seung-Hee Yoo
- Department of Biochemistry and Molecular Biology, UTHealth Houston, Houston, Texas, USA
| | - Mark J. Burish
- Department of Neurosurgery, UTHealth Houston, Houston, Texas, USA
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Nasser JS, Altahoo N, Almosawi S, Alhermi A, Butler AE. The Role of MicroRNA, Long Non-Coding RNA and Circular RNA in the Pathogenesis of Polycystic Ovary Syndrome: A Literature Review. Int J Mol Sci 2024; 25:903. [PMID: 38255975 PMCID: PMC10815174 DOI: 10.3390/ijms25020903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Revised: 01/04/2024] [Accepted: 01/06/2024] [Indexed: 01/24/2024] Open
Abstract
Polycystic ovary syndrome (PCOS) is the most common endocrine-metabolic disease in females of reproductive age, affecting 4-20% of pre-menopausal women worldwide. MicroRNAs (miRNAs) are endogenous, single-stranded, non-coding, regulatory ribonucleic acid molecules found in eukaryotic cells. Abnormal miRNA expression has been associated with several diseases and could possibly explain their underlying pathophysiology. MiRNAs have been extensively studied for their potential diagnostic, prognostic, and therapeutic uses in many diseases, such as type 2 diabetes, obesity, cardiovascular disease, PCOS, and endometriosis. In women with PCOS, miRNAs were found to be abnormally expressed in theca cells, follicular fluid, granulosa cells, peripheral blood leukocytes, serum, and adipose tissue when compared to those without PCOS, making miRNAs a useful potential biomarker for the disease. Key pathways involved in PCOS, such as folliculogenesis, steroidogenesis, and cellular adhesion, are regulated by miRNA. This also highlights their importance as potential prognostic markers. In addition, recent evidence suggests a role for miRNAs in regulating the circadian rhythm (CR). CR is crucial for regulating reproduction through the various functions of the hypothalamic-pituitary-gonadal (HPG) axis and the ovaries. A disordered CR affects reproductive outcomes by inducing insulin resistance, oxidative stress, and systemic inflammation. Moreover, miRNAs were demonstrated to interact with lncRNA and circRNAs, which are thought to play a role in the pathogenesis of PCOS. This review discusses what is currently understood about miRNAs in PCOS, the cellular pathways involved, and their potential role as biomarkers and therapeutic targets.
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Affiliation(s)
- Jenan Sh. Nasser
- School of Medicine, Royal College of Surgeons of Ireland, Busaiteen, Adliya 15503, Bahrain; (J.S.N.); (N.A.); (S.A.); (A.A.)
| | - Noor Altahoo
- School of Medicine, Royal College of Surgeons of Ireland, Busaiteen, Adliya 15503, Bahrain; (J.S.N.); (N.A.); (S.A.); (A.A.)
| | - Sayed Almosawi
- School of Medicine, Royal College of Surgeons of Ireland, Busaiteen, Adliya 15503, Bahrain; (J.S.N.); (N.A.); (S.A.); (A.A.)
| | - Abrar Alhermi
- School of Medicine, Royal College of Surgeons of Ireland, Busaiteen, Adliya 15503, Bahrain; (J.S.N.); (N.A.); (S.A.); (A.A.)
| | - Alexandra E. Butler
- Research Department, Royal College of Surgeons of Ireland, Busaiteen, Adliya 15503, Bahrain
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Millius A, Yamada RG, Fujishima H, Maeda K, Standley DM, Sumiyama K, Perrin D, Ueda HR. Circadian ribosome profiling reveals a role for the Period2 upstream open reading frame in sleep. Proc Natl Acad Sci U S A 2023; 120:e2214636120. [PMID: 37769257 PMCID: PMC10556633 DOI: 10.1073/pnas.2214636120] [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: 08/30/2022] [Accepted: 08/29/2023] [Indexed: 09/30/2023] Open
Abstract
Many mammalian proteins have circadian cycles of production and degradation, and many of these rhythms are altered posttranscriptionally. We used ribosome profiling to examine posttranscriptional control of circadian rhythms by quantifying RNA translation in the liver over a 24-h period from circadian-entrained mice transferred to constant darkness conditions and by comparing ribosome binding levels to protein levels for 16 circadian proteins. We observed large differences in ribosome binding levels compared to protein levels, and we observed delays between peak ribosome binding and peak protein abundance. We found extensive binding of ribosomes to upstream open reading frames (uORFs) in circadian mRNAs, including the core clock gene Period2 (Per2). An increase in the number of uORFs in the 5'UTR was associated with a decrease in ribosome binding in the main coding sequence and a reduction in expression of synthetic reporter constructs. Mutation of the Per2 uORF increased luciferase and fluorescence reporter expression in 3T3 cells and increased luciferase expression in PER2:LUC MEF cells. Mutation of the Per2 uORF in mice increased Per2 mRNA expression, enhanced ribosome binding on Per2, and reduced total sleep time compared to that in wild-type mice. These results suggest that uORFs affect mRNA posttranscriptionally, which can impact physiological rhythms and sleep.
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Affiliation(s)
- Arthur Millius
- Laboratory for Synthetic Biology, RIKEN Quantitative Biology Center, Suita, Osaka565-0871, Japan
- Laboratory for Host Defense, Immunology Frontier Research Center, Suita, Osaka565-0871, Japan
- Laboratory for Systems Immunology, Immunology Frontier Research Center, Suita, Osaka565-0871, Japan
| | - Rikuhiro G. Yamada
- Laboratory for Synthetic Biology, RIKEN Quantitative Biology Center, Suita, Osaka565-0871, Japan
| | - Hiroshi Fujishima
- Laboratory for Synthetic Biology, RIKEN Quantitative Biology Center, Suita, Osaka565-0871, Japan
| | - Kazuhiko Maeda
- Laboratory for Host Defense, Immunology Frontier Research Center, Suita, Osaka565-0871, Japan
| | - Daron M. Standley
- Laboratory for Systems Immunology, Immunology Frontier Research Center, Suita, Osaka565-0871, Japan
| | - Kenta Sumiyama
- Laboratory of Animal Genetics and Breeding, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya464-8601, Japan
| | - Dimitri Perrin
- School of Computer Science, Queensland University of Technology, BrisbaneQLD 4000, Australia
- Centre for Data Science, Queensland University of Technology, BrisbaneQLD 4000, Australia
| | - Hiroki R. Ueda
- Laboratory for Synthetic Biology, RIKEN Quantitative Biology Center, Suita, Osaka565-0871, Japan
- Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, Tokyo113-0033, Japan
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Gonçalves TM, Stewart CL, Baxley SD, Xu J, Li D, Gabel HW, Wang T, Avraham O, Zhao G. Towards a comprehensive regulatory map of Mammalian Genomes. RESEARCH SQUARE 2023:rs.3.rs-3294408. [PMID: 37841836 PMCID: PMC10571623 DOI: 10.21203/rs.3.rs-3294408/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2023]
Abstract
Genome mapping studies have generated a nearly complete collection of genes for the human genome, but we still lack an equivalently vetted inventory of human regulatory sequences. Cis-regulatory modules (CRMs) play important roles in controlling when, where, and how much a gene is expressed. We developed a training data-free CRM-prediction algorithm, the Mammalian Regulatory MOdule Detector (MrMOD) for accurate CRM prediction in mammalian genomes. MrMOD provides genome position-fixed CRM models similar to the fixed gene models for the mouse and human genomes using only genomic sequences as the inputs with one adjustable parameter - the significance p-value. Importantly, MrMOD predicts a comprehensive set of high-resolution CRMs in the mouse and human genomes including all types of regulatory modules not limited to any tissue, cell type, developmental stage, or condition. We computationally validated MrMOD predictions used a compendium of 21 orthogonal experimental data sets including thousands of experimentally defined CRMs and millions of putative regulatory elements derived from hundreds of different tissues, cell types, and stimulus conditions obtained from multiple databases. In ovo transgenic reporter assay demonstrates the power of our prediction in guiding experimental design. We analyzed CRMs located in the chromosome 17 using unsupervised machine learning and identified groups of CRMs with multiple lines of evidence supporting their functionality, linking CRMs with upstream binding transcription factors and downstream target genes. Our work provides a comprehensive base pair resolution annotation of the functional regulatory elements and non-functional regions in the mammalian genomes.
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Affiliation(s)
| | | | | | - Jason Xu
- Missouri University of Science & Technology
| | - Daofeng Li
- Washington University School of Medicine
| | | | - Ting Wang
- Washington University School of Medicine
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Panda K, Chinnapaiyan S, Rahman MS, Santiago MJ, Black SM, Unwalla HJ. Circadian-Coupled Genes Expression and Regulation in HIV-Associated Chronic Obstructive Pulmonary Disease (COPD) and Lung Comorbidities. Int J Mol Sci 2023; 24:9140. [PMID: 37298092 PMCID: PMC10253051 DOI: 10.3390/ijms24119140] [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: 04/24/2023] [Revised: 05/13/2023] [Accepted: 05/19/2023] [Indexed: 06/12/2023] Open
Abstract
People living with HIV (PLWH) have an elevated risk of chronic obstructive pulmonary disease (COPD) and are at a higher risk of asthma and worse outcomes. Even though the combination of antiretroviral therapy (cART) has significantly improved the life expectancy of HIV-infected patients, it still shows a higher incidence of COPD in patients as young as 40 years old. Circadian rhythms are endogenous 24 h oscillations that regulate physiological processes, including immune responses. Additionally, they play a significant role in health and diseases by regulating viral replication and its corresponding immune responses. Circadian genes play an essential role in lung pathology, especially in PLWH. The dysregulation of core clock and clock output genes plays an important role in chronic inflammation and aberrant peripheral circadian rhythmicity, particularly in PLWH. In this review, we explained the mechanism underlying circadian clock dysregulation in HIV and its effects on the development and progression of COPD. Furthermore, we discussed potential therapeutic approaches to reset the peripheral molecular clocks and mitigate airway inflammation.
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Affiliation(s)
- Kingshuk Panda
- Department of Immunology and Nanomedicine, Herbert Wertheim College of Medicine, Florida International University, 11200 SW 8th Street, Miami, FL 33199, USA; (K.P.); (S.C.); (M.S.R.); (M.J.S.)
| | - Srinivasan Chinnapaiyan
- Department of Immunology and Nanomedicine, Herbert Wertheim College of Medicine, Florida International University, 11200 SW 8th Street, Miami, FL 33199, USA; (K.P.); (S.C.); (M.S.R.); (M.J.S.)
| | - Md. Sohanur Rahman
- Department of Immunology and Nanomedicine, Herbert Wertheim College of Medicine, Florida International University, 11200 SW 8th Street, Miami, FL 33199, USA; (K.P.); (S.C.); (M.S.R.); (M.J.S.)
| | - Maria J. Santiago
- Department of Immunology and Nanomedicine, Herbert Wertheim College of Medicine, Florida International University, 11200 SW 8th Street, Miami, FL 33199, USA; (K.P.); (S.C.); (M.S.R.); (M.J.S.)
| | - Stephen M. Black
- Department of Cellular Biology & Pharmacology, Herbert Wertheim College of Medicine, Florida International University, 11200 SW 8th Street, Miami, FL 33199, USA;
| | - Hoshang J. Unwalla
- Department of Immunology and Nanomedicine, Herbert Wertheim College of Medicine, Florida International University, 11200 SW 8th Street, Miami, FL 33199, USA; (K.P.); (S.C.); (M.S.R.); (M.J.S.)
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8
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Mawatari K, Koike N, Nohara K, Wirianto M, Uebanso T, Shimohata T, Shikishima Y, Miura H, Nii Y, Burish MJ, Yagita K, Takahashi A, Yoo SH, Chen Z. The Polymethoxyflavone Sudachitin Modulates the Circadian Clock and Improves Liver Physiology. Mol Nutr Food Res 2023; 67:e2200270. [PMID: 36829302 DOI: 10.1002/mnfr.202200270] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 12/13/2022] [Indexed: 02/26/2023]
Abstract
SCOPE Polymethoxylated flavones (PMFs) are a group of natural compounds known to display a wide array of beneficial effects to promote physiological fitness. Recent studies reveal circadian clocks as an important cellular mechanism mediating preventive efficacy of the major PMF Nobiletin against metabolic disorders. Sudachitin is a PMF enriched in Citrus sudachi, and its functions and mechanism of action are poorly understood. METHODS AND RESULTS Using circadian reporter cells, it shows that Sudachitin modulates circadian amplitude and period of Bmal1 promoter-driven reporter rhythms, and real-time qPCR analysis shows that Sudachitin alters expression of core clock genes, notably Bmal1, at both transcript and protein levels. Mass-spec analysis reveals systemic exposure in vivo. In mice fed with high-fat diet with or without Sudachitin, it observes increased nighttime activity and daytime sleep, accompanied by significant metabolic improvements in a circadian time-dependent manner, including respiratory quotient, blood lipid and glucose profiles, and liver physiology. Focusing on liver, RNA-sequencing and metabolomic analyses reveal prevalent diurnal alteration in both gene expression and metabolite accumulation. CONCLUSION This study elucidates Sudachitin as a new clock-modulating PMF with beneficial effects to improve diurnal metabolic homeostasis and liver physiology, suggesting the circadian clock as a fundamental mechanism to safeguard physiological well-being.
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Affiliation(s)
- Kazuaki Mawatari
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston, 6431 Fannin St., Houston, TX, 77030, USA
- Department of Preventive Environment and Nutrition, Institute of Biomedical Sciences, Tokushima University Graduate School, Kuramoto-cho 3-18-15, Tokushima, 770-8503, Japan
| | - Nobuya Koike
- Department of Physiology and Systems Bioscience, Kyoto Prefectural University of Medicine, 465 Kamigyo-ku, Kyoto, 602-8566, Japan
| | - Kazunari Nohara
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston, 6431 Fannin St., Houston, TX, 77030, USA
| | - Marvin Wirianto
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston, 6431 Fannin St., Houston, TX, 77030, USA
| | - Takashi Uebanso
- Department of Preventive Environment and Nutrition, Institute of Biomedical Sciences, Tokushima University Graduate School, Kuramoto-cho 3-18-15, Tokushima, 770-8503, Japan
| | - Takaaki Shimohata
- Department of Preventive Environment and Nutrition, Institute of Biomedical Sciences, Tokushima University Graduate School, Kuramoto-cho 3-18-15, Tokushima, 770-8503, Japan
| | - Yasuhiro Shikishima
- Ikeda Yakusou Corporation, 1808-1 Shuzunakatsu, Ikeda-cho, Miyoshi-city, Tokushima, 778-0020, Japan
| | - Hiroyuki Miura
- Ikeda Yakusou Corporation, 1808-1 Shuzunakatsu, Ikeda-cho, Miyoshi-city, Tokushima, 778-0020, Japan
| | - Yoshitaka Nii
- Food and Biotechnology Division, Tokushima Prefectural Industrial Technology Center, 11-2 Nishibari, Saika-cho, Tokushima, 770-8021, Japan
| | - Mark J Burish
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston, 6431 Fannin St., Houston, TX, 77030, USA
| | - Kazuhiro Yagita
- Department of Physiology and Systems Bioscience, Kyoto Prefectural University of Medicine, 465 Kamigyo-ku, Kyoto, 602-8566, Japan
| | - Akira Takahashi
- Department of Preventive Environment and Nutrition, Institute of Biomedical Sciences, Tokushima University Graduate School, Kuramoto-cho 3-18-15, Tokushima, 770-8503, Japan
| | - Seung-Hee Yoo
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston, 6431 Fannin St., Houston, TX, 77030, USA
| | - Zheng Chen
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston, 6431 Fannin St., Houston, TX, 77030, USA
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Kim JY, Kim W, Lee KH. The role of microRNAs in the molecular link between circadian rhythm and autism spectrum disorder. Anim Cells Syst (Seoul) 2023; 27:38-52. [PMID: 36860270 PMCID: PMC9970207 DOI: 10.1080/19768354.2023.2180535] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2023] Open
Abstract
Circadian rhythm regulates physiological cycles of awareness and sleepiness. Melatonin production is primarily regulated by circadian regulation of gene expression and is involved in sleep homeostasis. If the circadian rhythm is abnormal, sleep disorders, such as insomnia and several other diseases, can occur. The term 'autism spectrum disorder (ASD)' is used to characterize people who exhibit a certain set of repetitive behaviors, severely constrained interests, social deficits, and/or sensory behaviors that start very early in life. Because many patients with ASD suffer from sleep disorders, sleep disorders and melatonin dysregulation are attracting attention for their potential roles in ASD. ASD is caused by abnormalities during the neurodevelopmental processes owing to various genetic or environmental factors. Recently, the role of microRNAs (miRNAs) in circadian rhythm and ASD have gained attraction. We hypothesized that the relationship between circadian rhythm and ASD could be explained by miRNAs that can regulate or be regulated by either or both. In this study, we introduced a possible molecular link between circadian rhythm and ASD. We performed a thorough literature review to understand their complexity.
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Affiliation(s)
- Ji Young Kim
- Department of Molecular Biology, Pusan National University, Busan, Republic of Korea
| | - Wanil Kim
- Department of Biochemistry, College of Medicine, Gyeongsang National University, Jinju-si, Republic of Korea, Wanil Kim Department of Biochemistry, College of Medicine, Gyeongsang National University, Jinju-si, Gyeongsangnam-do52727, Republic of Korea; Kyung-Ha Lee Department of Molecular Biology, Pusan National University, 2, Busandaehak-ro 63beon-gil, Geumjeong-gu, Busan46241, Republic of Korea
| | - Kyung-Ha Lee
- Department of Molecular Biology, Pusan National University, Busan, Republic of Korea, Wanil Kim Department of Biochemistry, College of Medicine, Gyeongsang National University, Jinju-si, Gyeongsangnam-do52727, Republic of Korea; Kyung-Ha Lee Department of Molecular Biology, Pusan National University, 2, Busandaehak-ro 63beon-gil, Geumjeong-gu, Busan46241, Republic of Korea
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10
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Olejárová S, Moravčík R, Herichová I. 2.4 GHz Electromagnetic Field Influences the Response of the Circadian Oscillator in the Colorectal Cancer Cell Line DLD1 to miR-34a-Mediated Regulation. Int J Mol Sci 2022; 23:13210. [PMID: 36361993 PMCID: PMC9656412 DOI: 10.3390/ijms232113210] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Revised: 10/26/2022] [Accepted: 10/27/2022] [Indexed: 10/15/2023] Open
Abstract
Radiofrequency electromagnetic fields (RF-EMF) exert pleiotropic effects on biological processes including circadian rhythms. miR-34a is a small non-coding RNA whose expression is modulated by RF-EMF and has the capacity to regulate clock gene expression. However, interference between RF-EMF and miR-34a-mediated regulation of the circadian oscillator has not yet been elucidated. Therefore, the present study was designed to reveal if 24 h exposure to 2.4 GHz RF-EMF influences miR-34a-induced changes in clock gene expression, migration and proliferation in colorectal cancer cell line DLD1. The effect of up- or downregulation of miR-34a on DLD1 cells was evaluated using real-time PCR, the scratch assay test and the MTS test. Administration of miR-34a decreased the expression of per2, bmal1, sirtuin1 and survivin and inhibited proliferation and migration of DLD1 cells. When miR-34a-transfected DLD1 cells were exposed to 2.4 GHz RF-EMF, an increase in cry1 mRNA expression was observed. The inhibitory effect of miR-34a on per2 and survivin was weakened and abolished, respectively. The effect of miR-34a on proliferation and migration was eliminated by RF-EMF exposure. In conclusion, RF-EMF strongly influenced regulation mediated by the tumour suppressor miR-34a on the peripheral circadian oscillator in DLD1 cells.
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Affiliation(s)
| | | | - Iveta Herichová
- Department of Animal Physiology and Ethology, Faculty of Natural Sciences, Comenius University Bratislava, 842 15 Bratislava, Slovakia
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11
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Patel R, Galagali H, Kim JK, Frand AR. Feedback between a retinoid-related nuclear receptor and the let-7 microRNAs controls the pace and number of molting cycles in C. elegans. eLife 2022; 11:e80010. [PMID: 35968765 PMCID: PMC9377799 DOI: 10.7554/elife.80010] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 07/22/2022] [Indexed: 11/13/2022] Open
Abstract
Animal development requires coordination among cyclic processes, sequential cell fate specifications, and once-a-lifetime morphogenic events, but the underlying timing mechanisms are not well understood. Caenorhabditis elegans undergoes four molts at regular 8 to 10 hour intervals. The pace of the cycle is governed by PERIOD/lin-42 and other as-yet unknown factors. Cessation of the cycle in young adults is controlled by the let-7 family of microRNAs and downstream transcription factors in the heterochronic pathway. Here, we characterize a negative feedback loop between NHR-23, the worm homolog of mammalian retinoid-related orphan receptors (RORs), and the let-7 family of microRNAs that regulates both the frequency and finite number of molts. The molting cycle is decelerated in nhr-23 knockdowns and accelerated in let-7(-) mutants, but timed similarly in let-7(-) nhr-23(-) double mutants and wild-type animals. NHR-23 binds response elements (ROREs) in the let-7 promoter and activates transcription. In turn, let-7 dampens nhr-23 expression across development via a complementary let-7-binding site (LCS) in the nhr-23 3' UTR. The molecular interactions between NHR-23 and let-7 hold true for other let-7 family microRNAs. Either derepression of nhr-23 transcripts by LCS deletion or high gene dosage of nhr-23 leads to protracted behavioral quiescence and extra molts in adults. NHR-23 and let-7 also coregulate scores of genes required for execution of the molts, including lin-42. In addition, ROREs and LCSs isolated from mammalian ROR and let-7 genes function in C. elegans, suggesting conservation of this feedback mechanism. We propose that this feedback loop unites the molting timer and the heterochronic gene regulatory network, possibly by functioning as a cycle counter.
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Affiliation(s)
- Ruhi Patel
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los AngelesLos AngelesUnited States
| | - Himani Galagali
- Department of Biology, Johns Hopkins UniversityBaltimoreUnited States
| | - John K Kim
- Department of Biology, Johns Hopkins UniversityBaltimoreUnited States
| | - Alison R Frand
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los AngelesLos AngelesUnited States
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12
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Melatonergic Receptors (Mt1/Mt2) as a Potential Additional Target of Novel Drugs for Depression. Neurochem Res 2022; 47:2909-2924. [PMID: 35689787 PMCID: PMC9187850 DOI: 10.1007/s11064-022-03646-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 05/21/2022] [Accepted: 05/25/2022] [Indexed: 11/06/2022]
Abstract
A complex pathogenesis involving several physiological systems is theorized to underline the development of depressive disorders. Depression is accompanied by circadian regulation disruption and interaction with the functioning of both central and peripheral oscillators. Many aspects of melatonin function unite these systems. The use of drugs for circadian rhythm disorders could inspire a potential treatment strategy for depression. Melatonin plays an essential role in the regulation of circadian rhythms. It exerts effect by activating two types of melatonin receptors, type 1A (MT1) and 1B (MT2). These are G-protein-coupled receptors, predominantly located in the central nervous system. MT1/MT2 agonists could be a useful treatment approach according to all three prevalent theories of the pathogenesis of depression involving either monoamines, synaptic remodeling, or immune/inflammatory events. MT1/MT2 receptors can be a potential target for novel antidepressants with impact on concentrations of neurotrophins or neurotransmitters, and reducing levels of pro-inflammatory cytokines. There is an interesting cross-talk mediated via the physical association of melatonin and serotonin receptors into functional heteromers. The antidepressive and neurogenetic effects of MT1/MT2 agonists can also be caused by the inhibition of the acid sphingomyelinase, leading to reduced ceramide, or increasing monoamine oxidase A levels in the hippocampus. Compounds targeting MT1 and MT2 receptors could have potential for new anti-depressants that may improve the quality of therapeutic interventions in treating depression and relieving symptoms. In particular, a combined effect on MT1 and/or MT2 receptors and neurotransmitter systems may be useful, since the normalization of the circadian rhythm through the melatonergic system will probably contribute to improved treatment. In this review, we discuss melatonergic receptors as a potential additional target for novel drugs for depression.
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13
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A time to heal: microRNA and circadian dynamics in cutaneous wound repair. Clin Sci (Lond) 2022; 136:579-597. [PMID: 35445708 PMCID: PMC9069467 DOI: 10.1042/cs20220011] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 04/01/2022] [Accepted: 04/04/2022] [Indexed: 12/11/2022]
Abstract
Many biological systems have evolved circadian rhythms based on the daily cycles of daylight and darkness on Earth. Such rhythms are synchronised or entrained to 24-h cycles, predominantly by light, and disruption of the normal circadian rhythms has been linked to elevation of multiple health risks. The skin serves as a protective barrier to prevent microbial infection and maintain homoeostasis of the underlying tissue and the whole organism. However, in chronic non-healing wounds such as diabetic foot ulcers (DFUs), pressure sores, venous and arterial ulcers, a variety of factors conspire to prevent wound repair. On the other hand, keloids and hypertrophic scars arise from overactive repair mechanisms that fail to cease in a timely fashion, leading to excessive production of extracellular matrix (ECM) components such as such as collagen. Recent years have seen huge increases in our understanding of the functions of microRNAs (miRNAs) in wound repair. Concomitantly, there has been growing recognition of miRNA roles in circadian processes, either as regulators or targets of clock activity or direct responders to external circadian stimuli. In addition, miRNAs are now known to function as intercellular signalling mediators through extracellular vesicles (EVs). In this review, we explore the intersection of mechanisms by which circadian and miRNA responses interact with each other in relation to wound repair in the skin, using keratinocytes, macrophages and fibroblasts as exemplars. We highlight areas for further investigation to support the development of translational insights to support circadian medicine in the context of these cells.
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14
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The role of cell-autonomous circadian oscillation of Cry transcription in circadian rhythm generation. Cell Rep 2022; 39:110703. [PMID: 35443162 DOI: 10.1016/j.celrep.2022.110703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 02/17/2022] [Accepted: 03/29/2022] [Indexed: 11/21/2022] Open
Abstract
The current model of the mammalian circadian clock describes cell-autonomous and negative feedback-driven circadian oscillation of Cry and Per transcription as the core circadian rhythm generator. However, the actual contribution of this oscillation to circadian rhythm generation remains undefined. Here we perform targeted disruption of cis elements indispensable for cell-autonomous Cry oscillation. Mice lacking overt cell-autonomous Cry oscillation show robust circadian rhythms in locomotor activity. In addition, tissue-autonomous circadian rhythms are robust in the absence of overt Cry oscillation. Unexpectedly, although the absence of overt Cry oscillation leads to severe attenuation of Per oscillation at the cell-autonomous level, circadian rhythms in Per2 accumulation remain robust. As a mechanism to explain this counterintuitive result, Per2 half-life shows cell-autonomous circadian rhythms independent of Cry and Per oscillation. The cell-autonomous circadian clock may therefore remain partially functional even in the absence of overt Cry and Per oscillation because of circadian oscillation in Per2 degradation.
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15
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D’Agostino Y, Frigato E, Noviello TM, Toni M, Frabetti F, Cigliano L, Ceccarelli M, Sordino P, Cerulo L, Bertolucci C, D’Aniello S. Loss of circadian rhythmicity in bdnf knockout zebrafish larvae. iScience 2022; 25:104054. [PMID: 35345456 PMCID: PMC8957028 DOI: 10.1016/j.isci.2022.104054] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Revised: 01/14/2022] [Accepted: 03/08/2022] [Indexed: 12/13/2022] Open
Abstract
Brain-derived neurotrophic factor (BDNF) plays a pivotal role in neuronal growth and differentiation, neuronal plasticity, learning, and memory. Using CRISPR/Cas9 technology, we generated a vital Bdnf null mutant line in zebrafish and carried out its molecular and behavioral characterization. Although no defects are evident on a morphological inspection, 66% of coding genes and 37% of microRNAs turned out to be differentially expressed in bdnf−/− compared with wild type sibling embryos. We deeply investigated the circadian clock pathway and confirmed changes in the rhythmic expression of clock (arntl1a, clock1a and clock2) and clock-controlled (aanat2) genes. The modulatory role of Bdnf on the zebrafish circadian clock was then validated by behavioral tests highlighting the absence of circadian activity rhythms in bdnf−/− larvae. The circadian behavior was partially rescued by pharmacological treatment. The bdnf−/− zebrafish line presented here is the first valuable and stable vertebrate model for the study of BDNF-related neurodevelopmental diseases Generation of a viable bdnf KO line in zebrafish Bdnf deficiency affects locomotor activity and thigmotaxis in larvae Differential RNA-seq analysis shows changes in expression of circadian clock genes Bdnf mutant fails in the generation of the behavioral circadian rhythmicity
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16
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Shkodina AD, Tan SC, Hasan MM, Abdelgawad M, Chopra H, Bilal M, Boiko DI, Tarianyk KA, Alexiou A. Roles of clock genes in the pathogenesis of Parkinson's disease. Ageing Res Rev 2022; 74:101554. [PMID: 34973458 DOI: 10.1016/j.arr.2021.101554] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 11/24/2021] [Accepted: 12/27/2021] [Indexed: 12/13/2022]
Abstract
Parkinson's disease (PD) is a common motor disorder that has become increasingly prevalent in the ageing population. Recent works have suggested that circadian rhythms disruption is a common event in PD patients. Clock genes regulate the circadian rhythm of biological processes in eukaryotic organisms, but their roles in PD remain unclear. Despite this, several lines of evidence point to the possibility that clock genes may have a significant impact on the development and progression of the disease. This review aims to consolidate recent understanding of the roles of clock genes in PD. We first summarized the findings of clock gene expression and epigenetic analyses in PD patients and animal models. We also discussed the potential contributory role of clock gene variants in the development of PD and/or its symptoms. We further reviewed the mechanisms by which clock genes affect mitochondrial dynamics as well as the rhythmic synthesis and secretion of endocrine hormones, the impairment of which may contribute to the development of PD. Finally, we discussed the limitations of the currently available studies, and suggested future potential studies to deepen our understanding of the roles of clock genes in PD pathogenesis.
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Affiliation(s)
| | - Shing Cheng Tan
- UKM Medical Molecular Biology Institute, Universiti Kebangsaan Malaysia, 56000 Cheras, Kuala Lumpur, Malaysia.
| | - Mohammad Mehedi Hasan
- Department of Biochemistry and Molecular Biology, Faculty of Life Science, Mawlana Bhashani Science and Technology University, Tangail 1902, Bangladesh
| | - Mai Abdelgawad
- Biotechnology and Life Sciences Department, Faculty of Postgraduate Studies for Advanced Sciences (PSAS), Beni-Suef University, Beni-Suef 62511, Egypt
| | - Hitesh Chopra
- Chitkara College of Pharmacy, Chitkara University, 140401 Punjab, India
| | - Muhammad Bilal
- College of Pharmacy, Liaquat University of Medical and Health Sciences, Jamshoro, Pakistan
| | | | | | - Athanasios Alexiou
- Novel Global Community Educational Foundation, Peterlee Place NSW2700, Australia; AFNP Med, Haidingergasse 29, 1030 Wien, Austria
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17
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Shkodina AD, Tan SC, Hasan MM, Abdelgawad M, Chopra H, Bilal M, Boiko DI, Tarianyk KA, Alexiou A. Roles of clock genes in the pathogenesis of Parkinson's disease. Ageing Res Rev 2022; 74:101554. [DOI: https:/doi.org/10.1016/j.arr.2021.101554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/30/2023]
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18
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Shkodina AD, Tan SC, Hasan MM, Abdelgawad M, Chopra H, Bilal M, Boiko DI, Tarianyk KA, Alexiou A. Roles of clock genes in the pathogenesis of Parkinson's disease. Ageing Res Rev 2022. [DOI: https://doi.org/10.1016/j.arr.2021.101554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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19
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Smith CB, van der Vinne V, McCartney E, Stowie AC, Leise TL, Martin-Burgos B, Molyneux PC, Garbutt LA, Brodsky MH, Davidson AJ, Harrington ME, Dallmann R, Weaver DR. Cell-Type-Specific Circadian Bioluminescence Rhythms in Dbp Reporter Mice. J Biol Rhythms 2022; 37:53-77. [PMID: 35023384 DOI: 10.1177/07487304211069452] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Circadian rhythms are endogenously generated physiological and molecular rhythms with a cycle length of about 24 h. Bioluminescent reporters have been exceptionally useful for studying circadian rhythms in numerous species. Here, we report development of a reporter mouse generated by modification of a widely expressed and highly rhythmic gene encoding D-site albumin promoter binding protein (Dbp). In this line of mice, firefly luciferase is expressed from the Dbp locus in a Cre recombinase-dependent manner, allowing assessment of bioluminescence rhythms in specific cellular populations. A mouse line in which luciferase expression was Cre-independent was also generated. The Dbp reporter alleles do not alter Dbp gene expression rhythms in liver or circadian locomotor activity rhythms. In vivo and ex vivo studies show the utility of the reporter alleles for monitoring rhythmicity. Our studies reveal cell-type-specific characteristics of rhythms among neuronal populations within the suprachiasmatic nuclei ex vivo. In vivo studies show Dbp-driven bioluminescence rhythms in the liver of Albumin-Cre;DbpKI/+ "liver reporter" mice. After a shift of the lighting schedule, locomotor activity achieved the proper phase relationship with the new lighting cycle more rapidly than hepatic bioluminescence did. As previously shown, restricting food access to the daytime altered the phase of hepatic rhythmicity. Our model allowed assessment of the rate of recovery from misalignment once animals were provided with food ad libitum. These studies confirm the previously demonstrated circadian misalignment following environmental perturbations and reveal the utility of this model for minimally invasive, longitudinal monitoring of rhythmicity from specific mouse tissues.
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Affiliation(s)
- Ciearra B Smith
- Department of Neurobiology, University of Massachusetts Chan Medical School, Worcester, Massachusetts.,Graduate Program in Neuroscience, University of Massachusetts Chan Medical School, Worcester, Massachusetts
| | - Vincent van der Vinne
- Department of Neurobiology, University of Massachusetts Chan Medical School, Worcester, Massachusetts.,Department of Biology, Williams College, Williamstown, Massachusetts
| | | | - Adam C Stowie
- Neuroscience Institute, Morehouse School of Medicine, Atlanta, Georgia
| | - Tanya L Leise
- Department of Mathematics & Statistics, Amherst College, Amherst, Massachusetts
| | | | | | - Lauren A Garbutt
- Division of Biomedical Sciences, Warwick Medical School, The University of Warwick, Coventry, UK
| | - Michael H Brodsky
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, Massachusetts
| | - Alec J Davidson
- Neuroscience Institute, Morehouse School of Medicine, Atlanta, Georgia
| | | | - Robert Dallmann
- Division of Biomedical Sciences, Warwick Medical School, The University of Warwick, Coventry, UK
| | - David R Weaver
- Department of Neurobiology, University of Massachusetts Chan Medical School, Worcester, Massachusetts.,Graduate Program in Neuroscience, University of Massachusetts Chan Medical School, Worcester, Massachusetts.,NeuroNexus Institute, University of Massachusetts Chan Medical School, Worcester, Massachusetts
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20
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Chen WH, Huang QY, Wang ZY, Zhuang XX, Lin S, Shi QY. Therapeutic potential of exosomes/miRNAs in polycystic ovary syndrome induced by the alteration of circadian rhythms. Front Endocrinol (Lausanne) 2022; 13:918805. [PMID: 36465652 PMCID: PMC9709483 DOI: 10.3389/fendo.2022.918805] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 10/19/2022] [Indexed: 11/17/2022] Open
Abstract
Polycystic ovary syndrome (PCOS) is a reproductive dysfunction associated with endocrine disorders and is most common in women of reproductive age. Clinical and/or biochemical manifestations include hyperandrogenism, persistent anovulation, polycystic ovary, insulin resistance, and obesity. Presently, the aetiology and pathogenesis of PCOS remain unclear. In recent years, the role of circadian rhythm changes in PCOS has garnered considerable attention. Changes in circadian rhythm can trigger PCOS through mechanisms such as oxidative stress and inflammation; however, the specific mechanisms are unclear. Exosomes are vesicles with sizes ranging from 30-120nm that mediate intercellular communication by transporting microRNAs (miRNAs), proteins, mRNAs, DNA, or lipids to target cells and are widely involved in the regulation of various physiological and pathological processes. Circadian rhythm can alter circulating exosomes, leading to a series of related changes and physiological dysfunctions. Therefore, we speculate that circadian rhythm-induced changes in circulating exosomes may be involved in PCOS pathogenesis. In this review, we summarize the possible roles of exosomes and their derived microRNAs in the occurrence and development of PCOS and discuss their possible mechanisms, providing insights into the potential role of exosomes for PCOS treatment.
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Affiliation(s)
- Wei-hong Chen
- Department of Gynaecology and Obstetrics, the Second Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian, China
| | - Qiao-yi Huang
- Department of Gynaecology and Obstetrics, the Second Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian, China
| | - Zhi-yi Wang
- Department of Gynaecology and Obstetrics, the Second Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian, China
| | - Xuan-xuan Zhuang
- Department of Gynaecology and Obstetrics, the Second Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian, China
| | - Shu Lin
- Centre of Neurological and Metabolic Research, the Second Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian, China
- Group of Neuroendocrinology, Garvan Institute of Medical Research, Sydney, NSW, Australia
- *Correspondence: Qi-yang Shi, ; Shu Lin,
| | - Qi-yang Shi
- Department of Gynaecology and Obstetrics, the Second Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian, China
- *Correspondence: Qi-yang Shi, ; Shu Lin,
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21
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Mohamed HMA, Takahashi A, Nishijima S, Adachi S, Murai I, Okamura H, Yamamoto T. CNOT1 regulates circadian behaviour through Per2 mRNA decay in a deadenylation-dependent manner. RNA Biol 2021; 19:703-718. [PMID: 35510877 PMCID: PMC9090297 DOI: 10.1080/15476286.2022.2071026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 04/15/2022] [Accepted: 04/20/2022] [Indexed: 11/18/2022] Open
Abstract
Circadian clocks are an endogenous internal timekeeping mechanism that drives the rhythmic expression of genes, controlling the 24 h oscillatory pattern in behaviour and physiology. It has been recently shown that post-transcriptional mechanisms are essential for controlling rhythmic gene expression. Controlling the stability of mRNA through poly(A) tail length modulation is one such mechanism. In this study, we show that Cnot1, encoding the scaffold protein of the CCR4-NOT deadenylase complex, is highly expressed in the suprachiasmatic nucleus, the master timekeeper. CNOT1 deficiency in mice results in circadian period lengthening and alterations in the mRNA and protein expression patterns of various clock genes, mainly Per2. Per2 mRNA exhibited a longer poly(A) tail and increased mRNA stability in Cnot1+/- mice. CNOT1 is recruited to Per2 mRNA through BRF1 (ZFP36L1), which itself oscillates in antiphase with Per2 mRNA. Upon Brf1 knockdown, Per2 mRNA is stabilized leading to increased PER2 expression levels. This suggests that CNOT1 plays a role in tuning and regulating the mammalian circadian clock.
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Affiliation(s)
| | - Akinori Takahashi
- Cell Signal Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Saori Nishijima
- Cell Signal Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Shungo Adachi
- Molecular Profiling Research Center for Drug Discovery, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
| | - Iori Murai
- Laboratory of Molecular Brain Science, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
| | - Hitoshi Okamura
- Laboratory of Molecular Brain Science, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
- Department of Neuroscience, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Tadashi Yamamoto
- Cell Signal Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
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22
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Cheng Q, Fan X, Liu Y, Xu L, Dong P, Song L, Qian R. miR-455-5p regulates circadian rhythms by accelerating the degradation of Clock mRNA. IUBMB Life 2021; 74:245-258. [PMID: 34904778 DOI: 10.1002/iub.2587] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Revised: 11/22/2021] [Accepted: 12/09/2021] [Indexed: 11/08/2022]
Abstract
Circadian rhythms are approximately 24-hr cycles generated by organisms to adapt to daily rhythms. Core circadian proteins such as CLOCK, BMAL1, PER1/2, and CRY1/2/3 form a transcription-translation feedback loop (TTFL) to maintain circadian rhythms. MicroRNAs are involved in regulating circadian rhythms; however, the detailed mechanisms remain unclear. Here, using miRNA-seq screening, we discovered that the expression level of miR-455 was controlled by CLOCK. Furthermore, miR-455-5p also binds to the 3' untranslated region (3'UTR) of Clock mRNA and regulates its stability. To further study whether such mutual regulation forms a feedback loop to regulate circadian rhythms, we recorded bioluminescence traces of Per2::Luc U2OS cells in real time and confirmed that overexpression of miR-455-5p lengthens the period and attenuates the amplitude of circadian rhythms in synchronized cells (and vice versa). We also discovered that miR-455-5p can function as a Clock modulator to induce a fine-orchestral circadian rhythm in vitro, as well as other known factors such as dexamethasone, horse serum, or temperature. In conclusion, miR-455-5p is essential for maintaining a normal circadian rhythm via regulating Clock mRNA stability. Our study reveals a new mutual regulatory mechanism between CLOCK protein, Clock mRNA, and miR-455-5p, which regulates circadian rhythms in cells.
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Affiliation(s)
- Qianyun Cheng
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Fudan University, Shanghai, China.,Research Center on Aging and Medicine, Fudan University, Shanghai, China
| | - Xinyi Fan
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Fudan University, Shanghai, China.,Research Center on Aging and Medicine, Fudan University, Shanghai, China
| | - Yutong Liu
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Fudan University, Shanghai, China.,Research Center on Aging and Medicine, Fudan University, Shanghai, China
| | - Lirong Xu
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Fudan University, Shanghai, China.,Research Center on Aging and Medicine, Fudan University, Shanghai, China
| | - Pengjuan Dong
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Fudan University, Shanghai, China.,Research Center on Aging and Medicine, Fudan University, Shanghai, China
| | - Liwen Song
- School of Medicine, Department of Obstetrics & Gynecology, Tongren Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Ruizhe Qian
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Fudan University, Shanghai, China.,Research Center on Aging and Medicine, Fudan University, Shanghai, China
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23
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Chen M, Chen M, Lu D, Wang Y, Zhang L, Wang Z, Wu B. Period 2 Regulates CYP2B10 Expression and Activity in Mouse Liver. Front Pharmacol 2021; 12:764124. [PMID: 34887762 PMCID: PMC8650840 DOI: 10.3389/fphar.2021.764124] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 11/03/2021] [Indexed: 01/08/2023] Open
Abstract
CYP2B10 is responsible for metabolism and detoxification of many clinical drugs. Here, we aimed to investigate a potential role of Period 2 (PER2) in regulating expression of hepatic CYP2B10. Regulatory effects of PER2 on hepatic expression of CYP2B10 and other enzymes were determined using Per2-deficient mice with exons 4-6 deleted (named Per2Del4-6 mice). In vitro and in vivo metabolic activities of CYP2B10 were probed using cyclophosphamide (CPA) as a specific substrate. Regulatory mechanism was investigated using luciferase reporter assays. Genotyping and Western blotting demonstrated loss of wild-type Per2 transcript and markedly reduced PER2 protein in Per2Del4-6 mice. Hepatic expression of a plenty of drug-metabolizing genes (including Cyp2a4/2a5, Cyp2b10, Ugt1a1, Ugt1a9, Ugt2b36, Sult1a1 and Sult1e1) were altered (and majority were down-regulated) in Per2Del4-6 mice. Of note, Cyp2b10, Ugt1a9 and Sult1a1 were three genes considerably affected with reduced expression. Decreased expression of CYP2B10 was translated to reduced metabolism and altered pharmacokinetics of CPA as well as attenuated CPA hepatotoxicity in Per2Del4-6 mice. Positive regulation of CYP2B10 by PER2 was further confirmed in both Hepa-1c1c7 and AML-12 cells. Based on luciferase reporter assays, it was shown that PER2 regulated Cyp2b10 transcription in a REV-ERBα-dependent manner. REV-ERBα was negatively regulated by PER2 (increased REV-ERBα expression in Per2Del4-6 mice) and itself was also a repressor of CYP2B10. In conclusion, PER2 positively regulates CYP2B10 expression and activity in mouse liver through inhibiting its repressor REV-ERBα.
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Affiliation(s)
- MengLin Chen
- College of Pharmacy, Jinan University, Guangzhou, China.,Institute of Molecular Rhythm and Metabolism, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Min Chen
- College of Pharmacy, Jinan University, Guangzhou, China.,Institute of Molecular Rhythm and Metabolism, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Danyi Lu
- Institute of Molecular Rhythm and Metabolism, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Yi Wang
- College of Pharmacy, Jinan University, Guangzhou, China.,Institute of Molecular Rhythm and Metabolism, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Li Zhang
- College of Pharmacy, Jinan University, Guangzhou, China.,Institute of Molecular Rhythm and Metabolism, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Zhigang Wang
- Department of Intensive Care Unit, First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Baojian Wu
- Institute of Molecular Rhythm and Metabolism, Guangzhou University of Chinese Medicine, Guangzhou, China
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24
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Martin-Burgos B, Wang W, William I, Tir S, Mohammad I, Javed R, Smith S, Cui Y, Arzavala J, Mora D, Smith CB, van der Vinne V, Molyneux PC, Miller SC, Weaver DR, Leise TL, Harrington ME. Methods for Detecting PER2:LUCIFERASE Bioluminescence Rhythms in Freely Moving Mice. J Biol Rhythms 2021; 37:78-93. [PMID: 34873943 DOI: 10.1177/07487304211062829] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Circadian rhythms are driven by daily oscillations of gene expression. An important tool for studying cellular and tissue circadian rhythms is the use of a gene reporter, such as bioluminescence from the reporter gene luciferase controlled by a rhythmically expressed gene of interest. Here we describe methods that allow measurement of circadian bioluminescence from a freely moving mouse housed in a standard cage. Using a LumiCycle In Vivo (Actimetrics), we determined conditions that allow detection of circadian rhythms of bioluminescence from the PER2 reporter, PER2::LUC, in freely behaving mice. The LumiCycle In Vivo applies a background subtraction that corrects for effects of room temperature on photomultiplier tube (PMT) output. We tested delivery of d-luciferin via a subcutaneous minipump and in the drinking water. We demonstrate spikes in bioluminescence associated with drinking bouts. Further, we demonstrate that a synthetic luciferase substrate, CycLuc1, can support circadian rhythms of bioluminescence, even when delivered at a lower concentration than d-luciferin, and can support longer-term studies. A small difference in phase of the PER2::LUC bioluminescence rhythms, with females phase leading males, can be detected with this technique. We share our analysis scripts and suggestions for further improvements in this method. This approach will be straightforward to apply to mice with tissue-specific reporters, allowing insights into responses of specific peripheral clocks to perturbations such as environmental or pharmacological manipulations.
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Affiliation(s)
| | - Wanqi Wang
- Neuroscience Program, Smith College, Northampton, Massachusetts
| | - Ivana William
- Neuroscience Program, Smith College, Northampton, Massachusetts
| | - Selma Tir
- Neuroscience Program, Smith College, Northampton, Massachusetts
| | - Innus Mohammad
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Chan Medical School, Worcester, Massachusetts
| | - Reja Javed
- Neuroscience Program, Smith College, Northampton, Massachusetts
| | - Stormi Smith
- Neuroscience Program, Smith College, Northampton, Massachusetts
| | - Yilin Cui
- Neuroscience Program, Smith College, Northampton, Massachusetts
| | | | - Dalilah Mora
- Neuroscience Program, Smith College, Northampton, Massachusetts
| | - Ciearra B Smith
- Graduate Program in Neuroscience, University of Massachusetts Chan Medical School, Worcester, Massachusetts.,Department of Neurobiology, University of Massachusetts Chan Medical School, Worcester, Massachusetts
| | - Vincent van der Vinne
- Department of Neurobiology, University of Massachusetts Chan Medical School, Worcester, Massachusetts.,Department of Biology, Williams College, Williamstown, Massachusetts
| | | | - Stephen C Miller
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Chan Medical School, Worcester, Massachusetts
| | - David R Weaver
- Graduate Program in Neuroscience, University of Massachusetts Chan Medical School, Worcester, Massachusetts.,Department of Neurobiology, University of Massachusetts Chan Medical School, Worcester, Massachusetts
| | - Tanya L Leise
- Department of Mathematics & Statistics, Amherst College, Amherst, Massachusetts
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25
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Gagliano O, Luni C, Li Y, Angiolillo S, Qin W, Panariello F, Cacchiarelli D, Takahashi JS, Elvassore N. Synchronization between peripheral circadian clock and feeding-fasting cycles in microfluidic device sustains oscillatory pattern of transcriptome. Nat Commun 2021; 12:6185. [PMID: 34702819 PMCID: PMC8548598 DOI: 10.1038/s41467-021-26294-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 07/26/2021] [Indexed: 12/13/2022] Open
Abstract
The circadian system cyclically regulates many physiological and behavioral processes within the day. Desynchronization between physiological and behavioral rhythms increases the risk of developing some, including metabolic, disorders. Here we investigate how the oscillatory nature of metabolic signals, resembling feeding-fasting cycles, sustains the cell-autonomous clock in peripheral tissues. By controlling the timing, period and frequency of glucose and insulin signals via microfluidics, we find a strong effect on Per2::Luc fibroblasts entrainment. We show that the circadian Per2 expression is better sustained via a 24 h period and 12 h:12 h frequency-encoded metabolic stimulation applied for 3 daily cycles, aligned to the cell-autonomous clock, entraining the expression of hundreds of genes mostly belonging to circadian rhythms and cell cycle pathways. On the contrary misaligned feeding-fasting cycles synchronize and amplify the expression of extracellular matrix-associated genes, aligned during the light phase. This study underlines the role of the synchronicity between life-style-associated metabolic signals and peripheral clocks on the circadian entrainment.
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Affiliation(s)
- Onelia Gagliano
- Department of Industrial Engineering (DII), University of Padova, Padova, Italy
- Venetian Institute of Molecular Medicine (VIMM), Padova, Italy
- Department of Neuroscience, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Camilla Luni
- Shanghai Institute for Advanced Immunochemical Studies (SIAIS), ShanghaiTech University, Shanghai, China
- Department of Civil, Chemical, Environmental and Materials Engineering (DICAM), University of Bologna, Bologna, Italy
| | - Yan Li
- Department of Neuroscience, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Silvia Angiolillo
- Department of Industrial Engineering (DII), University of Padova, Padova, Italy
- Venetian Institute of Molecular Medicine (VIMM), Padova, Italy
| | - Wei Qin
- Department of Industrial Engineering (DII), University of Padova, Padova, Italy
- Venetian Institute of Molecular Medicine (VIMM), Padova, Italy
| | - Francesco Panariello
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy
- Department of Translational Medicine, University of Naples "Federico II", Naples, Italy
| | - Davide Cacchiarelli
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy
- Department of Translational Medicine, University of Naples "Federico II", Naples, Italy
| | - Joseph S Takahashi
- Department of Neuroscience, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA.
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA.
| | - Nicola Elvassore
- Department of Industrial Engineering (DII), University of Padova, Padova, Italy.
- Venetian Institute of Molecular Medicine (VIMM), Padova, Italy.
- Stem Cell and Regenerative Medicine Section, University College London GOS Institute of Child Health, London, UK.
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26
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PER2 Regulates Reactive Oxygen Species Production in the Circadian Susceptibility to Ischemia/Reperfusion Injury in the Heart. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2021; 2021:6256399. [PMID: 34659637 PMCID: PMC8519710 DOI: 10.1155/2021/6256399] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 08/15/2021] [Accepted: 08/24/2021] [Indexed: 11/21/2022]
Abstract
The main objective of this study was to investigate the diurnal differences in Period 2 (PER2) expression in myocardial ischemia-reperfusion (I/R) injury. We investigated diurnal variations in oxidative stress and energy metabolism after myocardial I/R in vitro and in vivo. In addition, we also analyzed the effects of H2O2 treatment and serum shock in H9c2 cells transfected with silencing RNA against Per2 (siRNA-Per2) in vitro. We used C57BL/6 male mice to construct a model of I/R injury at zeitgeber time (ZT) 2 and ZT14 by synchronizing the circadian rhythms. Our in vivo analysis demonstrated that there were diurnal differences in the severity of injury caused by myocardial infarctions, with more injury occurring in the daytime. PER2 was significantly reduced in heart tissue in the daytime and was higher at night. Our results also showed that more severe injury of mitochondrial function in daytime produced more reactive oxygen species (ROS) and less ATP, which increased myocardial injury. In vitro, our findings presented a similar trend showing that apoptosis of H9c2 cells was increased when PER2 expression was lower. Meanwhile, downregulation of PER2 disrupted the oxidative balance by increasing ROS and mitochondrial injury. The result was a reduction in ATP and failure to provide sufficient energy protection for cardiomyocytes.
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27
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Anna G, Kannan NN. Post-transcriptional modulators and mediators of the circadian clock. Chronobiol Int 2021; 38:1244-1261. [PMID: 34056966 PMCID: PMC7611477 DOI: 10.1080/07420528.2021.1928159] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 04/26/2021] [Accepted: 05/03/2021] [Indexed: 01/04/2023]
Abstract
The endogenous circadian timekeeping system drives ~24-h rhythms in gene expression and rhythmically coordinates the physiology, metabolism and behavior in a wide range of organisms. Regulation at various levels is important for the accurate functioning of this circadian timing system. The core circadian oscillator consists of an interlocked transcriptional-translational negative feedback loop (TTFL) that imposes a substantial delay between the accumulation of clock gene mRNA and its protein to generate 24-h oscillations. This TTFL mediated daily oscillation of clock proteins is further fine-tuned by post-translational modifications that regulate the clock protein stability, interaction with other proteins and subcellular localization. Emerging evidence from various studies indicates that besides TTFL and post-translational modifications, post-transcriptional regulation plays a key role in shaping the rhythmicity of mRNAs and to delay the accumulation of clock proteins in relation to their mRNAs. In this review, we summarize the current knowledge on the importance of post-transcriptional regulatory mechanisms such as splicing, polyadenylation, the role of RNA-binding proteins, RNA methylation and microRNAs in the context of shaping the circadian rhythmicity in Drosophila and mammals. In particular, we discuss microRNAs, an important player in post-transcriptional regulation of core-clock machinery, circadian neural circuit, clock input, and output pathways. Furthermore, we provide an overview of the microRNAs that exhibit diurnal rhythm in expression and their role in mediating rhythmic physiological processes.
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Affiliation(s)
- Geo Anna
- Chronobiology Laboratory, School of Biology, Indian Institute of Science Education and Research (IISER), Thiruvananthapuram, Kerala 695551, India
| | - Nisha N Kannan
- Chronobiology Laboratory, School of Biology, Indian Institute of Science Education and Research (IISER), Thiruvananthapuram, Kerala 695551, India
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28
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Clock-Modulating Activities of the Anti-Arrhythmic Drug Moricizine. Clocks Sleep 2021; 3:351-365. [PMID: 34206497 PMCID: PMC8293187 DOI: 10.3390/clockssleep3030022] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 06/09/2021] [Accepted: 06/21/2021] [Indexed: 12/12/2022] Open
Abstract
Dysregulated circadian functions contribute to various diseases, including cardiovascular disease. Much progress has been made on chronotherapeutic applications of drugs against cardiovascular disease (CVD); however, the direct effects of various medications on the circadian system are not well characterized. We previously conducted high-throughput chemical screening for clock modulators and identified an off-patent anti-arrhythmic drug, moricizine, as a clock-period lengthening compound. In Per2:LucSV reporter fibroblast cells, we showed that under both dexamethasone and forskolin synchronization, moricizine was able to increase the circadian period length, with greater effects seen with the former. Titration studies revealed a dose-dependent effect of moricizine to lengthen the period. In contrast, flecainide, another Class I anti-arrhythmic, showed no effects on circadian reporter rhythms. Real-time qPCR analysis in fibroblast cells treated with moricizine revealed significant circadian time- and/or treatment-dependent expression changes in core clock genes, consistent with the above period-lengthening effects. Several clock-controlled cardiac channel genes also displayed altered expression patterns. Using tissue explant culture, we showed that moricizine was able to significantly prolong the period length of circadian reporter rhythms in atrial ex vivo cultures. Using wild-type C57BL/6J mice, moricizine treatment was found to promote sleep, alter circadian gene expression in the heart, and show a slight trend of increasing free-running periods. Together, these observations demonstrate novel clock-modulating activities of moricizine, particularly the period-lengthening effects on cellular oscillators, which may have clinical relevance against heart diseases.
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29
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Ralph MR, Shi SQ, Johnson CH, Houdek P, Shrestha TC, Crosby P, O’Neill JS, Sládek M, Stinchcombe AR, Sumová A. Targeted modification of the Per2 clock gene alters circadian function in mPer2luciferase (mPer2Luc) mice. PLoS Comput Biol 2021; 17:e1008987. [PMID: 34048425 PMCID: PMC8191895 DOI: 10.1371/journal.pcbi.1008987] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 06/10/2021] [Accepted: 04/20/2021] [Indexed: 11/19/2022] Open
Abstract
Modification of the Per2 clock gene in mPer2Luc reporter mice significantly alters circadian function. Behavioral period in constant dark is lengthened, and dissociates into two distinct components in constant light. Rhythms exhibit increased bimodality, enhanced phase resetting to light pulses, and altered entrainment to scheduled feeding. Mechanistic mathematical modelling predicts that enhanced protein interactions with the modified mPER2 C-terminus, combined with differential clock regulation among SCN subregions, can account for effects on circadian behavior via increased Per2 transcript and protein stability. PER2::LUC produces greater suppression of CLOCK:BMAL1 E-box activity than PER2. mPer2Luc carries a 72 bp deletion in exon 23 of Per2, and retains a neomycin resistance cassette that affects rhythm amplitude but not period. The results show that mPer2Luc acts as a circadian clock mutation illustrating a need for detailed assessment of potential impacts of c-terminal tags in genetically modified animal models.
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Affiliation(s)
- Martin R. Ralph
- Department of Psychology, University of Toronto, Toronto, Ontario, Canada
| | - Shu-qun Shi
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Carl H. Johnson
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Pavel Houdek
- Laboratory of Biological Rhythms, Institute of Physiology, the Czech Academy of Sciences, Prague, Czech Republic
| | - Tenjin C. Shrestha
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
| | - Priya Crosby
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - John S. O’Neill
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Martin Sládek
- Laboratory of Biological Rhythms, Institute of Physiology, the Czech Academy of Sciences, Prague, Czech Republic
| | | | - Alena Sumová
- Laboratory of Biological Rhythms, Institute of Physiology, the Czech Academy of Sciences, Prague, Czech Republic
- * E-mail:
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30
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Natural antisense transcript of Period2, Per2AS, regulates the amplitude of the mouse circadian clock. Genes Dev 2021; 35:899-913. [PMID: 34016691 PMCID: PMC8168560 DOI: 10.1101/gad.343541.120] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 04/26/2021] [Indexed: 12/20/2022]
Abstract
In mammals, a set of core clock genes form transcription-translation feedback loops to generate circadian oscillations. We and others recently identified a novel transcript at the Period2 (Per2) locus that is transcribed from the antisense strand of Per2 This transcript, Per2AS, is expressed rhythmically and antiphasic to Per2 mRNA, leading to our hypothesis that Per2AS and Per2 mutually inhibit each other's expression and form a double negative feedback loop. By perturbing the expression of Per2AS, we found that Per2AS transcription, but not transcript, represses Per2 However, Per2 does not repress Per2AS, as Per2 knockdown led to a decrease in the Per2AS level, indicating that Per2AS forms a single negative feedback loop with Per2 and maintains the level of Per2 within the oscillatory range. Per2AS also regulates the amplitude of the circadian clock, and this function cannot be solely explained through its interaction with Per2, as Per2 knockdown does not recapitulate the phenotypes of Per2AS perturbation. Overall, our data indicate that Per2AS is an important regulatory molecule in the mammalian circadian clock machinery. Our work also supports the idea that antisense transcripts of core clock genes constitute a common feature of circadian clocks, as they are found in other organisms.
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31
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de Assis LVM, Oster H. The circadian clock and metabolic homeostasis: entangled networks. Cell Mol Life Sci 2021; 78:4563-4587. [PMID: 33683376 PMCID: PMC8195959 DOI: 10.1007/s00018-021-03800-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 01/28/2021] [Accepted: 02/23/2021] [Indexed: 12/12/2022]
Abstract
The circadian clock exerts an important role in systemic homeostasis as it acts a keeper of time for the organism. The synchrony between the daily challenges imposed by the environment needs to be aligned with biological processes and with the internal circadian clock. In this review, it is provided an in-depth view of the molecular functioning of the circadian molecular clock, how this system is organized, and how central and peripheral clocks communicate with each other. In this sense, we provide an overview of the neuro-hormonal factors controlled by the central clock and how they affect peripheral tissues. We also evaluate signals released by peripheral organs and their effects in the central clock and other brain areas. Additionally, we evaluate a possible communication between peripheral tissues as a novel layer of circadian organization by reviewing recent studies in the literature. In the last section, we analyze how the circadian clock can modulate intracellular and tissue-dependent processes of metabolic organs. Taken altogether, the goal of this review is to provide a systemic and integrative view of the molecular clock function and organization with an emphasis in metabolic tissues.
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Affiliation(s)
| | - Henrik Oster
- Center of Brain, Behavior and Metabolism, University of Lübeck, Institute of Neurobiology, Marie Curie Street, 23562, Lübeck, Germany.
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32
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A genome-wide microRNA screen identifies the microRNA-183/96/182 cluster as a modulator of circadian rhythms. Proc Natl Acad Sci U S A 2021; 118:2020454118. [PMID: 33443164 DOI: 10.1073/pnas.2020454118] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
The regulatory mechanisms of circadian rhythms have been studied primarily at the level of the transcription-translation feedback loops of protein-coding genes. Regulatory modules involving noncoding RNAs are less thoroughly understood. In particular, emerging evidence has revealed the important role of microRNAs (miRNAs) in maintaining the robustness of the circadian system. To identify miRNAs that have the potential to modulate circadian rhythms, we conducted a genome-wide miRNA screen using U2OS luciferase reporter cells. Among 989 miRNAs in the library, 120 changed the period length in a dose-dependent manner. We further validated the circadian regulatory function of an miRNA cluster, miR-183/96/182, both in vitro and in vivo. We found that all three members of this miRNA cluster can modulate circadian rhythms. Particularly, miR-96 directly targeted a core circadian clock gene, PER2. The knockout of the miR-183/96/182 cluster in mice showed tissue-specific effects on circadian parameters and altered circadian rhythms at the behavioral level. This study identified a large number of miRNAs, including the miR-183/96/182 cluster, as circadian modulators. We provide a resource for further understanding the role of miRNAs in the circadian network and highlight the importance of miRNAs as a genome-wide layer of circadian clock regulation.
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33
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Ahmad SF, Shanaz S, Kumar A, Dar AH, Mohmad A, Bhushan B. Crosstalk of epigenetics with biological rhythmicity in animal kingdom. BIOL RHYTHM RES 2021. [DOI: 10.1080/09291016.2019.1607218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Sheikh Firdous Ahmad
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Bareilly, India
| | - Syed Shanaz
- Department of Animal Genetics and Breeding, Sher-i-Kashmir University of Agricultural Sciences and Technology, Srinagar, India
| | - Abhishek Kumar
- Division of Animal Reproduction, ICAR-Indian Veterinary Research Institute, Bareilly, India
| | - Aashaq Hussain Dar
- Department of Livestock Production and Management, Govind Ballabh Pant University of Agriculture and Technology, Pantnagar, Uttarakhand
| | - Aquil Mohmad
- Division of Parasitology, ICAR-Indian Veterinary Research Institute, Bareilly, India
| | - Bharat Bhushan
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Bareilly, India
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34
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Burish MJ, Han C, Mawatari K, Wirianto M, Kim E, Ono K, Parakramaweera R, Chen Z, Yoo SH. The first-line cluster headache medication verapamil alters the circadian period and elicits sex-specific sleep changes in mice. Chronobiol Int 2021; 38:839-850. [PMID: 33829951 DOI: 10.1080/07420528.2021.1892127] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Verapamil is the first-line preventive medication for cluster headache, an excruciating disorder with strong circadian features. Whereas second- and third-line preventives include known circadian modulators, such as melatonin, corticosteroids, and lithium, the circadian effects of verapamil are poorly understood. Here, we characterize the circadian features of verapamil using both in vitro and in vivo models. In Per2::LucSV reporter fibroblasts, treatment with verapamil (0.03-10 µM) showed a dose-dependent period shortening of the reporter rhythm which reached a nadir at 1 µM, and altered core clock gene expression at 10 µM. Mouse wheel-running activity with verapamil (1 mg/mL added to the drinking water) also resulted in significant period shortening and activity reduction in both male and female free-running wild-type C57BL6/J mice. The temporal patterns of activity reduction, however, differ between the two sexes. Importantly, piezo sleep recording revealed sexual dimorphism in the effects of verapamil on sleep timing and bout duration, with more pronounced adverse effects in female mice. We also found altered circadian clock gene expression in the cerebellum, hypothalamus, and trigeminal ganglion of verapamil-treated mice. Verapamil did not affect reporter rhythms in ex vivo suprachiasmatic nucleus (SCN) slices from Per2:Luc reporter mice, perhaps due to the exceptionally tight coupling in the SCN. Thus, verapamil affects both peripheral (trigeminal ganglion) and central (hypothalamus and cerebellum) nervous system structures involved in cluster headache pathophysiology, possibly with network effects instead of isolated SCN effects. These studies suggest that verapamil is a circadian modulator in laboratory models at both molecular and behavioral levels, and sex is an important biological variable for cluster headache medications. These observations highlight the circadian system as a potential convergent target for cluster headache medications with different primary mechanisms of action.
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Affiliation(s)
- Mark J Burish
- Department of Neurosurgery and Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston, Houston, USA
| | - Chorong Han
- Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston, Houston, USA
| | - Kazuaki Mawatari
- Department of Preventive Environment and Nutrition, Institute of Biomedical Sciences, Tokushima University Graduate School, Japan
| | - Marvin Wirianto
- Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston, Houston, USA
| | - Eunju Kim
- Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston, Houston, USA
| | - Kaori Ono
- Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston, Houston, USA
| | - Randika Parakramaweera
- Department of Neurosurgery and Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston, Houston, USA
| | - Zheng Chen
- Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston, Houston, USA
| | - Seung-Hee Yoo
- Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston, Houston, USA
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35
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Parnell AA, De Nobrega AK, Lyons LC. Translating around the clock: Multi-level regulation of post-transcriptional processes by the circadian clock. Cell Signal 2021; 80:109904. [PMID: 33370580 PMCID: PMC8054296 DOI: 10.1016/j.cellsig.2020.109904] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 12/20/2020] [Accepted: 12/21/2020] [Indexed: 12/11/2022]
Abstract
The endogenous circadian clock functions to maintain optimal physiological health through the tissue specific coordination of gene expression and synchronization between tissues of metabolic processes throughout the 24 hour day. Individuals face numerous challenges to circadian function on a daily basis resulting in significant incidences of circadian disorders in the United States and worldwide. Dysfunction of the circadian clock has been implicated in numerous diseases including cancer, diabetes, obesity, cardiovascular and hepatic abnormalities, mood disorders and neurodegenerative diseases. The circadian clock regulates molecular, metabolic and physiological processes through rhythmic gene expression via transcriptional and post-transcriptional processes. Mounting evidence indicates that post-transcriptional regulation by the circadian clock plays a crucial role in maintaining tissue specific biological rhythms. Circadian regulation affecting RNA stability and localization through RNA processing, mRNA degradation, and RNA availability for translation can result in rhythmic protein synthesis, even when the mRNA transcripts themselves do not exhibit rhythms in abundance. The circadian clock also targets the initiation and elongation steps of translation through multiple pathways. In this review, the influence of the circadian clock across the levels of post-transcriptional, translation, and post-translational modifications are examined using examples from humans to cyanobacteria demonstrating the phylogenetic conservation of circadian regulation. Lastly, we briefly discuss chronotherapies and pharmacological treatments that target circadian function. Understanding the complexity and levels through which the circadian clock regulates molecular and physiological processes is important for future advancement of therapeutic outcomes.
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Affiliation(s)
- Amber A Parnell
- Department of Biological Science, Program in Neuroscience, Florida State University, Tallahassee, FL 32306, USA
| | - Aliza K De Nobrega
- Department of Biological Science, Program in Neuroscience, Florida State University, Tallahassee, FL 32306, USA
| | - Lisa C Lyons
- Department of Biological Science, Program in Neuroscience, Florida State University, Tallahassee, FL 32306, USA.
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36
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Yi JS, Díaz NM, D'Souza S, Buhr ED. The molecular clockwork of mammalian cells. Semin Cell Dev Biol 2021; 126:87-96. [PMID: 33810978 DOI: 10.1016/j.semcdb.2021.03.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 03/15/2021] [Accepted: 03/17/2021] [Indexed: 12/20/2022]
Abstract
Most organisms contain self-sustained circadian clocks. These clocks can be synchronized by environmental stimuli, but can also oscillate indefinitely in isolation. In mammals this is true at the molecular level for the majority of cell types that have been examined. A core set of "clock genes" form a transcriptional/translational feedback loop (TTFL) which repeats with a period of approximately 24 h. The exact mechanism of the TTFL differs slightly in various cell types, but all involve similar family members of the core cohort of clock genes. The clock has many outputs which are unique for different tissues. Cells in diverse tissues will convert the timing signals provided by the TTFL into uniquely orchestrated transcriptional oscillations of many clock-controlled genes and cellular processes.
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Affiliation(s)
- Jonathan S Yi
- University of Washington, Dept. of Ophthalmology, 750 Republican St., Seattle, WA 98109, USA
| | - Nicolás M Díaz
- University of Washington, Dept. of Ophthalmology, 750 Republican St., Seattle, WA 98109, USA
| | - Shane D'Souza
- Center for Chronobiology, Abrahamson Pediatric Eye Institute, Division of Pediatric Ophthalmology, Cincinnati Children's Hospital, Cincinnati, OH 45229, USA
| | - Ethan D Buhr
- University of Washington, Dept. of Ophthalmology, 750 Republican St., Seattle, WA 98109, USA.
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37
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Ruan W, Yuan X, Eltzschig HK. Circadian rhythm as a therapeutic target. Nat Rev Drug Discov 2021; 20:287-307. [PMID: 33589815 DOI: 10.1038/s41573-020-00109-w] [Citation(s) in RCA: 179] [Impact Index Per Article: 59.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/09/2020] [Indexed: 12/20/2022]
Abstract
The circadian clock evolved in diverse organisms to integrate external environmental changes and internal physiology. The clock endows the host with temporal precision and robust adaptation to the surrounding environment. When circadian rhythms are perturbed or misaligned, as a result of jet lag, shiftwork or other lifestyle factors, adverse health consequences arise, and the risks of diseases such as cancer, cardiovascular diseases or metabolic disorders increase. Although the negative impact of circadian rhythm disruption is now well established, it remains underappreciated how to take advantage of biological timing, or correct it, for health benefits. In this Review, we provide an updated account of the circadian system and highlight several key disease areas with altered circadian signalling. We discuss environmental and lifestyle modifications of circadian rhythm and clock-based therapeutic strategies, including chronotherapy, in which dosing time is deliberately optimized for maximum therapeutic index, and pharmacological agents that target core clock components and proximal regulators. Promising progress in research, disease models and clinical applications should encourage a concerted effort towards a new era of circadian medicine.
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Affiliation(s)
- Wei Ruan
- Department of Anesthesiology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA.,Department of Anesthesiology, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Xiaoyi Yuan
- Department of Anesthesiology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Holger K Eltzschig
- Department of Anesthesiology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA.
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38
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Lee SB, Park J, Kwak Y, Park YU, Nhung TTM, Suh BK, Woo Y, Suh Y, Cho E, Cho S, Park SK. Disrupted-in-schizophrenia 1 enhances the quality of circadian rhythm by stabilizing BMAL1. Transl Psychiatry 2021; 11:110. [PMID: 33542182 PMCID: PMC7862247 DOI: 10.1038/s41398-021-01212-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 12/15/2020] [Accepted: 01/07/2021] [Indexed: 11/27/2022] Open
Abstract
Disrupted-in-schizophrenia 1 (DISC1) is a scaffold protein that has been implicated in multiple mental disorders. DISC1 is known to regulate neuronal proliferation, signaling, and intracellular calcium homeostasis, as well as neurodevelopment. Although DISC1 was linked to sleep-associated behaviors, whether DISC1 functions in the circadian rhythm has not been determined yet. In this work, we revealed that Disc1 expression exhibits daily oscillating pattern and is regulated by binding of circadian locomotor output cycles kaput (CLOCK) and Brain and muscle Arnt-like protein-1 (BMAL1) heterodimer to E-box sequences in its promoter. Interestingly, Disc1 deficiency increases the ubiquitination of BMAL1 and de-stabilizes it, thereby reducing its protein levels. DISC1 inhibits the activity of GSK3β, which promotes BMAL1 ubiquitination, suggesting that DISC1 regulates BMAL1 stability by inhibiting its ubiquitination. Moreover, Disc1-deficient cells and mice show reduced expression of other circadian genes. Finally, Disc1-LI (Disc1 knockout) mice exhibit damped circadian physiology and behaviors. Collectively, these findings demonstrate that the oscillation of DISC1 expression is under the control of CLOCK and BMAL1, and that DISC1 contributes to the core circadian system by regulating BMAL1 stability.
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Affiliation(s)
- Su Been Lee
- grid.49100.3c0000 0001 0742 4007Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Jihyun Park
- grid.289247.20000 0001 2171 7818Department of Physiology, College of Medicine, Kyung Hee University, Seoul, Republic of Korea
| | - Yongdo Kwak
- grid.49100.3c0000 0001 0742 4007Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea ,grid.507563.2Present Address: SK biopharmaceuticals Ltd, Seongnam-Si, Republic of Korea
| | - Young-Un Park
- grid.49100.3c0000 0001 0742 4007Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea ,grid.49606.3d0000 0001 1364 9317Present Address: Department of Pathology, College of Medicine, Hanyang University, Seoul, Korea
| | - Truong Thi My Nhung
- grid.49100.3c0000 0001 0742 4007Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Bo Kyoung Suh
- grid.49100.3c0000 0001 0742 4007Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Youngsik Woo
- grid.49100.3c0000 0001 0742 4007Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Yeongjun Suh
- grid.49100.3c0000 0001 0742 4007Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Eunbyul Cho
- grid.49100.3c0000 0001 0742 4007Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Sehyung Cho
- Department of Physiology, College of Medicine, Kyung Hee University, Seoul, Republic of Korea.
| | - Sang Ki Park
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea.
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Littleton ES, Childress ML, Gosting ML, Jackson AN, Kojima S. Genome-wide correlation analysis to identify amplitude regulators of circadian transcriptome output. Sci Rep 2020; 10:21839. [PMID: 33318596 PMCID: PMC7736363 DOI: 10.1038/s41598-020-78851-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Accepted: 11/20/2020] [Indexed: 02/07/2023] Open
Abstract
Cell-autonomous circadian system, consisting of core clock genes, generates near 24-h rhythms and regulates the downstream rhythmic gene expression. While it has become clear that the percentage of rhythmic genes varies among mouse tissues, it remains unclear how this variation can be generated, particularly when the clock machinery is nearly identical in all tissues. In this study, we sought to characterize circadian transcriptome datasets that are publicly available and identify the critical component(s) involved in creating this variation. We found that the relative amplitude of 13 genes and the average level of 197 genes correlated with the percentage of cycling genes. Of those, the correlation of Rorc in both relative amplitude and the average level was one of the strongest. In addition, the level of Per2AS, a novel non-coding transcript that is expressed at the Period 2 locus, was also linearly correlated, although with a much lesser degree compared to Rorc. Overall, our study provides insight into how the variation in the percentage of clock-controlled genes can be generated in mouse tissues and suggests that Rorc and potentially Per2AS are involved in regulating the amplitude of circadian transcriptome output.
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Affiliation(s)
- Evan S Littleton
- Department of Biological Sciences, Fralin Life Sciences Institute, Virginia Tech, Blacksburg, VA, USA
| | - Madison L Childress
- Department of Biological Sciences, Fralin Life Sciences Institute, Virginia Tech, Blacksburg, VA, USA
| | - Michaela L Gosting
- Department of Biological Sciences, Fralin Life Sciences Institute, Virginia Tech, Blacksburg, VA, USA
| | - Ayana N Jackson
- Department of Biological Sciences, Fralin Life Sciences Institute, Virginia Tech, Blacksburg, VA, USA
| | - Shihoko Kojima
- Department of Biological Sciences, Fralin Life Sciences Institute, Virginia Tech, Blacksburg, VA, USA.
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40
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Kelliher CM, Lambreghts R, Xiang Q, Baker CL, Loros JJ, Dunlap JC. PRD-2 directly regulates casein kinase I and counteracts nonsense-mediated decay in the Neurospora circadian clock. eLife 2020; 9:64007. [PMID: 33295874 PMCID: PMC7746235 DOI: 10.7554/elife.64007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 12/08/2020] [Indexed: 01/22/2023] Open
Abstract
Circadian clocks in fungi and animals are driven by a functionally conserved transcription–translation feedback loop. In Neurospora crassa, negative feedback is executed by a complex of Frequency (FRQ), FRQ-interacting RNA helicase (FRH), and casein kinase I (CKI), which inhibits the activity of the clock’s positive arm, the White Collar Complex (WCC). Here, we show that the prd-2 (period-2) gene, whose mutation is characterized by recessive inheritance of a long 26 hr period phenotype, encodes an RNA-binding protein that stabilizes the ck-1a transcript, resulting in CKI protein levels sufficient for normal rhythmicity. Moreover, by examining the molecular basis for the short circadian period of upf-1prd-6 mutants, we uncovered a strong influence of the Nonsense-Mediated Decay pathway on CKI levels. The finding that circadian period defects in two classically derived Neurospora clock mutants each arise from disruption of ck-1a regulation is consistent with circadian period being exquisitely sensitive to levels of casein kinase I.
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Affiliation(s)
- Christina M Kelliher
- Department of Molecular & Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, United States
| | - Randy Lambreghts
- Department of Molecular & Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, United States
| | - Qijun Xiang
- Department of Molecular & Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, United States
| | - Christopher L Baker
- Department of Molecular & Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, United States.,The Jackson Laboratory, Bar Harbor, United States
| | - Jennifer J Loros
- Department of Biochemistry & Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, United States
| | - Jay C Dunlap
- Department of Molecular & Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, United States
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41
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Ma Q, Mo G, Tan Y. Micro RNAs and the biological clock: a target for diseases associated with a loss of circadian regulation. Afr Health Sci 2020; 20:1887-1894. [PMID: 34394254 PMCID: PMC8351835 DOI: 10.4314/ahs.v20i4.46] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Background Circadian clocks are self-sustaining oscillators that coordinate behavior and physiology over a 24 hour period, achieving time-dependent homeostasis with the external environment. The molecular clocks driving circadian rhythmic changes are based on intertwined transcriptional/translational feedback loops that combine with a range of environmental and metabolic stimuli to generate daily internal programing. Understanding how biological rhythms are generated throughout the body and the reasons for their dysregulation can provide avenues for temporally directed therapeutics. Summary In recent years, microRNAs have been shown to play important roles in the regulation of the circadian clock, particularly in Drosophila, but also in some small animal and human studies. This review will summarize our current understanding of the role of miRNAs during clock regulation, with a particular focus on the control of clock regulated gene expression.
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Affiliation(s)
- Qianwen Ma
- Gynecology department, Zhenjiang Hospital Affiliated to Nanjing University of Chinese Medicine (Zhenjiang Hospital of Traditional Chinese Medicine), Zhenjiang, China
- Reproductive medicine department, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China
| | - Genlin Mo
- Advanced manufacturing institution, Jiangsu University, Zhenjiang, China
| | - Yong Tan
- Reproductive medicine department, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China
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Wang Z, Li F, Wei M, Zhang S, Wang T. Circadian Clock Protein PERIOD2 Suppresses the PI3K/Akt Pathway and Promotes Cisplatin Sensitivity in Ovarian Cancer. Cancer Manag Res 2020; 12:11897-11908. [PMID: 33244267 PMCID: PMC7683831 DOI: 10.2147/cmar.s278903] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 10/17/2020] [Indexed: 02/06/2023] Open
Abstract
Background The mortality rate of ovarian cancer is the highest among gynecological tumors. The two factors leading to high mortality of ovarian cancer are late clinical stage and chemotherapy resistance. It is very important to reverse or intervene chemotherapy resistance. Abnormal circadian rhythm is related to the occurrence of tumor, and circadian clock protein PERIOD2 (PER2) acts as a tumor suppressor in cancer; however, little is known about its involvement in chemosensitivity. Methods This study aimed to investigate the role and underlying mechanisms of PER2 in ovarian cancer sensitivity to cisplatin. Overexpression and knockdown of PER2 were performed to explore its role in ovarian cancer cell sensitivity to cisplatin both in vitro and in vivo. The protein levels of PI3K, AKT, caspase 3, E-cadherin, and other drug resistance-related molecules were determined in parental SKOV3 and SKOV3/DDP cells as well as in xenograft tumor tissues. Results Compared with parental cells, SKOV3/DDP cells had dramatically decreased PER2 expression, possibly due to hypermethylation in the PER2 promoter. PER2 overexpression significantly inhibited proliferation while promoting cisplatin-induced apoptosis in SKOV3 and SKOV3/DDP cells. In agreement, PER2-overexpressing SKOV3/DPP cells yielded significantly reduced tumor mass in cisplatin-treated mice compared with control cells. Mechanistically, PER2 overexpression remarkably reduced the protein amounts of PI3K, AKT, and MDR1 while increasing those of caspase 3 and E-cadherin in tumor tissues. Knockdown of PER2 exhibited opposite effects. PER2 overexpression also reduced the serum levels of TNF-α and IL-6 in tumor-bearing mice before the initiation of cisplatin treatment. Conclusion This study suggests that loss of PER2 contributes to cisplatin resistance in SKOV3 cells, possibly by activating the PI3K/AKT pathway and EMT, inhibiting apoptosis, and promoting drug efflux and inflammatory responses. Overexpression of PER2 could reverse these alterations and sensitize both parental SKOV3 and SKOV3/DDP cells to cisplatin.
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Affiliation(s)
- Zhaoxia Wang
- Department of Gynecology, First Hospital of Shanxi Medical University, Taiyuan, Shanxi, People's Republic of China
| | - Fengyan Li
- Department of Gynecology, First Hospital of Shanxi Medical University, Taiyuan, Shanxi, People's Republic of China
| | - Meiyan Wei
- Department of Gynecology, First Hospital of Shanxi Medical University, Taiyuan, Shanxi, People's Republic of China
| | - Sanyuan Zhang
- Department of Gynecology, First Hospital of Shanxi Medical University, Taiyuan, Shanxi, People's Republic of China
| | - Tong Wang
- Department of Health Statistics, School of Public Health, Shanxi Medical University, Taiyuan, Shanxi, People's Republic of China
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microRNA-25 as a novel modulator of circadian Period2 gene oscillation. Exp Mol Med 2020; 52:1614-1626. [PMID: 32968200 PMCID: PMC8080691 DOI: 10.1038/s12276-020-00496-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 06/22/2020] [Accepted: 07/06/2020] [Indexed: 01/02/2023] Open
Abstract
Circadian clock controls an organism’s biological rhythm and regulates its physiological processes in response to external time cues. Most living organisms have their own time-keeping mechanism that is maintained by transcriptional–translational autoregulatory feedback loops involving several core clock genes, such as Period. Recent studies have found the relevance between the modulation of circadian oscillation and posttranscriptional modifications by microRNAs (miRNAs). However, there are limited studies on candidate miRNAs that regulate circadian oscillation. Here, we characterize the functions of novel miRNA-25 regulating circadian Period2 (Per2) expression. Using several in silico algorithms, we identified novel miR-25-3p that, together with miR-24-3p, targets the Per2 gene. Luciferase reporter assays validated that miR-25-3p and miR-24-3p repressed Per2 expression and confirmed their predicted binding sites in the 3′-untranslated region (UTR) of Per2 mRNA. Real-time bioluminescence analyses using Per2::Luc mouse embryonic fibroblasts confirmed that PER2 protein oscillation patterns were responsive to miR-25-3p and miR-24-3. The overexpression of miR-25-3p or miR-24-3p resulted in the dampening and period shortening of the PER2::LUC oscillation, while inhibition of either miRNA increased the relative amplitude of the PER2::LUC oscillation. Notably, endogenous miR-25-3p expression in the suprachiasmatic nucleus (SCN) showed no circadian rhythmicity, but the expression levels differed in various brain regions and peripheral tissues. These results suggest that the posttranscriptional regulation of miR-25-3p and miR-24-3p may differ according to Per2 gene expression in different tissue regions. In summary, we found that novel miR-25-3p was involved in fine-tuning circadian rhythmicity by regulating Per2 oscillation at the posttranscriptional level and that it functioned synergistically with miR-24-3p to affect Per2 oscillation. A newly identified microRNA plays a key role in fine-tuning the genetic interactions governing the circadian rhythms in mammals, according to researchers in South Korea. Numerous studies have suggested that the Period genes, which negatively regulate the CLOCK and BMAL1 genes to produce a 24-hour feedback loop, may be further modified by microRNAs after they are transcribed. Kyungjin Kim at Daegu Gyeongbuk Institute of Science and Technology, South Korea, and co-workers confirmed that a novel microRNA, miR-25-3p, reduces the expression of a Period gene, Per2, in mice. When miR-25-3p is over-expressed, it dampens and shortens the oscillations of Per2 levels. Interestingly, the researchers showed that natural miR-25-3p expression levels varied across different parts of the brain, supporting the theory that different tissues of the body maintain their own unique circadian cycles.
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Crosby P, Partch CL. New insights into non-transcriptional regulation of mammalian core clock proteins. J Cell Sci 2020; 133:133/18/jcs241174. [PMID: 32934011 DOI: 10.1242/jcs.241174] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Mammalian circadian rhythms drive ∼24 h periodicity in a wide range of cellular processes, temporally coordinating physiology and behaviour within an organism, and synchronising this with the external day-night cycle. The canonical model for this timekeeping consists of a delayed negative-feedback loop, containing transcriptional activator complex CLOCK-BMAL1 (BMAL1 is also known as ARNTL) and repressors period 1, 2 and 3 (PER1, PER2 and PER3) and cryptochrome 1 and 2 (CRY1 and CRY2), along with a number of accessory factors. Although the broad strokes of this system are defined, the exact molecular mechanisms by which these proteins generate a self-sustained rhythm with such periodicity and fidelity remains a topic of much research. Recent studies have identified prominent roles for a number of crucial post-transcriptional, translational and, particularly, post-translational events within the mammalian circadian oscillator, providing an increasingly complex understanding of the activities and interactions of the core clock proteins. In this Review, we highlight such contemporary work on non-transcriptional events and set it within our current understanding of cellular circadian timekeeping.
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Affiliation(s)
- Priya Crosby
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA
| | - Carrie L Partch
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA
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Kinoshita C, Okamoto Y, Aoyama K, Nakaki T. MicroRNA: A Key Player for the Interplay of Circadian Rhythm Abnormalities, Sleep Disorders and Neurodegenerative Diseases. Clocks Sleep 2020; 2:282-307. [PMID: 33089205 PMCID: PMC7573810 DOI: 10.3390/clockssleep2030022] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 07/21/2020] [Indexed: 02/06/2023] Open
Abstract
Circadian rhythms are endogenous 24-h oscillators that regulate the sleep/wake cycles and the timing of biological systems to optimize physiology and behavior for the environmental day/night cycles. The systems are basically generated by transcription-translation feedback loops combined with post-transcriptional and post-translational modification. Recently, evidence is emerging that additional non-coding RNA-based mechanisms are also required to maintain proper clock function. MicroRNA is an especially important factor that plays critical roles in regulating circadian rhythm as well as many other physiological functions. Circadian misalignment not only disturbs the sleep/wake cycle and rhythmic physiological activity but also contributes to the development of various diseases, such as sleep disorders and neurodegenerative diseases. The patient with neurodegenerative diseases often experiences profound disruptions in their circadian rhythms and/or sleep/wake cycles. In addition, a growing body of recent evidence implicates sleep disorders as an early symptom of neurodegenerative diseases, and also suggests that abnormalities in the circadian system lead to the onset and expression of neurodegenerative diseases. The genetic mutations which cause the pathogenesis of familial neurodegenerative diseases have been well studied; however, with the exception of Huntington's disease, the majority of neurodegenerative diseases are sporadic. Interestingly, the dysfunction of microRNA is increasingly recognized as a cause of sporadic neurodegenerative diseases through the deregulated genes related to the pathogenesis of neurodegenerative disease, some of which are the causative genes of familial neurodegenerative diseases. Here we review the interplay of circadian rhythm disruption, sleep disorders and neurodegenerative disease, and its relation to microRNA, a key regulator of cellular processes.
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Affiliation(s)
- Chisato Kinoshita
- Department of Pharmacology, Teikyo University School of Medicine, 2-11-1 Kaga, Itabashi, Tokyo 173-8605, Japan; (C.K.); (Y.O.); (K.A.)
| | - Yayoi Okamoto
- Department of Pharmacology, Teikyo University School of Medicine, 2-11-1 Kaga, Itabashi, Tokyo 173-8605, Japan; (C.K.); (Y.O.); (K.A.)
- Teikyo University Support Center for Women Physicians and Researchers, 2-11-1 Kaga, Itabashi, Tokyo 173-8605, Japan
| | - Koji Aoyama
- Department of Pharmacology, Teikyo University School of Medicine, 2-11-1 Kaga, Itabashi, Tokyo 173-8605, Japan; (C.K.); (Y.O.); (K.A.)
| | - Toshio Nakaki
- Department of Pharmacology, Teikyo University School of Medicine, 2-11-1 Kaga, Itabashi, Tokyo 173-8605, Japan; (C.K.); (Y.O.); (K.A.)
- Faculty of Pharma-Science, Teikyo University, 2-11-1 Kaga, Itabashi, Tokyo 173-8605, Japan
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Kim HK, Lee SY, Koike N, Kim E, Wirianto M, Burish MJ, Yagita K, Lee HK, Chen Z, Chung JM, Abdi S, Yoo SH. Circadian regulation of chemotherapy-induced peripheral neuropathic pain and the underlying transcriptomic landscape. Sci Rep 2020; 10:13844. [PMID: 32796949 PMCID: PMC7427990 DOI: 10.1038/s41598-020-70757-w] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2020] [Accepted: 07/27/2020] [Indexed: 12/19/2022] Open
Abstract
Growing evidence demonstrates circadian rhythms of pain hypersensitivity in various chronic disorders. In chemotherapy-induced peripheral neuropathy (CIPN), agents such as paclitaxel are known to elicit chronic neuropathic pain in cancer patients and seriously compromise their quality of life. Here, we report that the mechanical threshold for allodynia in paclitaxel-treated rats exhibited a robust circadian oscillation, reaching the nadir during the daytime (inactive phase). Using Per2::LucSV circadian reporter mice expressing a PER2::LUC fusion protein, we isolated dorsal root ganglia (DRG), the primary sensory cell body for peripheral nerve injury generated hypersensitivity, and monitored ex vivo reporter bioluminescence. We observed strong circadian reporter rhythms in DRG neurons which are highly entrainable by external cues. Paclitaxel treatment significantly lengthened DRG circadian periods, with little effects on the amplitude of oscillation. We further observed the core protein BMAL1 and PER2 in DRG neurons and satellite cells. Using DRG and dorsal horn (DH; another key structure for CIPN pain response) tissues from vehicle and paclitaxel treated rats, we performed RNA-sequencing and identified diurnal expression of core clock genes as well as clock-controlled genes in both sites. Interestingly, 20.1% and 30.4% of diurnal differentially expressed genes (DEGs) overlapped with paclitaxel-induced DEGs in the DRG and the DH respectively. In contrast, paclitaxel-induced DEGs displayed only a modest overlap between daytime and nighttime (Zeitgeber Time 8 and 20). Furthermore, paclitaxel treatment induced de novo diurnal DEGs, suggesting reciprocal interaction of circadian rhythms and chemotherapy. Our study therefore demonstrates a circadian oscillation of CIPN and its underlying transcriptomic landscape.
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Affiliation(s)
- Hee Kee Kim
- Division of Anesthesiology, Critical Care and Pain Medicine, Department of Pain Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Sun-Yeul Lee
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center At Houston, 6431 Fannin St., Houston, TX, 77030, USA
- Department of Anesthesiology and Pain Medicine, Chungnam National University Hospital, Daejeon, South Korea
| | - Nobuya Koike
- Department of Physiology and Systems Bioscience, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Eunju Kim
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center At Houston, 6431 Fannin St., Houston, TX, 77030, USA
| | - Marvin Wirianto
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center At Houston, 6431 Fannin St., Houston, TX, 77030, USA
| | - Mark J Burish
- Department of Neurosurgery, The University of Texas Health Science Center at Houston, 6400 Fannin St., Houston, TX, 77030, USA
| | - Kazuhiro Yagita
- Department of Physiology and Systems Bioscience, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Hyun Kyoung Lee
- Department of Pediatrics, Baylor College of Medicine, Neurological Research Institute, Texas Children's Hospital, Houston, TX, 77030, USA
| | - Zheng Chen
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center At Houston, 6431 Fannin St., Houston, TX, 77030, USA
| | - Jin Mo Chung
- Department of Neuroscience, Cell Biology and Anatomy, University of Texas Medical Branch, Galveston, TX, USA
| | - Salahadin Abdi
- Division of Anesthesiology, Critical Care and Pain Medicine, Department of Pain Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Seung-Hee Yoo
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center At Houston, 6431 Fannin St., Houston, TX, 77030, USA.
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Li Y, Shan Y, Kilaru GK, Berto S, Wang GZ, Cox KH, Yoo SH, Yang S, Konopka G, Takahashi JS. Epigenetic inheritance of circadian period in clonal cells. eLife 2020; 9:54186. [PMID: 32459177 PMCID: PMC7289596 DOI: 10.7554/elife.54186] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 05/26/2020] [Indexed: 12/22/2022] Open
Abstract
Circadian oscillations are generated via transcriptional-translational negative feedback loops. However, individual cells from fibroblast cell lines have heterogeneous rhythms, oscillating independently and with different period lengths. Here we showed that heterogeneity in circadian period is heritable and used a multi-omics approach to investigate underlying mechanisms. By examining large-scale phenotype-associated gene expression profiles in hundreds of mouse clonal cell lines, we identified and validated multiple novel candidate genes involved in circadian period determination in the absence of significant genomic variants. We also discovered differentially co-expressed gene networks that were functionally associated with period length. We further demonstrated that global differential DNA methylation bidirectionally regulated these same gene networks. Interestingly, we found that depletion of DNMT1 and DNMT3A had opposite effects on circadian period, suggesting non-redundant roles in circadian gene regulation. Together, our findings identify novel gene candidates involved in periodicity, and reveal DNA methylation as an important regulator of circadian periodicity.
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Affiliation(s)
- Yan Li
- Department of Neuroscience, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, United States
| | - Yongli Shan
- Department of Neuroscience, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, United States
| | - Gokhul Krishna Kilaru
- Department of Neuroscience, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, United States
| | - Stefano Berto
- Department of Neuroscience, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, United States
| | - Guang-Zhong Wang
- Department of Neuroscience, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, United States
| | - Kimberly H Cox
- Department of Neuroscience, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, United States
| | - Seung-Hee Yoo
- Department of Neuroscience, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, United States
| | - Shuzhang Yang
- Department of Neuroscience, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, United States
| | - Genevieve Konopka
- Department of Neuroscience, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, United States
| | - Joseph S Takahashi
- Department of Neuroscience, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, United States.,Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, United States
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Abstract
Our findings have revealed a previously unrecognized link between circadian oscillations and intercellular variation and provide experimental evidence that stochastic transcriptional noise contributes significantly to cell-autonomous circadian periodicity. Interestingly, in separate studies, aging and cancer have been associated with increased transcriptional noise and less robust circadian rhythms. Here, we establish a direct association between transcriptional noise and circadian period. These findings may provide additional directions for researchers in the aging and cancer fields. Furthermore, circadian period may also be used as an indicator of variance in heterogeneity research and drug screening for noise control. Nongenetic cellular heterogeneity is associated with aging and disease. However, the origins of cell-to-cell variability are complex and the individual contributions of different factors to total phenotypic variance are still unclear. Here, we took advantage of clear phenotypic heterogeneity of circadian oscillations in clonal cell populations to investigate the underlying mechanisms of cell-to-cell variability. Using a fully automated tracking and analysis pipeline, we examined circadian period length in thousands of single cells and hundreds of clonal cell lines and found that longer circadian period is associated with increased intercellular heterogeneity. Based on our experimental results, we then estimated the contributions of heritable and nonheritable factors to this variation in circadian period length using a variance partitioning model. We found that nonheritable noise predominantly drives intercellular circadian period variation in clonal cell lines, thereby revealing a previously unrecognized link between circadian oscillations and intercellular heterogeneity. Moreover, administration of a noise-enhancing drug reversibly increased both period length and variance. These findings suggest that circadian period may be used as an indicator of cellular noise and drug screening for noise control.
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Ku K, Park I, Kim D, Kim J, Jang S, Choi M, Choe HK, Kim K. Gut Microbial Metabolites Induce Changes in Circadian Oscillation of Clock Gene Expression in the Mouse Embryonic Fibroblasts. Mol Cells 2020; 43:276-285. [PMID: 32155689 PMCID: PMC7103884 DOI: 10.14348/molcells.2020.2309] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 01/31/2020] [Accepted: 02/10/2020] [Indexed: 12/17/2022] Open
Abstract
Circadian rhythm is an endogenous oscillation of about 24-h period in many physiological processes and behaviors. This daily oscillation is maintained by the molecular clock machinery with transcriptional-translational feedback loops mediated by clock genes including Period2 (Per2) and Bmal1. Recently, it was revealed that gut microbiome exerts a significant impact on the circadian physiology and behavior of its host; however, the mechanism through which it regulates the molecular clock has remained elusive. 3-(4-hydroxyphenyl)propionic acid (4-OH-PPA) and 3-phenylpropionic acid (PPA) are major metabolites exclusively produced by Clostridium sporogenes and may function as unique chemical messengers communicating with its host. In the present study, we examined if two C. sporogenes-derived metabolites can modulate the oscillation of mammalian molecular clock. Interestingly, 4-OH-PPA and PPA increased the amplitude of both PER2 and Bmal1 oscillation in a dosedependent manner following their administration immediately after the nadir or the peak of their rhythm. The phase of PER2 oscillation responded differently depending on the mode of administration of the metabolites. In addition, using an organotypic slice culture ex vivo, treatment with 4-OH-PPA increased the amplitude and lengthened the period of PER2 oscillation in the suprachiasmatic nucleus and other tissues. In summary, two C. sporogenes-derived metabolites are involved in the regulation of circadian oscillation of Per2 and Bmal1 clock genes in the host's peripheral and central clock machineries.
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Affiliation(s)
- Kyojin Ku
- Department of Brain and Cognitive Sciences, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu 42988, Korea
| | - Inah Park
- Department of Brain and Cognitive Sciences, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu 42988, Korea
| | - Doyeon Kim
- Department of Brain and Cognitive Sciences, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu 42988, Korea
| | - Jeongah Kim
- Department of Brain and Cognitive Sciences, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu 42988, Korea
| | - Sangwon Jang
- Department of Brain and Cognitive Sciences, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu 42988, Korea
| | - Mijung Choi
- Department of Brain and Cognitive Sciences, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu 42988, Korea
| | - Han Kyoung Choe
- Department of Brain and Cognitive Sciences, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu 42988, Korea
| | - Kyungjin Kim
- Department of Brain and Cognitive Sciences, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu 42988, Korea
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Pilorz V, Astiz M, Heinen KO, Rawashdeh O, Oster H. The Concept of Coupling in the Mammalian Circadian Clock Network. J Mol Biol 2020; 432:3618-3638. [PMID: 31926953 DOI: 10.1016/j.jmb.2019.12.037] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 12/22/2019] [Accepted: 12/23/2019] [Indexed: 12/13/2022]
Abstract
The circadian clock network regulates daily rhythms in mammalian physiology and behavior to optimally adapt the organism to the 24-h day/night cycle. A central pacemaker, the hypothalamic suprachiasmatic nucleus (SCN), coordinates subordinate cellular oscillators in the brain, as well as in peripheral organs to align with each other and external time. Stability and coordination of this vast network of cellular oscillators is achieved through different levels of coupling. Although coupling at the molecular level and across the SCN is well established and believed to define its function as pacemaker structure, the notion of coupling in other tissues and across the whole system is less well understood. In this review, we describe the different levels of coupling in the mammalian circadian clock system - from molecules to the whole organism. We highlight recent advances in gaining knowledge of the complex organization and function of circadian network regulation and its significance for the generation of stable but plastic intrinsic 24-h rhythms.
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Affiliation(s)
- Violetta Pilorz
- University of Lübeck, Institute of Neurobiology, Center of Brain, Behavior and Metabolism, Marie-Curie-Strasse, 23562, Luebeck, Germany
| | - Mariana Astiz
- University of Lübeck, Institute of Neurobiology, Center of Brain, Behavior and Metabolism, Marie-Curie-Strasse, 23562, Luebeck, Germany
| | - Keno Ole Heinen
- University of Lübeck, Institute of Neurobiology, Center of Brain, Behavior and Metabolism, Marie-Curie-Strasse, 23562, Luebeck, Germany
| | - Oliver Rawashdeh
- The University of Queensland, School of Biomedical Sciences, Faculty of Medicine, St Lucia Qld, 4071, Australia
| | - Henrik Oster
- University of Lübeck, Institute of Neurobiology, Center of Brain, Behavior and Metabolism, Marie-Curie-Strasse, 23562, Luebeck, Germany.
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