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Fishman B, Tauber E. Epigenetics and seasonal timing in animals: a concise review. J Comp Physiol A Neuroethol Sens Neural Behav Physiol 2024; 210:565-574. [PMID: 37695537 PMCID: PMC11226475 DOI: 10.1007/s00359-023-01673-3] [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: 05/07/2023] [Revised: 08/27/2023] [Accepted: 09/01/2023] [Indexed: 09/12/2023]
Abstract
Seasonal adaptation in animals is a complex process that involves genetic, epigenetic, and environmental factors. The present review explores recent studies on epigenetic mechanisms implicated in seasonal adaptation in animals. The review is divided into three main sections, each focusing on a different epigenetic mechanism: DNA methylation, histone modifications, and non-coding RNA. Additionally, the review delves into the current understanding of how these epigenetic factors contribute to the regulation of circadian and seasonal cycles. Understanding these molecular mechanisms provides the first step in deciphering the complex interplay between genetics, epigenetics, and the environment in driving seasonal adaptation in animals. By exploring these mechanisms, a better understanding of how animals adapt to changing environmental conditions can be achieved.
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Affiliation(s)
- Bettina Fishman
- Department of Evolutionary and Environmental Biology, Institute of Evolution, University of Haifa, Haifa, Israel
| | - Eran Tauber
- Department of Evolutionary and Environmental Biology, Institute of Evolution, University of Haifa, Haifa, Israel.
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2
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Curtis L, Piggins HD. Diverse genetic alteration dysregulates neuropeptide and intracellular signalling in the suprachiasmatic nuclei. Eur J Neurosci 2024. [PMID: 38924215 DOI: 10.1111/ejn.16443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 05/12/2024] [Accepted: 05/31/2024] [Indexed: 06/28/2024]
Abstract
In mammals, intrinsic 24 h or circadian rhythms are primarily generated by the suprachiasmatic nuclei (SCN). Rhythmic daily changes in the transcriptome and proteome of SCN cells are controlled by interlocking transcription-translation feedback loops (TTFLs) of core clock genes and their proteins. SCN cells function as autonomous circadian oscillators, which synchronize through intercellular neuropeptide signalling. Physiological and behavioural rhythms can be severely disrupted by genetic modification of a diverse range of genes and proteins in the SCN. With the advent of next generation sequencing, there is unprecedented information on the molecular profile of the SCN and how it is affected by genetically targeted alteration. However, whether the expression of some genes is more readily affected by genetic alteration of the SCN is unclear. Here, using publicly available datasets from recent RNA-seq assessments of the SCN from genetically altered and control mice, we evaluated whether there are commonalities in transcriptome dysregulation. This was completed for four different phases across the 24 h cycle and was augmented by Gene Ontology Molecular Function (GO:MF) and promoter analysis. Common differentially expressed genes (DEGs) and/or enriched GO:MF terms included signalling molecules, their receptors, and core clock components. Finally, examination of the JASPAR database indicated that E-box and CRE elements in the promoter regions of several commonly dysregulated genes. From this analysis, we identify differential expression of genes coding for molecules involved in SCN intra- and intercellular signalling as a potential cause of abnormal circadian rhythms.
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Affiliation(s)
- Lucy Curtis
- School of Biological Sciences, University of Bristol, Bristol, UK
- School of Physiology, Pharmacology, and Neuroscience, University of Bristol, Bristol, UK
| | - Hugh D Piggins
- School of Physiology, Pharmacology, and Neuroscience, University of Bristol, Bristol, UK
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3
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Pierre-Ferrer S, Collins B, Lukacsovich D, Wen S, Cai Y, Winterer J, Yan J, Pedersen L, Földy C, Brown SA. A phosphate transporter in VIPergic neurons of the suprachiasmatic nucleus gates locomotor activity during the light/dark transition in mice. Cell Rep 2024; 43:114220. [PMID: 38735047 DOI: 10.1016/j.celrep.2024.114220] [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: 07/22/2023] [Revised: 02/23/2024] [Accepted: 04/25/2024] [Indexed: 05/14/2024] Open
Abstract
The suprachiasmatic nucleus (SCN) encodes time of day through changes in daily firing; however, the molecular mechanisms by which the SCN times behavior are not fully understood. To identify factors that could encode day/night differences in activity, we combine patch-clamp recordings and single-cell sequencing of individual SCN neurons in mice. We identify PiT2, a phosphate transporter, as being upregulated in a population of Vip+Nms+ SCN neurons at night. Although nocturnal and typically showing a peak of activity at lights off, mice lacking PiT2 (PiT2-/-) do not reach the activity level seen in wild-type mice during the light/dark transition. PiT2 loss leads to increased SCN neuronal firing and broad changes in SCN protein phosphorylation. PiT2-/- mice display a deficit in seasonal entrainment when moving from a simulated short summer to longer winter nights. This suggests that PiT2 is responsible for timing activity and is a driver of SCN plasticity allowing seasonal entrainment.
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Affiliation(s)
- Sara Pierre-Ferrer
- Chronobiology and Sleep Research Group, Institute of Pharmacology and Toxicology, Faculties of Medicine and Science, University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland.
| | - Ben Collins
- Chronobiology and Sleep Research Group, Institute of Pharmacology and Toxicology, Faculties of Medicine and Science, University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland; Department of Biology, Sacred Heart University, 5151 Park Ave., Fairfield, CT 06825, USA
| | - David Lukacsovich
- Laboratory of Neural Connectivity, Brain Research Institute, Faculties of Medicine and Science, University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Shao'Ang Wen
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yuchen Cai
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Jochen Winterer
- Laboratory of Neural Connectivity, Brain Research Institute, Faculties of Medicine and Science, University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Jun Yan
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Lene Pedersen
- Department of Molecular Biology and Genetics, Aarhus University, Universitetsbyen 81, 8000 Aarhus, Denmark
| | - Csaba Földy
- Laboratory of Neural Connectivity, Brain Research Institute, Faculties of Medicine and Science, University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland.
| | - Steven A Brown
- Chronobiology and Sleep Research Group, Institute of Pharmacology and Toxicology, Faculties of Medicine and Science, University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
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4
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Yu Q, Zuo X, Bai H, Zhang S, Luan J, Zhao Q, Zhao X, Feng X. Alleviative effects of the parthenolide derivative ACT001 on insulin resistance induced by sodium propionate combined with a high-fat diet and its potential mechanisms. Eur J Pharmacol 2024; 971:176529. [PMID: 38554931 DOI: 10.1016/j.ejphar.2024.176529] [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: 10/29/2023] [Revised: 03/21/2024] [Accepted: 03/22/2024] [Indexed: 04/02/2024]
Abstract
The increasing side effects of traditional medications used to treat type II diabetes have made research into the development of safer and more effective natural medications necessary. ACT001, a derivative of parthenolide, has been shown to have good anti-inflammatory and antitumor effects; however, its role in diabetes is unclear. The short-chain fatty acid propionate is a common food preservative that has been found to cause disturbances in glucose metabolism in mice and humans. This study aimed to investigate whether sodium propionate could aggravate insulin resistance in obese mice and cause diabetes and to study the alleviative effects and potential mechanisms of action of ACT001 on insulin resistance in diabetic mice. Type II diabetic mice were adminietered sodium propionate combined with a high-fat diet (HFD + propionate) by gavage daily for four weeks. Biochemical analysis showed that ACT001 significantly affected blood glucose concentration in diabetic mice, mainly by downregulating the expression of phosphoenolpyruvate carboxykinase 2 and glucose-6-phosphatase. Meanwhile, the level of fatty acid-binding protein 4 in the liver was significantly decreased. ACT001 has a protective effect on the liver and adipose tissue of mice. In addition, the results of the running wheel experiment indicated that ACT001 alleviated the circadian rhythm disorder caused by insulin resistance to a certain extent. This study revealed the potential mechanism by which ACT001 alleviates insulin resistance and provides ideas for developing natural antidiabetic drugs.
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Affiliation(s)
- Qian Yu
- College of Life Science, State Key Laboratory of Medicinal Chemical Biology, The Key Laboratory of Bioactive Materials, Ministry of Education, Nankai University, Tianjin, 300071, China
| | - Xiang Zuo
- College of Life Science, State Key Laboratory of Medicinal Chemical Biology, The Key Laboratory of Bioactive Materials, Ministry of Education, Nankai University, Tianjin, 300071, China
| | - Huijuan Bai
- College of Life Science, State Key Laboratory of Medicinal Chemical Biology, The Key Laboratory of Bioactive Materials, Ministry of Education, Nankai University, Tianjin, 300071, China
| | - Shuhui Zhang
- College of Life Science, State Key Laboratory of Medicinal Chemical Biology, The Key Laboratory of Bioactive Materials, Ministry of Education, Nankai University, Tianjin, 300071, China
| | - Jialu Luan
- College of Life Science, State Key Laboratory of Medicinal Chemical Biology, The Key Laboratory of Bioactive Materials, Ministry of Education, Nankai University, Tianjin, 300071, China
| | - Qili Zhao
- Institute of Robotics & Automatic Information System, College of Artificial Intelligence, Nankai University, Tianjin, 300071, China
| | - Xin Zhao
- Institute of Robotics & Automatic Information System, College of Artificial Intelligence, Nankai University, Tianjin, 300071, China
| | - Xizeng Feng
- College of Life Science, State Key Laboratory of Medicinal Chemical Biology, The Key Laboratory of Bioactive Materials, Ministry of Education, Nankai University, Tianjin, 300071, China.
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5
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de Oliveira Melo NC, Cuevas-Sierra A, Souto VF, Martínez JA. Biological Rhythms, Chrono-Nutrition, and Gut Microbiota: Epigenomics Insights for Precision Nutrition and Metabolic Health. Biomolecules 2024; 14:559. [PMID: 38785965 PMCID: PMC11117887 DOI: 10.3390/biom14050559] [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: 04/17/2024] [Revised: 05/02/2024] [Accepted: 05/03/2024] [Indexed: 05/25/2024] Open
Abstract
Circadian rhythms integrate a finely tuned network of biological processes recurring every 24 h, intricately coordinating the machinery of all cells. This self-regulating system plays a pivotal role in synchronizing physiological and behavioral responses, ensuring an adaptive metabolism within the environmental milieu, including dietary and physical activity habits. The systemic integration of circadian homeostasis involves a balance of biological rhythms, each synchronically linked to the central circadian clock. Central to this orchestration is the temporal dimension of nutrient and food intake, an aspect closely interwoven with the neuroendocrine circuit, gut physiology, and resident microbiota. Indeed, the timing of meals exerts a profound influence on cell cycle regulation through genomic and epigenetic processes, particularly those involving gene expression, DNA methylation and repair, and non-coding RNA activity. These (epi)genomic interactions involve a dynamic interface between circadian rhythms, nutrition, and the gut microbiota, shaping the metabolic and immune landscape of the host. This research endeavors to illustrate the intricate (epi)genetic interplay that modulates the synchronization of circadian rhythms, nutritional signaling, and the gut microbiota, unravelling the repercussions on metabolic health while suggesting the potential benefits of feed circadian realignment as a non-invasive therapeutic strategy for systemic metabolic modulation via gut microbiota. This exploration delves into the interconnections that underscore the significance of temporal eating patterns, offering insights regarding circadian rhythms, gut microbiota, and chrono-nutrition interactions with (epi)genomic phenomena, thereby influencing diverse aspects of metabolic, well-being, and quality of life outcomes.
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Affiliation(s)
| | - Amanda Cuevas-Sierra
- Precision Nutrition Program, Research Institute on Food and Health Sciences IMDEA Food, CSIC-UAM, 28049 Madrid, Spain;
| | - Vitória Felício Souto
- Department of Nutrition at the Federal University of Pernambuco, Recife 50670-901, PE, Brazil; (N.C.d.O.M.); (V.F.S.)
| | - J. Alfredo Martínez
- Precision Nutrition Program, Research Institute on Food and Health Sciences IMDEA Food, CSIC-UAM, 28049 Madrid, Spain;
- Centro de Investigación Biomédica en Red Fisiopatología de la Obesidad y la Nutrición (CIBEROBN), Instituto de Salud Carlos III, 28029 Madrid, Spain
- Centre of Medicine and Endocrinology, University of Valladolid, 47002 Valladolid, Spain
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6
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Chiu JC. Editorial: Rising stars in chronobiology 2022. Front Physiol 2024; 15:1412956. [PMID: 38725565 PMCID: PMC11079284 DOI: 10.3389/fphys.2024.1412956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2024] [Accepted: 04/11/2024] [Indexed: 05/12/2024] Open
Affiliation(s)
- Joanna C. Chiu
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California, Davis, CA, United States
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7
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Fu Y, Lai D, Xu Y, Liu J, Wang Y, Jiang D, Pan J, Ouyang H, Tian Y, Huang Y, Shen X. The DNA methylation status of the vitamin A signaling associated with testicular degeneration induced by long-day photoperiods in Magang geese. Poult Sci 2024; 103:103769. [PMID: 38917605 DOI: 10.1016/j.psj.2024.103769] [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: 02/15/2024] [Revised: 04/10/2024] [Accepted: 04/10/2024] [Indexed: 06/27/2024] Open
Abstract
Magang geese are typical short-day breeders whose reproductive behaviors are significantly influenced by photoperiod. Exposure to a long-day photoperiod results in testicular regression and spermatogenesis arrest in Magang geese. To investigate the epigenetic influence of DNA methylation on the seasonal testicular regression in Magang geese, we conducted whole-genome bisulfite sequencing and transcriptome sequencing of testes across 3 reproductive phases during a long-day photoperiod. A total of 250,326 differentially methylated regions (DMR) were identified among the 3 comparison groups, with a significant number showing hypermethylation, especially in intronic regions of the genome. Integrating bisulfite sequencing with transcriptome sequencing data revealed that DMR-associated genes tend to be differentially expressed in the testes, highlighting a potential regulatory role for DNA methylation in gene expression. Furthermore, there was a significant negative correlation between changes in the methylation of CG DMRs and changes in the expression of their associated genes in the testes. A total of 3,359 DMR-associated differentially expressed genes (DEG) were identified; functional enrichment analyses revealed that motor proteins, MAPK signaling pathway, ECM-receptor interaction, phagosome, TGF-beta signaling pathway, and calcium signaling might contribute to the testicular regression process. GSEA revealed that the significantly enriched activated hallmark gene set was associated with apoptosis and estrogen response during testicular regression, while the repressed hallmark gene set was involved in spermatogenesis. Our study also revealed that methylation changes significantly impacted the expression level of vitamin A metabolism-related genes during testicular degeneration, with hypermethylation of STRA6 and increased calmodulin levels indicating vitamin A efflux during the testicular regression. These findings were corroborated by pyrosequencing and real-time qPCR, which revealed that the vitamin A metabolic pathway plays a pivotal role in testicular degeneration under long-day conditions. Additionally, metabolomics analysis revealed an insufficiency of vitamin A and an abnormally high level of oxysterols accumulated in the testes during testicular regression. In conclusion, our study demonstrated that testicular degeneration in Magang geese induced by a long-day photoperiod is linked to vitamin A homeostasis disruption, which manifests as the hypermethylation status of STRA6, vitamin A efflux, and a high level of oxysterol accumulation. These findings offer new insights into the effects of DNA methylation on the seasonal testicular regression that occurs during long-day photoperiods in Magang geese.
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Affiliation(s)
- Yuting Fu
- College of Animal Science and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
| | - Diyu Lai
- College of Animal Science and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
| | - Yanglong Xu
- College of Animal Science and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
| | - Jiaxin Liu
- College of Animal Science and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
| | - Yushuai Wang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, Guangdong, China
| | - Danli Jiang
- College of Animal Science and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
| | - Jianqiu Pan
- College of Animal Science and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
| | - Hongjia Ouyang
- College of Animal Science and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
| | - Yunbo Tian
- College of Animal Science and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
| | - Yunmao Huang
- College of Animal Science and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
| | - Xu Shen
- College of Animal Science and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China.
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8
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Kundu S, Ray A, Das Gupta S, Biswas A, Roy S, Kumar Tiwari N, Kumar VS, Das BK. Environmental bisphenol A disrupts methylation of steroidogenic genes in the ovary of Paradise threadfin Polynemus paradiseus via abnormal DNA methylation: Implications for human exposure and health risk assessment. CHEMOSPHERE 2024; 351:141236. [PMID: 38237780 DOI: 10.1016/j.chemosphere.2024.141236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 01/10/2024] [Accepted: 01/15/2024] [Indexed: 01/26/2024]
Abstract
Bisphenol A, endocrine-disrupting chemicals (EDCs) impacting disease development via epigenetic modifications, is crucial in transcriptional regulation. However, ecotoxicology's limited exploration of epigenetics prompted our study's objective: examining the extended exposure of riverine Bisphenol A (BPA), a potent EDC, on DNA methylation during female paradise threadfin (Polynemus paradiseus) reproductive maturation. Assessing BPA contamination in riverine water, we collected fish samples from two locations with distinct contamination levels. In the highly contaminated region (Hc), we observed elevated DNA methylation in aromatase (7.5-fold), 20β-HSD (3-fold), and FSHR (2-fold) genes. Hormone receptor investigation highlighted an escalating connection between transcriptional hyper-methylation and contamination levels. Additionally, our study revealed a positive correlation between oocyte growth and global DNA methylation, suggesting BPA's potential to modify DNA methylation in female paradise threadfins. This effect likely occurs through changes in hormone receptor expression, persisting throughout oocyte maturation. Notably, our research, the first of its kind in estuarine areas, confirmed BPA contamination in paradise threadfins, raising concerns about potential health risks for humans.
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Affiliation(s)
- Sourav Kundu
- ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata, 700 120, West Bengal, India
| | - Archisman Ray
- ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata, 700 120, West Bengal, India
| | - Subhadeep Das Gupta
- ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata, 700 120, West Bengal, India
| | - Ayan Biswas
- ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata, 700 120, West Bengal, India
| | - Shreya Roy
- ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata, 700 120, West Bengal, India
| | - Nitish Kumar Tiwari
- ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata, 700 120, West Bengal, India
| | - V Santhana Kumar
- ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata, 700 120, West Bengal, India
| | - Basanta Kumar Das
- ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata, 700 120, West Bengal, India.
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9
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Lee JU, Chang HS, Shim JS, Kim MH, Cho YJ, Kim MK, Park SL, Lee SJ, Park JS, Park CS. Aspirin Challenge-Induced Genome-Wide DNA Methylation Profile of Peripheral Blood Lymphocytes in Aspirin-Exacerbated Respiratory Disease. DNA Cell Biol 2024; 43:132-140. [PMID: 38386995 DOI: 10.1089/dna.2023.0218] [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] [Indexed: 02/24/2024] Open
Abstract
Genetic variation and epigenetic factors are thought to contribute to the development of hypersensitivity to aspirin. DNA methylation fluctuates dynamically throughout the day. To discover new CpG methylation in lymphocytes associated with aspirin-exacerbated respiratory disease (AERD), we evaluated changes in global CpG methylation profiles from before to after an oral aspirin challenge in patients with AERD and aspirin-tolerant asthma (ATA). Whole-genome CpG methylation levels of peripheral blood mononuclear cells were quantified with an Illumina 860K Infinium Methylation EPIC BeadChip array and then adjusted for inferred lymphocyte fraction (ILF) with GLINT and Tensor Composition Analysis. Among the 866,091 CpGs in the array, differentially methylated CpGs (DMCs) were found in 6 CpGs in samples from all 12 patients with asthma included in the study (AERD, n = 6; ATA, n = 6). DMCs were found in 3 CpGs in the 6 ATA samples and in 615 CpGs in the 6 AERD samples. A total of 663 DMCs in 415 genes and 214 intergenic regions differed significantly in the AERD compared with the ATA. In promoters, 126 CpG loci were predicted to bind to 38 transcription factors (TFs), many of which were factors already known to be involved in the pathogenesis of asthma and immune responses. In conclusion, we identified 615 new CpGs methylated in peripheral blood lymphocytes by oral aspirin challenge in AERD but not in ATA. These findings indicate that oral aspirin challenge induces epigenetic changes in ILFs, specifically in AERD patients, possibly via changes in TF binding, which may have epigenetic effects on the development of AERD.
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Affiliation(s)
- Jong-Uk Lee
- Division of Allergy and Respiratory Medicine, Department of Internal Medicine, Soonchunhyang University Bucheon Hospital, Bucheon, Korea
| | - Hun Soo Chang
- Department of Microbiology and BK21 FOUR Project, College of Medicine, Soonchunhyang University, Cheonan, Korea
| | - Ji-Su Shim
- Department of Internal Medicine, Ewha Womans University College of Medicine, Seoul, Korea
| | - Min-Hye Kim
- Department of Internal Medicine, Ewha Womans University College of Medicine, Seoul, Korea
| | - Young-Joo Cho
- Department of Internal Medicine, Ewha Womans University College of Medicine, Seoul, Korea
| | - Min Kyung Kim
- Department of Interdisciplinary Program in Biomedical Science Major, Soonchuhyang University, Asan, Korea
| | - Seung-Lee Park
- Department of Interdisciplinary Program in Biomedical Science Major, Soonchuhyang University, Asan, Korea
| | - Sun Ju Lee
- Department of Interdisciplinary Program in Biomedical Science Major, Soonchuhyang University, Asan, Korea
| | - Jong-Sook Park
- Division of Allergy and Respiratory Medicine, Department of Internal Medicine, Soonchunhyang University Bucheon Hospital, Bucheon, Korea
| | - Choon-Sik Park
- Division of Allergy and Respiratory Medicine, Department of Internal Medicine, Soonchunhyang University Bucheon Hospital, Bucheon, Korea
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10
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Regmi P, Young M, Minigo G, Milic N, Gyawali P. Photoperiod and metabolic health: evidence, mechanism, and implications. Metabolism 2024; 152:155770. [PMID: 38160935 DOI: 10.1016/j.metabol.2023.155770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 12/23/2023] [Accepted: 12/25/2023] [Indexed: 01/03/2024]
Abstract
Circadian rhythms are evolutionarily programmed biological rhythms that are primarily entrained by the light cycle. Disruption of circadian rhythms is an important risk factor for several metabolic disorders. Photoperiod is defined as total duration of light exposure in a day. With the extended use of indoor/outdoor light, smartphones, television, computers, and social jetlag people are exposed to excessive artificial light at night increasing their photoperiod. Importantly long photoperiod is not limited to any geographical region, season, age, or socioeconomic group, it is pervasive. Long photoperiod is an established disrupter of the circadian rhythm and can induce a range of chronic health conditions including adiposity, altered hormonal signaling and metabolism, premature ageing, and poor psychological health. This review discusses the impact of exposure to long photoperiod on circadian rhythms, metabolic and mental health, hormonal signaling, and ageing and provides a perspective on possible preventive and therapeutic approaches for this pervasive challenge.
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Affiliation(s)
- Prashant Regmi
- Faculty of Health, Charles Darwin University, Australia.
| | - Morag Young
- Cardiovascular Endocrinology Laboratory, Baker IDI Heart and Diabetes Institute, Australia
| | | | - Natalie Milic
- Faculty of Health, Charles Darwin University, Australia
| | - Prajwal Gyawali
- Centre of Health Research and School of Health and Medical Sciences, University of Southern Queensland, Australia
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11
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Liu XL, Duan Z, Yu M, Liu X. Epigenetic control of circadian clocks by environmental signals. Trends Cell Biol 2024:S0962-8924(24)00028-X. [PMID: 38423855 DOI: 10.1016/j.tcb.2024.02.005] [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: 12/14/2023] [Revised: 02/01/2024] [Accepted: 02/05/2024] [Indexed: 03/02/2024]
Abstract
Circadian clocks have evolved to enable organisms to respond to daily environmental changes. Maintaining a robust circadian rhythm under various perturbations and stresses is essential for the fitness of an organism. In the core circadian oscillator conserved in eukaryotes (from fungi to mammals), a negative feedback loop based on both transcription and translation drives circadian rhythms. The expression of circadian clock genes depends both on the binding of transcription activators at the promoter and on the chromatin state of the clock genes, and epigenetic modifications of chromatin are crucial for transcriptional regulation of circadian clock genes. Herein we review current knowledge of epigenetic regulation of circadian clock mechanisms and discuss how environmental cues can control clock gene expression by affecting chromatin states.
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Affiliation(s)
- Xiao-Lan Liu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Zeyu Duan
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Muqun Yu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xiao Liu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China; College of Life Sciences, University of the Chinese Academy of Sciences, Beijing, 100049, China.
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12
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Apsley AT, Ye Q, Etzel L, Wolf S, Hastings WJ, Mattern BC, Siegel SR, Shalev I. Biological stability of DNA methylation measurements over varying intervals of time and in the presence of acute stress. Epigenetics 2023; 18:2230686. [PMID: 37393564 PMCID: PMC10316737 DOI: 10.1080/15592294.2023.2230686] [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: 03/23/2023] [Revised: 06/13/2023] [Accepted: 06/21/2023] [Indexed: 07/04/2023] Open
Abstract
Identifying factors that influence the stability of DNA methylation measurements across biological replicates is of critical importance in basic and clinical research. Using a within-person between-group experimental design (n = 31, number of observations = 192), we report the stability of biological replicates over a variety of unique temporal scenarios, both in the absence and presence of acute psychosocial stress, and between individuals who have experienced early life adversity (ELA) and non-exposed individuals. We found that varying time intervals, acute stress, and ELA exposure influenced the stability of repeated DNA methylation measurements. In the absence of acute stress, probes were less stable as time passed; however, stress exerted a stabilizing influence on probes over longer time intervals. Compared to non-exposed individuals, ELA-exposed individuals had significantly lower probe stability immediately following acute stress. Additionally, we found that across all scenarios, probes used in most epigenetic-based algorithms for estimating epigenetic age or immune cell proportions had average or below-average stability, except for the Principal Component and DunedinPACE epigenetic ageing clocks, which were enriched for more stable probes. Finally, using highly stable probes in the absence of stress, we identified multiple probes that were hypomethylated in the presence of acute stress, regardless of ELA status. Two hypomethylated probes are located near the transcription start site of the glutathione-disulfide reductase gene (GSR), which has previously been shown to be an integral part of the stress response to environmental toxins. We discuss implications for future studies concerning the reliability and reproducibility of DNA methylation measurements.Abbreviations: DNAm - DNA methylation, CpG - 5'-cytosine-phosphate-guanine-3,' ICC - Interclass correlation coefficient, ELA - Early-life adversity, PBMCs - Peripheral blood mononuclear cells, mQTL - Methylation quantitative trait loci, TSS - Transcription start site, GSR - Glutathione-disulfide reductase gene, TSST - Trier social stress test, PC - Principal component.
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Affiliation(s)
- Abner T. Apsley
- Department of Biobehavioral Health, The Pennsylvania State University, University Park, PA, USA
- Department of Molecular, Cellular and Integrative Biological Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Qiaofeng Ye
- Department of Biobehavioral Health, The Pennsylvania State University, University Park, PA, USA
| | - Laura Etzel
- Department of Biobehavioral Health, The Pennsylvania State University, University Park, PA, USA
| | - Sarah Wolf
- Department of Biobehavioral Health, The Pennsylvania State University, University Park, PA, USA
| | - Waylon J. Hastings
- Department of Psychiatry, Tulane University School of Medicine, New Orleans, LA, USA
| | - Brooke C. Mattern
- Department of Biobehavioral Health, The Pennsylvania State University, University Park, PA, USA
| | - Sue Rutherford Siegel
- Department of Biobehavioral Health, The Pennsylvania State University, University Park, PA, USA
| | - Idan Shalev
- Department of Biobehavioral Health, The Pennsylvania State University, University Park, PA, USA
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13
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Ashokan M, Jayanthi KV, Elango K, Sneha K, Ramesha KP, Reshma RS, Saravanan KA, Naveen KGS. Biological methylation: redefining the link between genotype and phenotype. Anim Biotechnol 2023; 34:3174-3186. [PMID: 35468300 DOI: 10.1080/10495398.2022.2065999] [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] [Indexed: 11/01/2022]
Abstract
The central dogma of molecular biology is responsible for the crucial flow of genetic information from DNA to protein through the transcription and translation process. Although the sequence of DNA is constant in all organs, the difference in protein and variation in the phenotype is mainly due to the quality and quantity of tissue-specific gene expression and methylation pattern. The term methylation has been defined and redefined by various scientists in the last fifty years. There is always huge excitement around this field because the inheritance of something is beyond its DNA sequence. Advanced gene methylation studies have redefined molecular genetics and these tools are considered de novo in alleviating challenges of animal disease and production. Recent emerging evidence has shown that the impact of DNA, RNA, and protein methylation is crucial for embryonic development, cell proliferation, cell differentiation, and phenotype production. Currently, many researchers are focusing their work on methylation to understand its significant role in expression, disease-resistant traits, productivity, and longevity. The main aim of the present review is to provide an overview of DNA, RNA, and protein methylation, current research output from different sources, methodologies, factors responsible for methylation of genes, and future prospects in animal genetics.
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Affiliation(s)
- M Ashokan
- Animal Genetics and Breeding Division, Veterinary College, Hassan, KVAFSU, Karnataka, India
| | - K V Jayanthi
- Animal Genetics and Breeding Division, Veterinary College, Hassan, KVAFSU, Karnataka, India
| | - K Elango
- Southern Regional Station, ICAR-National Dairy Research Institute, Bangalore, India
| | - Kadimetla Sneha
- Animal Genetics and Breeding Division, Veterinary College, Hassan, KVAFSU, Karnataka, India
| | - K P Ramesha
- Southern Regional Station, ICAR-National Dairy Research Institute, Bangalore, India
| | - Raj S Reshma
- Southern Regional Station, ICAR-National Dairy Research Institute, Bangalore, India
| | - K A Saravanan
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Bareilly, India
| | - Kumar G S Naveen
- Animal Genetics and Breeding Division, Veterinary College, Hassan, KVAFSU, Karnataka, India
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14
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Barone I, Gilette NM, Hawks-Mayer H, Handy J, Zhang KJ, Chifamba FF, Mostafa E, Johnson-Venkatesh EM, Sun Y, Gibson JM, Rotenberg A, Umemori H, Tsai PT, Lipton JO. Synaptic BMAL1 phosphorylation controls circadian hippocampal plasticity. SCIENCE ADVANCES 2023; 9:eadj1010. [PMID: 37878694 PMCID: PMC10599629 DOI: 10.1126/sciadv.adj1010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 09/25/2023] [Indexed: 10/27/2023]
Abstract
The time of day strongly influences adaptive behaviors like long-term memory, but the correlating synaptic and molecular mechanisms remain unclear. The circadian clock comprises a canonical transcription-translation feedback loop (TTFL) strictly dependent on the BMAL1 transcription factor. We report that BMAL1 rhythmically localizes to hippocampal synapses in a manner dependent on its phosphorylation at Ser42 [pBMAL1(S42)]. pBMAL1(S42) regulates the autophosphorylation of synaptic CaMKIIα and circadian rhythms of CaMKIIα-dependent molecular interactions and LTP but not global rest/activity behavior. Therefore, our results suggest a model in which repurposing of the clock protein BMAL1 to synapses locally gates the circadian timing of plasticity.
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Affiliation(s)
- Ilaria Barone
- Department of Neurology and F.M. Kirby Center for Neurobiology, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Nicole M. Gilette
- Department of Neurology and F.M. Kirby Center for Neurobiology, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Hannah Hawks-Mayer
- Department of Neurology and F.M. Kirby Center for Neurobiology, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Jonathan Handy
- Department of Neurology and F.M. Kirby Center for Neurobiology, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Kevin J. Zhang
- Department of Neurology and F.M. Kirby Center for Neurobiology, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Fortunate F. Chifamba
- Department of Neurology and F.M. Kirby Center for Neurobiology, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Engie Mostafa
- Department of Neurology and F.M. Kirby Center for Neurobiology, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Erin M. Johnson-Venkatesh
- Department of Neurology and F.M. Kirby Center for Neurobiology, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Yan Sun
- Department of Neurology and F.M. Kirby Center for Neurobiology, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Jennifer M. Gibson
- Departments of Neurology, Neuroscience, Pediatrics, and Psychiatry, University of Texas at Southwestern, Dallas, TX 75390, USA
| | - Alexander Rotenberg
- Department of Neurology and F.M. Kirby Center for Neurobiology, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Hisashi Umemori
- Department of Neurology and F.M. Kirby Center for Neurobiology, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Peter T. Tsai
- Departments of Neurology, Neuroscience, Pediatrics, and Psychiatry, University of Texas at Southwestern, Dallas, TX 75390, USA
| | - Jonathan O. Lipton
- Department of Neurology and F.M. Kirby Center for Neurobiology, Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Neurology and Division of Sleep Medicine, Harvard Medical School, Boston, MA 02115, USA
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15
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Tomotani BM, Timpen F, Spoelstra K. Ingrained city rhythms: flexible activity timing but more persistent circadian pace in urban birds. Proc Biol Sci 2023; 290:20222605. [PMID: 37192668 PMCID: PMC10188242 DOI: 10.1098/rspb.2022.2605] [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: 12/31/2022] [Accepted: 04/24/2023] [Indexed: 05/18/2023] Open
Abstract
Urbanization dramatically increases the amount of light at night, which may disrupt avian circadian organization. We measured activity patterns of great tits breeding in the city and forest, and subsequently measured two clock properties of these birds under controlled conditions: tau (endogenous circadian clock speed) and after-effects (history dependency of the clock relative to previous conditions). City and forest birds showed a high repeatability of activity onset (0.60 and 0.41, respectively), with no difference between habitats after controlling for date effects. Activity duration and offset showed more variance, without a difference between birds from the two habitats. Tau did not differ between city and forest birds, however, city birds showed stronger after-effects, taking more days to revert to their endogenous circadian period. Finally, onset of activity was correlated with clocks speed in both habitats. Our results suggest that potential differences in activity timing of city birds is not caused by different clock speeds, but by a direct response to light. Persistence in after-effects suggests a reduced sensitivity of the clock to light at night. Urbanization may select for clock properties that increase the inertia of the endogenous circadian system to improve accuracy of activity rhythms when exposed to noisier lighting cues.
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Affiliation(s)
- Barbara M. Tomotani
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, Tromsø, Norway
| | - Fabian Timpen
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | - Kamiel Spoelstra
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
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16
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Ortega-Campos SM, Verdugo-Sivianes EM, Amiama-Roig A, Blanco JR, Carnero A. Interactions of circadian clock genes with the hallmarks of cancer. Biochim Biophys Acta Rev Cancer 2023; 1878:188900. [PMID: 37105413 DOI: 10.1016/j.bbcan.2023.188900] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 04/12/2023] [Accepted: 04/20/2023] [Indexed: 04/29/2023]
Abstract
The molecular machinery of the circadian clock regulates the expression of many genes and processes in the organism, allowing the adaptation of cellular activities to the daily light-dark cycles. Disruption of the circadian rhythm can lead to various pathologies, including cancer. Thus, disturbance of the normal circadian clock at both genetic and environmental levels has been described as an independent risk factor for cancer. In addition, researchers have proposed that circadian genes may have a tissue-dependent and/or context-dependent role in tumorigenesis and may function both as tumor suppressors and oncogenes. Finally, circadian clock core genes may trigger or at least be involved in different hallmarks of cancer. Hence, expanding the knowledge of the molecular basis of the circadian clock would be helpful to identify new prognostic markers of tumorigenesis and potential therapeutic targets.
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Affiliation(s)
- Sara M Ortega-Campos
- Instituto de Biomedicina de Sevilla (IBIS), Hospital Universitario Virgen del Rocío (HUVR), Consejo Superior de Investigaciones Científicas, Universidad de Sevilla, Seville 41013, Spain; CIBERONC, Instituto de Salud Carlos III, Madrid 28029, Spain
| | - Eva M Verdugo-Sivianes
- Instituto de Biomedicina de Sevilla (IBIS), Hospital Universitario Virgen del Rocío (HUVR), Consejo Superior de Investigaciones Científicas, Universidad de Sevilla, Seville 41013, Spain; CIBERONC, Instituto de Salud Carlos III, Madrid 28029, Spain
| | - Ana Amiama-Roig
- Hospital Universitario San Pedro, Logroño 26006, Spain; Centro de Investigación Biomédica de La Rioja (CIBIR), Logroño 26006, Spain
| | - José R Blanco
- Hospital Universitario San Pedro, Logroño 26006, Spain; Centro de Investigación Biomédica de La Rioja (CIBIR), Logroño 26006, Spain
| | - Amancio Carnero
- Instituto de Biomedicina de Sevilla (IBIS), Hospital Universitario Virgen del Rocío (HUVR), Consejo Superior de Investigaciones Científicas, Universidad de Sevilla, Seville 41013, Spain; CIBERONC, Instituto de Salud Carlos III, Madrid 28029, Spain.
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17
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Amidfar M, Garcez ML, Kim YK. The shared molecular mechanisms underlying aging of the brain, major depressive disorder, and Alzheimer's disease: The role of circadian rhythm disturbances. Prog Neuropsychopharmacol Biol Psychiatry 2023; 123:110721. [PMID: 36702452 DOI: 10.1016/j.pnpbp.2023.110721] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 01/07/2023] [Accepted: 01/19/2023] [Indexed: 01/24/2023]
Abstract
An association with circadian clock function and pathophysiology of aging, major depressive disorder (MDD), and Alzheimer's disease (AD) is well established and has been proposed as a factor in the development of these diseases. Depression and changes in circadian rhythm have been increasingly suggested as the two primary overlapping and interpenetrating changes that occur with aging. The relationship between AD and depression in late life is not completely understood and probably is complex. Patients with major depression or AD suffer from disturbed sleep/wake cycles and altered rhythms in daily activities. Although classical monoaminergic hypotheses are traditionally proposed to explain the pathophysiology of MDD, several clinical and preclinical studies have reported a strong association between circadian rhythm and mood regulation. In addition, a large body of evidence supports an association between disruption of circadian rhythm and AD. Some clock genes are dysregulated in rodent models of depression. If aging, AD, and MDD share a common biological basis in pathophysiology, common therapeutic tools could be investigated for their prevention and treatment. Nitro-oxidative stress (NOS), for example, plays a fundamental role in aging, as well as in the pathogenesis of AD and MDD and is associated with circadian clock disturbances. Thus, development of therapeutic possibilities with these NOS-related conditions is advisable. This review describes recent findings that link disrupted circadian clocks to aging, MDD, and AD and summarizes the experimental evidence that supports connections between the circadian clock and molecular pathologic factors as shared common pathophysiological mechanisms underlying aging, AD, and MDD.
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Affiliation(s)
- Meysam Amidfar
- Department of Neuroscience, Shahroud University of Medical Sciences, Shahroud, Iran
| | - Michelle Lima Garcez
- Laboratory of Translational Neuroscience, Department of Biochemistry, Federal University of Santa Catarina (UFSC), Florianópolis, Santa Catarina, Brazil
| | - Yong-Ku Kim
- Department of Psychiatry, College of Medicine, Korea University, Seoul, South Korea.
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18
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Schibler U, Dibner C, Ripperger J. Steve Brown. J Biol Rhythms 2023; 38:119-124. [PMID: 36762620 PMCID: PMC10037542 DOI: 10.1177/07487304231152275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Affiliation(s)
- Ueli Schibler
- Ueli Schibler, Department
of Molecular and Cellular Biology, University of Geneva, 30, Quai Ernest
Ansermet, Geneva, CH-1211, Switzerland; e-mail:
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19
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Zhang F, Niu L, Zhong R, Li S, Le W. Chronic Sleep Disturbances Alters Sleep Structure and Tau Phosphorylation in AβPP/PS1 AD Mice and Their Wild-Type Littermates. J Alzheimers Dis 2023; 92:1341-1355. [PMID: 37038814 DOI: 10.3233/jad-221048] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
Abstract
Background: Emerging evidence indicates that sleep disorders are the common non-cognitive symptoms of Alzheimer’s disease (AD), and they may contribute to the pathogenesis of this disease. Objective: In this study, we aim to investigate the effect of chronic sleep deprivation (CSD) on AD-related pathologies with a focus on tau phosphorylation and the underlying DNA methylation regulation. Methods: AβPPswe/PS1ΔE9 AD mice and their wild-type (WT) littermates were subjected to a two-month CSD followed by electroencephalography and electromyography recording. The mice were examined for learning and memory evaluation, then pathological, biochemical, and epigenetic assessments including western blotting, immunofluorescence, dot blotting, and bisulfite sequencing. Results: The results show that CSD caused sleep disorders shown as sleep pattern change, poor sleep maintenance, and increased sleep fragmentation. CSD increased tau phosphorylation at different sites and increased the level of tau kinases in AD and WT mice. The increased expression of cyclin-dependent kinase 5 (CDK5) may result from decreased DNA methylation of CpG sites in the promoter region of CDK5 gene, which might be associated with the downregulation of DNA methyltransferase 3A and 3B. Conclusion: CSD altered AD-related tau phosphorylation through epigenetic modification of tau kinase gene. The findings in this study may give insights into the mechanisms underlying the effects of sleep disorders on AD pathology and provide new therapeutic targets for the treatment of this disease.
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Affiliation(s)
- Feng Zhang
- Center for Clinical and Translational Medicine, Shanghai University of Medicine and Health Sciences, Shanghai, China
- Shanghai University of Medicine and Health Sciences Affiliated Zhoupu Hospital, Shanghai, China
| | - Long Niu
- Center for Clinical Research on Neurological Diseases, the First Affiliated Hospital, Dalian Medical University, Dalian, China
| | - Rujia Zhong
- Shanghai University of Medicine and Health Sciences Affiliated Zhoupu Hospital, Shanghai, China
| | - Song Li
- Center for Clinical Research on Neurological Diseases, the First Affiliated Hospital, Dalian Medical University, Dalian, China
| | - Weidong Le
- Center for Clinical and Translational Medicine, Shanghai University of Medicine and Health Sciences, Shanghai, China
- Shanghai University of Medicine and Health Sciences Affiliated Zhoupu Hospital, Shanghai, China
- Center for Clinical Research on Neurological Diseases, the First Affiliated Hospital, Dalian Medical University, Dalian, China
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20
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Handschuh PA, Murgaš M, Vraka C, Nics L, Hartmann AM, Winkler-Pjrek E, Baldinger-Melich P, Wadsak W, Winkler D, Hacker M, Rujescu D, Domschke K, Lanzenberger R, Spies M. Effect of MAOA DNA Methylation on Human in Vivo Protein Expression Measured by [11C]harmine Positron Emission Tomography. Int J Neuropsychopharmacol 2023; 26:116-124. [PMID: 36573644 PMCID: PMC9926052 DOI: 10.1093/ijnp/pyac085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 12/26/2022] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Epigenetic modifications like DNA methylation are understood as an intermediary between environmental factors and neurobiology. Cerebral monoamine oxidase A (MAO-A) levels are altered in depression, as are DNA methylation levels within the MAOA gene, particularly in the promoter/exon I/intron I region. An effect of MAOA methylation on peripheral protein expression was shown, but the extent to which methylation affects brain MAO-A levels is not fully understood. METHODS Here, the influence of MAOA promoter/exon I/intron I region DNA methylation on global MAO-A distribution volume (VT), an index of MAO-A density, was assessed via [11C]harmine positron emission tomography in 22 patients (14 females) suffering from seasonal affective disorder and 30 healthy controls (17 females). RESULTS No significant influence of MAOA DNA methylation on global MAO-A VT was found, despite correction for health status, sex, season, and MAOA variable number of tandem repeat genotype. However, season affected average methylation in women, with higher levels in spring and summer (Puncorr = .03). We thus did not find evidence for an effect of MAOA DNA methylation on brain MAO-A VT. CONCLUSIONS In contrast to a previous study demonstrating an effect of methylation of a MAOA promoter region located further 5' on brain MAO-A, MAOA methylation of the region assessed here appears to affect brain protein levels to a limited extent at most. The observed effect of season on methylation levels is in accordance with extensive evidence for seasonal effects within the serotonergic system. CLINICALTRIALS.GOV IDENTIFIER NCT02582398 (https://clinicaltrials.gov/ct2/show/NCT02582398).
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Affiliation(s)
- Patricia A Handschuh
- Department of Psychiatry and Psychotherapy, Medical University of Vienna, Austria
| | - Matej Murgaš
- Department of Psychiatry and Psychotherapy, Medical University of Vienna, Austria
| | - Chrysoula Vraka
- Department of Biomedical Imaging and Image-guided Therapy, Division of Nuclear Medicine, Medical University of Vienna, Austria
| | - Lukas Nics
- Department of Biomedical Imaging and Image-guided Therapy, Division of Nuclear Medicine, Medical University of Vienna, Austria
| | - Annette M Hartmann
- Department of Psychiatry and Psychotherapy, Medical University of Vienna, Austria
| | - Edda Winkler-Pjrek
- Department of Psychiatry and Psychotherapy, Medical University of Vienna, Austria
| | - Pia Baldinger-Melich
- Department of Psychiatry and Psychotherapy, Medical University of Vienna, Austria
| | - Wolfgang Wadsak
- Department of Biomedical Imaging and Image-guided Therapy, Division of Nuclear Medicine, Medical University of Vienna, Austria
- Center for Biomarker Research in Medicine (CBmed), Graz, Austria
| | - Dietmar Winkler
- Department of Psychiatry and Psychotherapy, Medical University of Vienna, Austria
| | - Marcus Hacker
- Department of Biomedical Imaging and Image-guided Therapy, Division of Nuclear Medicine, Medical University of Vienna, Austria
| | - Dan Rujescu
- Department of Psychiatry and Psychotherapy, Medical University of Vienna, Austria
| | - Katharina Domschke
- Department of Psychiatry and Psychotherapy, Medical Center – University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Centre for Basics in Neuromodulation, Faculty of Medicine, University of Freiburg, Germany
| | - Rupert Lanzenberger
- Department of Psychiatry and Psychotherapy, Medical University of Vienna, Austria
| | - Marie Spies
- Department of Psychiatry and Psychotherapy, Medical University of Vienna, Austria
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21
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Kompotis K, Landolt HP. In memoriam: Professor Steven A. Brown, PhD (1970-2022). J Sleep Res 2023:e13836. [PMID: 36756725 DOI: 10.1111/jsr.13836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 01/12/2023] [Indexed: 02/10/2023]
Affiliation(s)
- Konstantinos Kompotis
- Section of Chronobiology and Sleep Research, Institute of Pharmacology and Toxicology, University of Zürich, Zürich, Switzerland
| | - Hans-Peter Landolt
- Section of Chronobiology and Sleep Research, Institute of Pharmacology and Toxicology, University of Zürich, Zürich, Switzerland
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22
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Chrono-Nutrition: Circadian Rhythm and Personalized Nutrition. Int J Mol Sci 2023; 24:ijms24032571. [PMID: 36768893 PMCID: PMC9916946 DOI: 10.3390/ijms24032571] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 01/23/2023] [Accepted: 01/25/2023] [Indexed: 01/31/2023] Open
Abstract
The human circadian system has a period of approximately 24 h and studies on the consequences of "chornodisruption" have greatly expanded. Lifestyle and environmental factors of modern societies (i.e., artificial lighting, jetlag, shift work, and around-the-clock access to energy-dense food) can induce disruptions of the circadian system and thereby adversely affect individual health. Growing evidence demonstrates a complex reciprocal relationship between metabolism and the circadian system, in which perturbations in one system affect the other one. From a nutritional genomics perspective, genetic variants in clock genes can both influence metabolic health and modify the individual response to diet. Moreover, an interplay between the circadian rhythm, gut microbiome, and epigenome has been demonstrated, with the diet in turn able to modulate this complex link suggesting a remarkable plasticity of the underlying mechanisms. In this view, the study of the impact of the timing of eating by matching elements from nutritional research with chrono-biology, that is, chrono-nutrition, could have significant implications for personalized nutrition in terms of reducing the prevalence and burden of chronic diseases. This review provides an overview of the current evidence on the interactions between the circadian system and nutrition, highlighting how this link could in turn influence the epigenome and microbiome. In addition, possible nutritional strategies to manage circadian-aligned feeding are suggested.
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23
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Hitrec T, Petit C, Cryer E, Muir C, Tal N, Fustin JM, Hughes AT, Piggins HD. Timed exercise stabilizes behavioral rhythms but not molecular programs in the brain's suprachiasmatic clock. iScience 2023; 26:106002. [PMID: 36866044 PMCID: PMC9971895 DOI: 10.1016/j.isci.2023.106002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 11/25/2022] [Accepted: 01/13/2023] [Indexed: 01/20/2023] Open
Abstract
Timed daily access to a running-wheel (scheduled voluntary exercise; SVE) synchronizes rodent circadian rhythms and promotes stable, 24h rhythms in animals with genetically targeted impairment of neuropeptide signaling (Vipr2 -/- mice). Here we used RNA-seq and/or qRT-PCR to assess how this neuropeptide signaling impairment as well as SVE shapes molecular programs in the brain clock (suprachiasmatic nuclei; SCN) and peripheral tissues (liver and lung). Compared to Vipr2 +/+ animals, the SCN transcriptome of Vipr2 -/- mice showed extensive dysregulation which included core clock components, transcription factors, and neurochemicals. Furthermore, although SVE stabilized behavioral rhythms in these animals, the SCN transcriptome remained dysregulated. The molecular programs in the lung and liver of Vipr2 -/- mice were partially intact, although their response to SVE differed to that of these peripheral tissues in the Vipr2 +/+ mice. These findings highlight that SVE can correct behavioral abnormalities in circadian rhythms without causing large scale alterations to the SCN transcriptome.
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Affiliation(s)
- Timna Hitrec
- School of Physiology, Pharmacology, and Neuroscience, Faculty of Life Sciences, University of Bristol, Bristol BS8 1TD, UK
| | - Cheryl Petit
- School of Medical Sciences, Faculty of Biology, Medicine, and Health, University of Manchester, Manchester M13 9PT, UK
| | - Emily Cryer
- School of Biological Sciences, Faculty of Life Sciences, University of Bristol, Bristol BS8 1TQ, UK
| | - Charlotte Muir
- School of Physiology, Pharmacology, and Neuroscience, Faculty of Life Sciences, University of Bristol, Bristol BS8 1TD, UK
| | - Natalie Tal
- School of Medical Sciences, Faculty of Biology, Medicine, and Health, University of Manchester, Manchester M13 9PT, UK
| | - Jean-Michel Fustin
- School of Medical Sciences, Faculty of Biology, Medicine, and Health, University of Manchester, Manchester M13 9PT, UK
| | - Alun T.L. Hughes
- School of Medical Sciences, Faculty of Biology, Medicine, and Health, University of Manchester, Manchester M13 9PT, UK,School of Biological and Environmental Sciences, Faculty of Science, Liverpool John Moores University, Liverpool L3 3AF, UK,Corresponding author
| | - Hugh D. Piggins
- School of Physiology, Pharmacology, and Neuroscience, Faculty of Life Sciences, University of Bristol, Bristol BS8 1TD, UK,School of Medical Sciences, Faculty of Biology, Medicine, and Health, University of Manchester, Manchester M13 9PT, UK,Corresponding author
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The Effect of Diet on the Cardiac Circadian Clock in Mice: A Systematic Review. Metabolites 2022; 12:metabo12121273. [PMID: 36557311 PMCID: PMC9786298 DOI: 10.3390/metabo12121273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 11/19/2022] [Accepted: 11/23/2022] [Indexed: 12/23/2022] Open
Abstract
Circadian rhythms play important roles in regulating physiological and behavioral processes. These are adjusted by environmental cues, such as diet, which acts by synchronizing or attenuating the circadian rhythms of peripheral clocks, such as the liver, intestine, pancreas, white and brown adipose tissue, lungs, kidneys, as well as the heart. Some studies point to the influence of diet composition, feeding timing, and dietary restriction on metabolic homeostasis and circadian rhythms at various levels. Therefore, this systematic review aimed to discuss studies addressing the effect of diet on the heart clock in animal models and, additionally, the chronodisruption of the clock and its relation to the development of cardiovascular disorders in the last 15 years. A search was conducted in the PubMed, Scopus, and Embase databases. The PRISMA guide was used to construct the article. Nineteen studies met all inclusion and exclusion criteria. In summary, these studies have linked the circadian clock to cardiovascular health and suggested that maintaining a robust circadian system may reduce the risks of cardiometabolic and cardiovascular diseases. The effect of time-of-day-dependent eating on the modulation of circadian rhythms of the cardiac clock and energy homeostasis is notable, among its deleterious effects predominantly in the sleep (light) phase and/or at the end of the active phase.
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Renthlei Z, Yatung S, Lalpekhlui R, Trivedi AK. Seasonality in tropical birds. JOURNAL OF EXPERIMENTAL ZOOLOGY. PART A, ECOLOGICAL AND INTEGRATIVE PHYSIOLOGY 2022; 337:952-966. [PMID: 35982509 DOI: 10.1002/jez.2649] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 07/18/2022] [Accepted: 08/03/2022] [Indexed: 06/15/2023]
Abstract
The survival of offspring depends on environmental conditions. Many organisms have evolved with seasonality, characterized as initiation-termination-reinitiation of several physiological processes (i.e., body fattening, molt, plumage coloration, reproduction, etc). It is an adaptation for the survival of many species. Predominantly seasonal breeders use photoperiod as the most reliable environmental cue to adapt to seasonal changes but supplementary factors like temperature and food are synergistically involved in seasonal processes. Studies from diverse vertebrate systems have contributed to understanding the mechanism involved in seasonal reproduction at the molecular and endocrine levels. Long-day induced thyrotropin (thyroid-stimulating hormone) released from the pars tuberalis of the pituitary gland triggers local thyroid hormone activation within the mediobasal hypothalamus. This locally produced thyroid hormone, T3, regulates seasonal gonadotropin-releasing hormone secretion. Most of the bird species studied are seasonal in reproduction and linked behavior and, therefore, need to adjust reproductive decisions to environmental fluctuations. Reproductive strategies of the temperate zone breeders are well-documented, but less is known about tropical birds' reproduction and factors stimulating the annual breeding strategies. Here, we address seasonality in tropical birds with reference to seasonal reproduction and the various environmental factors influencing seasonal breeding.
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Affiliation(s)
| | - Subu Yatung
- Department of Zoology, Mizoram University, Aizawl, Mizoram, India
| | - Ruth Lalpekhlui
- Department of Zoology, Mizoram University, Aizawl, Mizoram, India
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26
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Yadav A, Kumar R, Tiwari J, Vaish V, Malik S, Rani S. Effect of artificial light at night on sleep and metabolism in weaver birds. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:80422-80435. [PMID: 35716297 DOI: 10.1007/s11356-022-20875-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 05/12/2022] [Indexed: 06/15/2023]
Abstract
Artificial light at night is constantly minimizing the span of dark nights from the natural light-dark cycle of earth. Over the past century, the "lightscape" of earth has completely changed owing to technological advancements which subsequently changed the lifestyle of human as well as the nearby animal species. This motivated the present study, wherein we investigated the impact of light at night (LAN) on behavior and physiology of a diurnal passerine finch, baya weaver (Ploceus philippinus). A group of bird (N=10) exposed to 12L:12D photoperiod was initially subjected to dark nights (0 lux) for a period of 1.5 weeks followed by 5 lux, night light for a span of 4 weeks. The first week in LAN served as acute treatment with respect to the fourth week (chronic). The results reveal significant increase in nighttime activity and sleep loss with respect to acute LAN, while significant inclusion of drowsiness behavior during the day in response to chronic LAN. Besides these behavioral alterations, changes in physiological parameters such as reduction in body mass, loss of gradient between pre- and post- prandial blood glucose levels, and elevation in plasma corticosterone levels were more prominent during acute exposure of LAN. Plasma metabolites such as triglycerides, total protein, serum glutamic-oxaloacetic transaminase (SGOT), and creatinine concentrations also hiked in response to acute LAN treatment. Thus, acute exposure of LAN seems to serve as a novel environment for the bird leading to more pronounced impacts on behavioral and physiological observations during the experiment. In chronic exposure, the birds sort of adapted themselves to the prevailing circumstances as evident by decreased nighttime activity, rebound of sleep and corticosterone levels, etc. Thus, the study clearly demonstrates the differential impact of acute and chronic exposure of LAN on behavior and physiology of birds.
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Affiliation(s)
- Anupama Yadav
- Department of Zoology, University of Lucknow, Uttar Pradesh, 226007, Lucknow, India
| | - Raj Kumar
- Department of Zoology, University of Lucknow, Uttar Pradesh, 226007, Lucknow, India
| | - Jyoti Tiwari
- Department of Zoology, University of Lucknow, Uttar Pradesh, 226007, Lucknow, India
| | - Vaibhav Vaish
- Department of Zoology, University of Lucknow, Uttar Pradesh, 226007, Lucknow, India
| | - Shalie Malik
- Department of Zoology, University of Lucknow, Uttar Pradesh, 226007, Lucknow, India
| | - Sangeeta Rani
- Department of Zoology, University of Lucknow, Uttar Pradesh, 226007, Lucknow, India.
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27
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Samad M, Agostinelli F, Sato T, Shimaji K, Baldi P. CircadiOmics: circadian omic web portal. Nucleic Acids Res 2022; 50:W183-W190. [PMID: 35657089 PMCID: PMC9252794 DOI: 10.1093/nar/gkac419] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Revised: 04/14/2022] [Accepted: 06/01/2022] [Indexed: 11/12/2022] Open
Abstract
Circadian rhythms are a foundational aspect of biology. These rhythms are found at the molecular level in every cell of every living organism and they play a fundamental role in homeostasis and a variety of physiological processes. As a result, biomedical research of circadian rhythms continues to expand at a rapid pace. To support this research, CircadiOmics (http://circadiomics.igb.uci.edu/) is the largest annotated repository and analytic web server for high-throughput omic (e.g. transcriptomic, metabolomic, proteomic) circadian time series experimental data. CircadiOmics contains over 290 experiments and over 100 million individual measurements, across >20 unique tissues/organs, and 11 different species. Users are able to visualize and mine these datasets by deriving and comparing periodicity statistics for oscillating molecular species including: period, amplitude, phase, P-value and q-value. These statistics are obtained from BIO_CYCLE and JTK_CYCLE and are intuitively aggregated and displayed for comparison. CircadiOmics is the most up-to-date and cutting-edge web portal for searching and analyzing circadian omic data and is used by researchers around the world.
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Affiliation(s)
- Muntaha Samad
- Department of Computer Science, University of California Irvine, Irvine, CA 92697, USA.,Institute for Genomics and Bioinformatics, University of California, Irvine CA 92697, USA
| | - Forest Agostinelli
- Department of Computer Science and Engineering, University of South Carolina, Columbia, SC 29208, USA
| | - Tomoki Sato
- Department of Biological Chemistry, Center for Epigenetics and Metabolism, School of Medicine, University of California, Irvine, CA 92697, USA
| | - Kohei Shimaji
- Department of Biological Chemistry, Center for Epigenetics and Metabolism, School of Medicine, University of California, Irvine, CA 92697, USA
| | - Pierre Baldi
- Department of Computer Science, University of California Irvine, Irvine, CA 92697, USA.,Institute for Genomics and Bioinformatics, University of California, Irvine CA 92697, USA
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28
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Ritonja JA, Aronson KJ, Leung M, Flaten L, Topouza DG, Duan QL, Durocher F, Tranmer JE, Bhatti P. Investigating the relationship between melatonin patterns and methylation in circadian genes among day shift and night shift workers. Occup Environ Med 2022; 79:oemed-2021-108111. [PMID: 35501127 DOI: 10.1136/oemed-2021-108111] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 04/16/2022] [Indexed: 11/04/2022]
Abstract
OBJECTIVES Mechanisms underlying the carcinogenicity of night shift work remain uncertain. One compelling yet understudied cancer mechanism may involve altered DNA methylation in circadian genes due to melatonin secretion patterns. The objective of this study was to explore the relationship between melatonin secretion patterns and circadian gene methylation among day and night shift workers. METHODS Female healthcare employees (n=38 day workers, n=36 night shift workers) for whom we had urinary 6-sulfatoxymelatonin secretion data from a previous study were recontacted. New blood samples were collected and used to measure methylation levels at 1150 CpG loci across 22 circadian genes using the Illumina Infinium MethylationEPIC beadchip. Linear regression was used to examine the association between melatonin (acrophase and mesor) and M values for each CpG site (false discovery rate, q=0.2), while testing for effect modification by shift work status. RESULTS Among night shift workers, a higher mesor (24 hours of mean production of melatonin) was associated with increased methylation in the body of RORA (q=0.02) and decreased methylation in the putative promoter region of MTNR1A (q=0.03). Later acrophase (ie, time of peak concentration) was associated with increased methylation in the putative promoter region of MTNR1A (q=0.20) and decreased methylation in the body of PER3 (q=0.20). No associations were identified among day workers. CONCLUSIONS In conclusion, patterns in melatonin secretion were associated with differential circadian gene methylation among night shift workers. Melatonin and alteration of DNA methylation in circadian genes may be one pathway towards increased cancer risk, although larger-scale studies examining multiple time points are needed.
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Affiliation(s)
- Jennifer A Ritonja
- Department of Public Health Sciences, Queen's University, Kingston, Ontario, Canada
| | - Kristan J Aronson
- Department of Public Health Sciences, Queen's University, Kingston, Ontario, Canada
- Division of Cancer Care and Epidemiology, Queen's University Cancer Research Institute, Kingston, Ontario, Canada
| | - Michael Leung
- Department of Epidemiology, Harvard University T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Lisa Flaten
- Department of Public Health Sciences, Queen's University, Kingston, Ontario, Canada
| | - Danai G Topouza
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, Canada
| | - Qing Ling Duan
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, Canada
- School of Computing, Queen's University, Kingston, Ontario, Canada
| | - Francine Durocher
- Département de Médecine Moléculaire, Faculté de Médecine, Université Laval, Quebec, Quebec, Canada
- Centre de Recherche sur le Cancer, Centre de recherche du CHU de Québec-Université Laval, Quebec, Quebec, Canada
| | - Joan E Tranmer
- Department of Public Health Sciences, Queen's University, Kingston, Ontario, Canada
- School of Nursing, Queen's University, Kingston, Ontario, Canada
| | - Parveen Bhatti
- Cancer Control Research, BC Cancer Agency, Vancouver, British Columbia, Canada
- School of Population and Public Health, The University of British Columbia, Vancouver, British Columbia, Canada
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29
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Seale K, Horvath S, Teschendorff A, Eynon N, Voisin S. Making sense of the ageing methylome. Nat Rev Genet 2022; 23:585-605. [PMID: 35501397 DOI: 10.1038/s41576-022-00477-6] [Citation(s) in RCA: 66] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/18/2022] [Indexed: 12/22/2022]
Abstract
Over time, the human DNA methylation landscape accrues substantial damage, which has been associated with a broad range of age-related diseases, including cardiovascular disease and cancer. Various age-related DNA methylation changes have been described, including at the level of individual CpGs, such as differential and variable methylation, and at the level of the whole methylome, including entropy and correlation networks. Here, we review these changes in the ageing methylome as well as the statistical tools that can be used to quantify them. We detail the evidence linking DNA methylation to ageing phenotypes and the longevity strategies aimed at altering both DNA methylation patterns and machinery to extend healthspan and lifespan. Lastly, we discuss theories on the mechanistic causes of epigenetic ageing.
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Affiliation(s)
- Kirsten Seale
- Institute for Health and Sport (iHeS), Victoria University, Footscray, Melbourne, Victoria, Australia
| | - Steve Horvath
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA.,Altos Labs, San Diego, CA, USA
| | - Andrew Teschendorff
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, China.,UCL Cancer Institute, University College London, London, UK
| | - Nir Eynon
- Institute for Health and Sport (iHeS), Victoria University, Footscray, Melbourne, Victoria, Australia.
| | - Sarah Voisin
- Institute for Health and Sport (iHeS), Victoria University, Footscray, Melbourne, Victoria, Australia.
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30
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Sympatric speciation of the spiny mouse from Evolution Canyon in Israel substantiated genomically and methylomically. Proc Natl Acad Sci U S A 2022; 119:e2121822119. [PMID: 35320043 PMCID: PMC9060526 DOI: 10.1073/pnas.2121822119] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
SignificanceWhether sympatric speciation (SS) is rare or common is still debated. Two populations of the spiny mouse, Acomys cahirinus, from Evolution Canyon I (EC I) in Israel have been depicted earlier as speciating sympatrically by molecular markers and transcriptome. Here, we investigated SS both genomically and methylomically, demonstrating that the opposite populations of spiny mice are sister taxa and split from the common ancestor around 20,000 years ago without an allopatric history. Mate choice, olfactory receptors, and speciation genes contributed to prezygotic/postzygotic reproductive isolation. The two populations showed different methylation patterns, facilitating adaptation to their local environment. They cope with abiotic and biotic stresses, due to high solar interslope radiation differences. We conclude that our new genomic and methylomic data substantiated SS.
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31
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Silverthorne T, Oh ES, Stinchcombe AR. Promoter methylation in a mixed feedback loop circadian clock model. Phys Rev E 2022; 105:034411. [PMID: 35428061 DOI: 10.1103/physreve.105.034411] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 02/27/2022] [Indexed: 06/14/2023]
Abstract
We investigate how epigenetic modifications to clock gene promoters affect transcriptomic activity in the circadian clock. Motivated by experimental observations that link DNA methylation with the behavior of the clock, we introduce and analyze an extension of the mixed feedback loop (MFL) model of François and Hakim. We extend the original model to include an additional methylated promoter state and allow for reversible protein sequestration, an important feature for circadian applications. First, working with the general form of the MFL model, we find that the qualitative behavior of the model is dictated by the promoter state with the highest transcription rate. We then build on the work of Kim and Forger, who analyzed the stability of the mammalian circadian clock by using a reduced form of the MFL model. We present a rigorous procedure for translating between the MFL model and the reduction of Kim and Forger. We then propose a model reduction more appropriate for the study of oscillatory promoter states, making use of a fully coupled quasi-steady-state approximation rather than the standard partially uncoupled quasi-steady-state approach. Working with the novel reduced form of the model, we find substantial differences in the transcription function and show that, although methylation contributes to period control, excessive methylation can abolish rhythmicity. Altogether our results show that even in a minimal clock model, DNA methylation has a nontrivial influence on the system's ability to oscillate.
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Affiliation(s)
- Turner Silverthorne
- Department of Mathematics, University of Toronto, Toronto, M5S 2E4 Ontario, Canada
- The Krembil Family Epigenetics Laboratory, The Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, M5T 1R8 Ontario, Canada
| | - Edward Saehong Oh
- The Krembil Family Epigenetics Laboratory, The Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, M5T 1R8 Ontario, Canada
| | - Adam R Stinchcombe
- Department of Mathematics, University of Toronto, Toronto, M5S 2E4 Ontario, Canada
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32
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Govoni S, Fagiani F, Lanni C, Allegri N. The Frailty Puzzle: Searching for Immortality or for Knowledge Survival? Front Cell Neurosci 2022; 16:838447. [PMID: 35250489 PMCID: PMC8891148 DOI: 10.3389/fncel.2022.838447] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 01/25/2022] [Indexed: 12/18/2022] Open
Abstract
What is the value of assessing the biological age and frailty and predicting residual lifespan and health status? The benefit is obvious if we have means to alter the pace of aging and the development of frailty. So far, limited but increasing examples of interventions altering the predicted status indicate that, at least in some cases, this is possible through interventions spanning from the economic-social through drug treatments. Thus, why searching for biological markers, when some clinical and socio-economic indicators do already provide sufficiently accurate predictions? Indeed, the search of frailty biomarkers and of their biological clocks helps to build up a mechanistic frame that may orientate the design of interventions and the time window of their efficacy. Among the candidate biomarkers identified, several studies converge to indicate epigenetic clocks as a promising sensitive biomarker of the aging process. Moreover, it will help to establish the relationship between personal aging and health trajectories and to individuate the check points beyond which biological changes are irreversible.
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Affiliation(s)
- Stefano Govoni
- Department of Drug Sciences (Pharmacology Section), University of Pavia, Pavia, Italy
- CEFAT (Center of Pharmaceuticals Economics and Medical Technologies Evaluation), University of Pavia, Pavia, Italy
| | - Francesca Fagiani
- Department of Drug Sciences (Pharmacology Section), University of Pavia, Pavia, Italy
| | - Cristina Lanni
- Department of Drug Sciences (Pharmacology Section), University of Pavia, Pavia, Italy
| | - Nicola Allegri
- CEFAT (Center of Pharmaceuticals Economics and Medical Technologies Evaluation), University of Pavia, Pavia, Italy
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33
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Zhang S, Feng X. Effect of 17β-trenbolone exposure during adolescence on the circadian rhythm in male mice. CHEMOSPHERE 2022; 288:132496. [PMID: 34627821 DOI: 10.1016/j.chemosphere.2021.132496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Revised: 09/28/2021] [Accepted: 10/05/2021] [Indexed: 06/13/2023]
Abstract
The suprachiasmatic nucleus (SCN) is the main control area of the clock rhythm in the mammalian brain. It drives daily behaviours and rhythms by synchronizing or suppressing the oscillations of clock genes in peripheral tissue. It is an important brain tissue structure that affects rhythm stability. SCN has high plasticity and is easily affected by the external environment. In this experiment, we found that exposure to the endocrine disruptor 17β-trenbolone (17β-TBOH) affects the rhythmic function of SCN in the brains of adolescent male balb/c mice. Behavioural results showed that exposure to 17β-TBOH disrupted daily activity-rest rhythms, reduced the robustness of endogenous rhythms, altered sleep-wake-related behaviours, and increased the stress to light stimulation. At the cellular level, exposure to 17β-TBOH decreased the c-fos immune response of SCN neurons to the large phase shift, indicating that it affected the coupling ability of SCN neurons. At the molecular level, exposure to 17β-TBOH interfered with the daily expression of hormones, changed the expression levels of the core clock genes and cell communication genes in the SCN, and affected the expression of wake-up genes in the hypothalamus. Finally, we observed the effect of exposure to 17β-TBOH on energy metabolism. The results showed that 17β-TBOH reduced the metabolic response and affected the metabolic function of the liver. This study revealed the influence of environmental endocrine disrupting chemicals (EDCs) on rhythms and metabolic disorders, and provides references for follow-up research.
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Affiliation(s)
- Shaozhi Zhang
- College of Life Science, The Key Laboratory of Bioactive Materials, Ministry of Education, State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300071, China; Research Institute of Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan, Shandong, 250355, China
| | - Xizeng Feng
- College of Life Science, The Key Laboratory of Bioactive Materials, Ministry of Education, State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300071, China.
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Shi F, Qiu J, Zhang S, Zhao X, Feng D, Feng X. Exogenous melatonin protects preimplantation embryo development from decabromodiphenyl ethane-induced circadian rhythm disorder and endogenous melatonin reduction. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 292:118445. [PMID: 34737029 DOI: 10.1016/j.envpol.2021.118445] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 10/14/2021] [Accepted: 10/29/2021] [Indexed: 06/13/2023]
Abstract
Decabromodiphenyl ethane (DBDPE) is a novel flame retardant that is widely used in plastics, electronic products, building materials and textiles. Our previous studies have revealed the oocyte toxicity of DBDPE, but the effect of DBDPE on preimplantation embryo development has not been reported. Here, we investigated whether and how DBDPE exposure affects preimplantation embryo development. Adult female mice were orally exposed to DBDPE (0, 5, 50, 500 μg/kg bw/day) for 14 days. First, we found that after DBDPE exposure, mice showed obvious circadian rhythm disorder. Moreover, the development of preimplantation embryos was inhibited in DBDPE-exposed mice after pregnancy. Then, we further explored and revealed that DBDPE exposure reduced the endogenous melatonin (MLT) level during pregnancy, thereby inhibiting the development of preimplantation embryos. Furthermore, we discovered that exogenous MLT supplementation (15 mg/kg bw/day) rescued the inhibition of preimplantation embryo development induced by DBDPE, and a mechanistic study demonstrated that exogenous MLT inhibited the overexpression of ROS and DNA methylation at the 5-position of cytosine (5-mC) in DBDPE-exposed preimplantation embryos. Simultaneously, MLT ameliorated the DBDPE-induced mitochondrial dysfunction by increasing the mitochondrial membrane potential (MMP), ATP, and Trp1 expression. Additionally, MLT restored DBDPE-induced changes in zona pellucida (ZP) hardness and trophectoderm (TE) cortical tension. Finally, the protective effect of MLT on embryos ameliorated the adverse reproductive outcomes (dead fetus, fetus with abnormal liver, fetal weight loss) induced by DBDPE. Collectively, DBDPE induced preimplantation embryo damage leading to adverse reproductive outcomes, and MLT has emerged as a potential tool to rescue adverse reproductive outcomes induced by DBDPE.
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Affiliation(s)
- Feifei Shi
- College of Life Science, The Key Laboratory of Bioactive Materials, Ministry of Education, State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300071, China
| | - Jinyu Qiu
- The Institute of Robotics and Automatic Information Systems, Nankai University, Tianjin, 300071, China
| | - Shaozhi Zhang
- College of Life Science, The Key Laboratory of Bioactive Materials, Ministry of Education, State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300071, China
| | - Xin Zhao
- The Institute of Robotics and Automatic Information Systems, Nankai University, Tianjin, 300071, China
| | - Daofu Feng
- Department of General Surgery, Tianjin Medical University General Hospital, No. 154 Anshan Road, Tianjin, 300052, China
| | - Xizeng Feng
- College of Life Science, The Key Laboratory of Bioactive Materials, Ministry of Education, State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300071, China.
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35
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Zhou J, Wang J, Zhang X, Tang Q. New Insights Into Cancer Chronotherapies. Front Pharmacol 2021; 12:741295. [PMID: 34966277 PMCID: PMC8710512 DOI: 10.3389/fphar.2021.741295] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 11/25/2021] [Indexed: 02/01/2023] Open
Abstract
Circadian clocks participate in the coordination of various metabolic and biological activities to maintain homeostasis. Disturbances in the circadian rhythm and cancers are closely related. Circadian clock genes are differentially expressed in many tumors, and accelerate the development and progression of tumors. In addition, tumor tissues exert varying biological activities compared to normal tissues due to resetting of altered rhythms. Thus, chronotherapeutics used for cancer treatment should exploit the timing of circadian rhythms to achieve higher efficacy and mild toxicity. Due to interpatient differences in circadian functions, our findings advocate an individualized precision approach to chronotherapy. Herein, we review the specific association between circadian clocks and cancers. In addition, we focus on chronotherapies in cancers and personalized biomarkers for the development of precision chronotherapy. The understanding of circadian clocks in cancer will provide a rationale for more effective clinical treatment of tumors.
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Affiliation(s)
- Jingxuan Zhou
- Department of Stomatology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,School of Stomatology, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Hubei Province Key Laboratory of Oral and Maxillofacial Development and Regeneration, Wuhan, China
| | - Jiechen Wang
- Department of Stomatology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,School of Stomatology, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Hubei Province Key Laboratory of Oral and Maxillofacial Development and Regeneration, Wuhan, China
| | - Xiaozhao Zhang
- Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing, China.,Beijing Institute of Ophthalmology, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Qingming Tang
- Department of Stomatology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,School of Stomatology, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Hubei Province Key Laboratory of Oral and Maxillofacial Development and Regeneration, Wuhan, China
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36
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Kim S, McMahon DG. Light sets the brain's daily clock by regional quickening and slowing of the molecular clockworks at dawn and dusk. eLife 2021; 10:70137. [PMID: 34927581 PMCID: PMC8687663 DOI: 10.7554/elife.70137] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 12/11/2021] [Indexed: 12/15/2022] Open
Abstract
How daily clocks in the brain are set by light to local environmental time and encode the seasons is not fully understood. The suprachiasmatic nucleus (SCN) is a central circadian clock in mammals that orchestrates physiology and behavior in tune with daily and seasonal light cycles. Here, we have found that optogenetically simulated light input to explanted mouse SCN changes the waveform of the molecular clockworks from sinusoids in free-running conditions to highly asymmetrical shapes with accelerated synthetic (rising) phases and extended degradative (falling) phases marking clock advances and delays at simulated dawn and dusk. Daily waveform changes arise under ex vivo entrainment to simulated winter and summer photoperiods, and to non-24 hr periods. Ex vivo SCN imaging further suggests that acute waveform shifts are greatest in the ventrolateral SCN, while period effects are greatest in the dorsomedial SCN. Thus, circadian entrainment is encoded by SCN clock gene waveform changes that arise from spatiotemporally distinct intrinsic responses within the SCN neural network.
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Affiliation(s)
- Suil Kim
- Vanderbilt Brain Institute, Vanderbilt University, Nashville, United States
| | - Douglas G McMahon
- Vanderbilt Brain Institute, Vanderbilt University, Nashville, United States.,Department of Biological Sciences, Vanderbilt University, Nashville, United States
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Zhang S, Jiao Z, Zhao X, Sun M, Feng X. Environmental exposure to 17β-trenbolone during adolescence inhibits social interaction in male mice. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 289:117710. [PMID: 34243057 DOI: 10.1016/j.envpol.2021.117710] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 06/10/2021] [Accepted: 07/02/2021] [Indexed: 06/13/2023]
Abstract
Puberty is a critical period for growth and development. This period is sensitive to external stimuli, which ultimately affects the development of nerves and the formation of social behaviour. 17β-Trenbolone (17β-TBOH) is an endocrine disrupting chemicals (EDCs), which had been widely reported in aquatic vertebrates. But there is little known about the effects of 17β-TBOH on mammals, especially on adolescent neurodevelopment. In this study, we found that 17β-TBOH acute 1 h exposure can cause the activation of the dopamine circuit in pubertal male balb/c mice. At present, there is little known about the effects of puberty exposure of endocrine disruptors on these neurons/nerve pathways. Through a series of behavioural tests, exposure to 80 μgkg-1 d-1 of 17β-TBOH during adolescence increased the anxiety-like behaviour of mice and reduced the control of wheel-running behaviour and the response of social interaction behaviour. The results of TH immunofluorescence staining showed that exposure to 17β-TBOH reduced dopamine axon growth in the medial prefrontal cortex (mPFC). In addition, the results of real-time PCR showed that exposure to 17β-TBOH not only down-regulated the expression of dopamine axon development genes, but also affected the balance of excitatory/inhibitory signals in mPFC. In this research, we reveal the effects of 17β-TBOH exposure during adolescence on mammalian behaviour and neurodevelopment, and provide a reference for studying the origin of adolescent diseases.
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Affiliation(s)
- Shaozhi Zhang
- College of Life Science, The Key Laboratory of Bioactive Materials, Ministry of Education, State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300071, China
| | - Zihao Jiao
- The Institute of Robotics and Automatic Information Systems, Nankai University, Tianjin, 300071, China
| | - Xin Zhao
- The Institute of Robotics and Automatic Information Systems, Nankai University, Tianjin, 300071, China
| | - Mingzhu Sun
- The Institute of Robotics and Automatic Information Systems, Nankai University, Tianjin, 300071, China
| | - Xizeng Feng
- College of Life Science, The Key Laboratory of Bioactive Materials, Ministry of Education, State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300071, China.
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Brenna A, Ripperger JA, Saro G, Glauser DA, Yang Z, Albrecht U. PER2 mediates CREB-dependent light induction of the clock gene Per1. Sci Rep 2021; 11:21766. [PMID: 34741086 PMCID: PMC8571357 DOI: 10.1038/s41598-021-01178-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 10/25/2021] [Indexed: 01/05/2023] Open
Abstract
Light affects many physiological processes in mammals such as entrainment of the circadian clock, regulation of mood, and relaxation of blood vessels. At the molecular level, a stimulus such as light initiates a cascade of kinases that phosphorylate CREB at various sites, including serine 133 (S133). This modification leads CREB to recruit the co-factor CRCT1 and the histone acetyltransferase CBP to stimulate the transcription of genes containing a CRE element in their promoters, such as Period 1 (Per1). However, the details of this pathway are poorly understood. Here we provide evidence that PER2 acts as a co-factor of CREB to facilitate the formation of a transactivation complex on the CRE element of the Per1 gene regulatory region in response to light or forskolin. Using in vitro and in vivo approaches, we show that PER2 modulates the interaction between CREB and its co-regulator CRTC1 to support complex formation only after a light or forskolin stimulus. Furthermore, the absence of PER2 abolished the interaction between the histone acetyltransferase CBP and CREB. This process was accompanied by a reduction of histone H3 acetylation and decreased recruitment of RNA Pol II to the Per1 gene. Collectively, our data show that PER2 supports the stimulus-dependent induction of the Per1 gene via modulation of the CREB/CRTC1/CBP complex.
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Affiliation(s)
- Andrea Brenna
- Department of Biology, Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland.,Laboratory of Cardiovascular and Aging Research, Department of Endocrinology, Metabolism, Cardiovascular System, Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland
| | - Jürgen A Ripperger
- Department of Biology, Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland
| | - Gabriella Saro
- Department of Biology, Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland
| | - Dominique A Glauser
- Department of Biology, Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland
| | - Zhihong Yang
- Laboratory of Cardiovascular and Aging Research, Department of Endocrinology, Metabolism, Cardiovascular System, Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland
| | - Urs Albrecht
- Department of Biology, Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland.
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39
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Tabibzadeh S. CircadiOmic medicine and aging. Ageing Res Rev 2021; 71:101424. [PMID: 34389481 DOI: 10.1016/j.arr.2021.101424] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 07/22/2021] [Accepted: 08/05/2021] [Indexed: 01/15/2023]
Abstract
The earth displays daily, seasonal and annual environmental cycles that have led to evolutionarily adapted ultradian, circadian and infradian rhythmicities in the entire biosphere. All biological organisms must adapt to these cycles that synchronize the function of their circadiome. The objective of this review is to discuss the latest knowledge regarding the role of circadiomics in health and aging. The biological timekeepers are responsive to the environmental cues at microsecond to seasonal time-scales and act with precision of a clock machinery. The robustness of these rhythms is essential to normal daily function of cells, tissues and organs. Mis-alignment of circadian rhythms makes the individual prone to aging, sleep disorders, cancer, diabetes, and neuro-degenerative diseases. Circadian and CircadiOmic medicine are emerging fields that leverage our in-depth understanding of health issues, that arise as a result of disturbances in circadian rhythms, towards establishing better therapeutic approaches in personalized medicine and for geroprotection.
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Affiliation(s)
- Siamak Tabibzadeh
- Frontiers in Bioscience Research Institute in Aging and Cancer, 16471 Scientific Way, Irvine, CA 92618, United States.
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40
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Samoilova EM, Belopasov VV, Ekusheva EV, Zhang C, Troitskiy AV, Baklaushev VP. Epigenetic Clock and Circadian Rhythms in Stem Cell Aging and Rejuvenation. J Pers Med 2021; 11:1050. [PMID: 34834402 PMCID: PMC8620936 DOI: 10.3390/jpm11111050] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 10/12/2021] [Accepted: 10/14/2021] [Indexed: 12/12/2022] Open
Abstract
This review summarizes the current understanding of the interaction between circadian rhythms of gene expression and epigenetic clocks characterized by the specific profile of DNA methylation in CpG-islands which mirror the senescence of all somatic cells and stem cells in particular. Basic mechanisms of regulation for circadian genes CLOCK-BMAL1 as well as downstream clock-controlled genes (ССG) are also discussed here. It has been shown that circadian rhythms operate by the finely tuned regulation of transcription and rely on various epigenetic mechanisms including the activation of enhancers/suppressors, acetylation/deacetylation of histones and other proteins as well as DNA methylation. Overall, up to 20% of all genes expressed by the cell are subject to expression oscillations associated with circadian rhythms. Additionally included in the review is a brief list of genes involved in the regulation of circadian rhythms, along with genes important for cell aging, and oncogenesis. Eliminating some of them (for example, Sirt1) accelerates the aging process, while the overexpression of Sirt1, on the contrary, protects against age-related changes. Circadian regulators control a number of genes that activate the cell cycle (Wee1, c-Myc, p20, p21, and Cyclin D1) and regulate histone modification and DNA methylation. Approaches for determining the epigenetic age from methylation profiles across CpG islands in individual cells are described. DNA methylation, which characterizes the function of the epigenetic clock, appears to link together such key biological processes as regeneration and functioning of stem cells, aging and malignant transformation. Finally, the main features of adult stem cell aging in stem cell niches and current possibilities for modulating the epigenetic clock and stem cells rejuvenation as part of antiaging therapy are discussed.
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Affiliation(s)
- Ekaterina M. Samoilova
- Federal Research and Clinical Center of Specialized Medical Care and Medical Technologies, FMBA of Russia, 115682 Moscow, Russia; (A.V.T.); (V.P.B.)
| | | | - Evgenia V. Ekusheva
- Academy of Postgraduate Education of the Federal Scientific and Clinical Center for Specialized Types of Medical Care and Medical Technologies, FMBA of Russia, 125371 Moscow, Russia;
| | - Chao Zhang
- Tianjin’s Clinical Research Center for Cancer, Tianjin 300060, China;
| | - Alexander V. Troitskiy
- Federal Research and Clinical Center of Specialized Medical Care and Medical Technologies, FMBA of Russia, 115682 Moscow, Russia; (A.V.T.); (V.P.B.)
| | - Vladimir P. Baklaushev
- Federal Research and Clinical Center of Specialized Medical Care and Medical Technologies, FMBA of Russia, 115682 Moscow, Russia; (A.V.T.); (V.P.B.)
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Bertucci EM, Mason MW, Rhodes OE, Parrott BB. Exposure to ionizing radiation disrupts normal epigenetic aging in Japanese medaka. Aging (Albany NY) 2021; 13:22752-22771. [PMID: 34644261 PMCID: PMC8544305 DOI: 10.18632/aging.203624] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 09/03/2021] [Indexed: 02/06/2023]
Abstract
Alterations to the epigenome are a hallmark of biological aging and age-dependent patterning of the DNA methylome ("epigenetic aging") can be modeled to produce epigenetic age predictors. Rates of epigenetic aging vary amongst individuals and correlate to the onset of age-related disease and all-cause mortality. Yet, the origins of epigenetic-to-chronological age discordance are not empirically resolved. Here, we investigate the relationship between aging, DNA methylation, and environmental exposures in Japanese medaka (Oryzias latipes). We find age-associated DNA methylation patterning enriched in genomic regions of low CpG density and that, similar to mammals, most age-related changes occur during early life. We construct an epigenetic clock capable of predicting chronological age with a mean error of 61.1 days (~8.4% of average lifespan). To test the role of environmental factors in driving epigenetic age variation, we exposed medaka to chronic, environmentally relevant doses of ionizing radiation. Because most organisms share an evolutionary history with ionizing radiation, we hypothesized that exposure would reveal fundamental insights into environment-by-epigenetic aging interactions. Radiation exposure disrupted epigenetic aging by accelerating and decelerating normal age-associated patterning and was most pronounced in cytosines that were moderately associated with age. These findings empirically demonstrate the role of DNA methylation in integrating environmental factors into aging trajectories.
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Affiliation(s)
- Emily M. Bertucci
- Odum School of Ecology, University of Georgia, Athens, GA 30602, USA
- Savannah River Ecology Laboratory, University of Georgia, Aiken, SC 29802, USA
| | - Marilyn W. Mason
- Savannah River Ecology Laboratory, University of Georgia, Aiken, SC 29802, USA
| | - Olin E. Rhodes
- Odum School of Ecology, University of Georgia, Athens, GA 30602, USA
- Savannah River Ecology Laboratory, University of Georgia, Aiken, SC 29802, USA
| | - Benjamin B. Parrott
- Odum School of Ecology, University of Georgia, Athens, GA 30602, USA
- Savannah River Ecology Laboratory, University of Georgia, Aiken, SC 29802, USA
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42
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Buck JM, Yu L, Knopik VS, Stitzel JA. DNA methylome perturbations: an epigenetic basis for the emergingly heritable neurodevelopmental abnormalities associated with maternal smoking and maternal nicotine exposure†. Biol Reprod 2021; 105:644-666. [PMID: 34270696 PMCID: PMC8444709 DOI: 10.1093/biolre/ioab138] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 06/29/2021] [Accepted: 07/14/2021] [Indexed: 11/13/2022] Open
Abstract
Maternal smoking during pregnancy is associated with an ensemble of neurodevelopmental consequences in children and therefore constitutes a pressing public health concern. Adding to this burden, contemporary epidemiological and especially animal model research suggests that grandmaternal smoking is similarly associated with neurodevelopmental abnormalities in grandchildren, indicative of intergenerational transmission of the neurodevelopmental impacts of maternal smoking. Probing the mechanistic bases of neurodevelopmental anomalies in the children of maternal smokers and the intergenerational transmission thereof, emerging research intimates that epigenetic changes, namely DNA methylome perturbations, are key factors. Altogether, these findings warrant future research to fully elucidate the etiology of neurodevelopmental impairments in the children and grandchildren of maternal smokers and underscore the clear potential thereof to benefit public health by informing the development and implementation of preventative measures, prophylactics, and treatments. To this end, the present review aims to encapsulate the burgeoning evidence linking maternal smoking to intergenerational epigenetic inheritance of neurodevelopmental abnormalities, to identify the strengths and weaknesses thereof, and to highlight areas of emphasis for future human and animal model research therein.
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Affiliation(s)
- Jordan M Buck
- Institute for Behavioral Genetics, University of Colorado Boulder, Boulder, CO, USA
- Department of Integrative Physiology, University of Colorado, Boulder, Boulder, CO, USA
| | - Li Yu
- Department of Human Development and Family Studies, Purdue University, West Lafayette, IN, USA
| | - Valerie S Knopik
- Department of Human Development and Family Studies, Purdue University, West Lafayette, IN, USA
| | - Jerry A Stitzel
- Institute for Behavioral Genetics, University of Colorado Boulder, Boulder, CO, USA
- Department of Integrative Physiology, University of Colorado, Boulder, Boulder, CO, USA
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43
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Saad L, Zwiller J, Kalsbeek A, Anglard P. Epigenetic Regulation of Circadian Clocks and Its Involvement in Drug Addiction. Genes (Basel) 2021; 12:1263. [PMID: 34440437 PMCID: PMC8394526 DOI: 10.3390/genes12081263] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 08/04/2021] [Accepted: 08/11/2021] [Indexed: 12/19/2022] Open
Abstract
Based on studies describing an increased prevalence of addictive behaviours in several rare sleep disorders and shift workers, a relationship between circadian rhythms and addiction has been hinted for more than a decade. Although circadian rhythm alterations and molecular mechanisms associated with neuropsychiatric conditions are an area of active investigation, success is limited so far, and further investigations are required. Thus, even though compelling evidence connects the circadian clock to addictive behaviour and vice-versa, yet the functional mechanism behind this interaction remains largely unknown. At the molecular level, multiple mechanisms have been proposed to link the circadian timing system to addiction. The molecular mechanism of the circadian clock consists of a transcriptional/translational feedback system, with several regulatory loops, that are also intricately regulated at the epigenetic level. Interestingly, the epigenetic landscape shows profound changes in the addictive brain, with significant alterations in histone modification, DNA methylation, and small regulatory RNAs. The combination of these two observations raises the possibility that epigenetic regulation is a common plot linking the circadian clocks with addiction, though very little evidence has been reported to date. This review provides an elaborate overview of the circadian system and its involvement in addiction, and we hypothesise a possible connection at the epigenetic level that could further link them. Therefore, we think this review may further improve our understanding of the etiology or/and pathology of psychiatric disorders related to drug addiction.
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Affiliation(s)
- Lamis Saad
- Laboratoire de Neurosciences Cognitives et Adaptatives (LNCA), UMR 7364 CNRS, Université de Strasbourg, Neuropôle de Strasbourg, 67000 Strasbourg, France; (L.S.); (J.Z.)
- The Netherlands Institute for Neuroscience (NIN), Royal Netherlands Academy of Arts and Sciences (KNAW), 1105 BA Amsterdam, The Netherlands;
- Department of Endocrinology and Metabolism, Amsterdam University Medical Center, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
| | - Jean Zwiller
- Laboratoire de Neurosciences Cognitives et Adaptatives (LNCA), UMR 7364 CNRS, Université de Strasbourg, Neuropôle de Strasbourg, 67000 Strasbourg, France; (L.S.); (J.Z.)
- Centre National de la Recherche Scientifique (CNRS), 75016 Paris, France
| | - Andries Kalsbeek
- The Netherlands Institute for Neuroscience (NIN), Royal Netherlands Academy of Arts and Sciences (KNAW), 1105 BA Amsterdam, The Netherlands;
- Department of Endocrinology and Metabolism, Amsterdam University Medical Center, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
| | - Patrick Anglard
- Laboratoire de Neurosciences Cognitives et Adaptatives (LNCA), UMR 7364 CNRS, Université de Strasbourg, Neuropôle de Strasbourg, 67000 Strasbourg, France; (L.S.); (J.Z.)
- Institut National de la Santé et de la Recherche Médicale (INSERM), 75013 Paris, France
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44
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Abstract
Circadian rhythms, present in most phyla across life, are biological oscillations occurring on a daily cycle. Since the discovery of their molecular foundations in model organisms, many inputs that modify this tightly controlled system in humans have been identified. Polygenic variations and environmental factors influence each person's circadian rhythm, contributing to the trait known as chronotype, which manifests as the degree of morning or evening preference in an individual. Despite normal variation in chronotype, much of society operates on a "one size fits all" schedule that can be difficult to adjust to, especially for certain individuals whose endogenous circadian phase is extremely advanced or delayed. This is a public health concern, as phase misalignment in humans is associated with a number of adverse health outcomes. Additionally, modern technology (such as electric lights and computer, tablet, and phone screens that emit blue light) and lifestyles (such as shift or irregular work schedules) are disrupting circadian consistency in an increasing number of people. Though medical and lifestyle interventions can alleviate some of these issues, growing research on endogenous circadian variability and sensitivity suggests that broader social changes may be necessary to minimize the impact of circadian misalignment on health.
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Affiliation(s)
| | | | - Ying-Hui Fu
- Department of Neurology
- Institute for Human Genetics
- Weill Institute for Neurosciences, and
- Kavli Institute for Fundamental Neuroscience, UCSF, San Francisco, California, USA
| | - Louis J. Ptáček
- Department of Neurology
- Institute for Human Genetics
- Weill Institute for Neurosciences, and
- Kavli Institute for Fundamental Neuroscience, UCSF, San Francisco, California, USA
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45
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Abstract
Epigenetics has enriched human disease studies by adding new interpretations to disease features that cannot be explained by genetic and environmental factors. However, identifying causal mechanisms of epigenetic origin has been challenging. New opportunities have risen from recent findings in intra-individual and cyclical epigenetic variation, which includes circadian epigenetic oscillations. Cytosine modifications display deterministic temporal rhythms, which may drive ageing and complex disease. Temporality in the epigenome, or the 'chrono' dimension, may help the integration of epigenetic, environmental and genetic disease studies, and reconcile several disparities stemming from the arbitrarily delimited research fields. The ultimate goal of chrono-epigenetics is to predict disease risk, age of onset and disease dynamics from within individual-specific temporal dynamics of epigenomes.
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The effect of season of birth on brain epigenome-wide DNA methylation of older adults. J Dev Orig Health Dis 2021; 13:367-377. [PMID: 34308828 DOI: 10.1017/s2040174421000453] [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] [Indexed: 11/07/2022]
Abstract
Perinatal light exposure predisposes towards health and behaviour in adulthood. Season of birth is associated with psychiatric, allergic, cardiovascular and metabolic problems. It has been proposed that early-life environmental light disrupts the development of biological rhythms which, in turn, influence later-life health. However, the mechanisms linking perinatal seasonal light to later-life biological rhythm and health in humans are unknown. In this study, we investigated the association between season of birth and epigenome-wide DNA methylation of two postmortem human brain regions (16 hypothalamus, 14 temporal cortex). We did not find statistically significant differences at the whole epigenome level, either because we lacked statistical power or that no association exists. However, when we examined 24 CpG sites that had the highest significance or differential methylation, we identified regions which may be associated with circadian rhythm entrainment, cholinergic neurotransmission and neural development. Amongst methylation of the core clock genes, we identified that hypothalamus Neuronal PAS Domain Protein 2 (NPAS2) gene has hypermethylated regions in long photoperiod-born individuals. In addition, we found nominal associations between season of birth and genes linked to chronotype and narcolepsy. Season of birth-related brain DNA methylation profile was different than a previously reported blood methylation profile, suggesting a tissue-specific mechanism of perinatal light programming. Overall, we are the first to analyse the relationship between season of birth and human brain DNA methylation. Further studies with larger sample sizes are required to confirm an imprinting effect of perinatal light on the circadian clock.
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47
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Sato T, Greco CM. Expanding the link between circadian rhythms and redox metabolism of epigenetic control. Free Radic Biol Med 2021; 170:50-58. [PMID: 33450380 DOI: 10.1016/j.freeradbiomed.2021.01.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 12/23/2020] [Accepted: 01/06/2021] [Indexed: 12/13/2022]
Abstract
Circadian rhythms play a central role in physiological and metabolic processes. This is mostly achieved through rhythmic regulation of myriad genes via dynamic epigenome changes. Accumulating evidence indicates that oxidative stress and redox balance are under circadian control and feedback on the clock system. Circadian perturbations induce oxidative stress accumulation and disturb redox balance. Along with these changes, epigenomic landscape changes are a remarkable hallmark of clock disruption. This review aims to summarize evidence supporting the link between the circadian clock and redox metabolism, focusing on possible connections through epigenetic mechanisms.
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Affiliation(s)
- Tomoki Sato
- Department of Biological Chemistry, Center for Epigenetics and Metabolism, School of Medicine, University of California, Irvine, CA, 92697, USA
| | - Carolina Magdalen Greco
- Department of Biological Chemistry, Center for Epigenetics and Metabolism, School of Medicine, University of California, Irvine, CA, 92697, USA.
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48
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Bano-Otalora B, Martial F, Harding C, Bechtold DA, Allen AE, Brown TM, Belle MDC, Lucas RJ. Bright daytime light enhances circadian amplitude in a diurnal mammal. Proc Natl Acad Sci U S A 2021; 118:e2100094118. [PMID: 34031246 PMCID: PMC8179182 DOI: 10.1073/pnas.2100094118] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Mammalian circadian rhythms are orchestrated by a master pacemaker in the hypothalamic suprachiasmatic nuclei (SCN), which receives information about the 24 h light-dark cycle from the retina. The accepted function of this light signal is to reset circadian phase in order to ensure appropriate synchronization with the celestial day. Here, we ask whether light also impacts another key property of the circadian oscillation, its amplitude. To this end, we measured circadian rhythms in behavioral activity, body temperature, and SCN electrophysiological activity in the diurnal murid rodent Rhabdomys pumilio following stable entrainment to 12:12 light-dark cycles at four different daytime intensities (ranging from 18 to 1,900 lx melanopic equivalent daylight illuminance). R. pumilio showed strongly diurnal activity and body temperature rhythms in all conditions, but measures of rhythm robustness were positively correlated with daytime irradiance under both entrainment and subsequent free run. Whole-cell and extracellular recordings of electrophysiological activity in ex vivo SCN revealed substantial differences in electrophysiological activity between dim and bright light conditions. At lower daytime irradiance, daytime peaks in SCN spontaneous firing rate and membrane depolarization were substantially depressed, leading to an overall marked reduction in the amplitude of circadian rhythms in spontaneous activity. Our data reveal a previously unappreciated impact of daytime light intensity on SCN physiology and the amplitude of circadian rhythms and highlight the potential importance of daytime light exposure for circadian health.
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Affiliation(s)
- Beatriz Bano-Otalora
- Centre for Biological Timing, Faculty of Biology Medicine and Health, University of Manchester, Manchester M13 9PT, United Kingdom
- Division of Neuroscience and Experimental Psychology, Faculty of Biology Medicine and Health, University of Manchester, Manchester M13 9PT, United Kingdom
| | - Franck Martial
- Division of Neuroscience and Experimental Psychology, Faculty of Biology Medicine and Health, University of Manchester, Manchester M13 9PT, United Kingdom
| | - Court Harding
- Division of Neuroscience and Experimental Psychology, Faculty of Biology Medicine and Health, University of Manchester, Manchester M13 9PT, United Kingdom
| | - David A Bechtold
- Centre for Biological Timing, Faculty of Biology Medicine and Health, University of Manchester, Manchester M13 9PT, United Kingdom
- Division of Diabetes, Endocrinology and Gastroenterology, Faculty of Biology Medicine and Health, University of Manchester, Manchester M13 9PT, United Kingdom
| | - Annette E Allen
- Centre for Biological Timing, Faculty of Biology Medicine and Health, University of Manchester, Manchester M13 9PT, United Kingdom
- Division of Neuroscience and Experimental Psychology, Faculty of Biology Medicine and Health, University of Manchester, Manchester M13 9PT, United Kingdom
| | - Timothy M Brown
- Centre for Biological Timing, Faculty of Biology Medicine and Health, University of Manchester, Manchester M13 9PT, United Kingdom
- Division of Diabetes, Endocrinology and Gastroenterology, Faculty of Biology Medicine and Health, University of Manchester, Manchester M13 9PT, United Kingdom
| | - Mino D C Belle
- Institute of Biomedical and Clinical Sciences, University of Exeter Medical School, University of Exeter, Exeter EX4 4PS, United Kingdom
| | - Robert J Lucas
- Centre for Biological Timing, Faculty of Biology Medicine and Health, University of Manchester, Manchester M13 9PT, United Kingdom
- Division of Neuroscience and Experimental Psychology, Faculty of Biology Medicine and Health, University of Manchester, Manchester M13 9PT, United Kingdom
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49
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Forsburg ZR, Guzman A, Gabor CR. Artificial light at night (ALAN) affects the stress physiology but not the behavior or growth of Rana berlandieri and Bufo valliceps. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 277:116775. [PMID: 33639600 DOI: 10.1016/j.envpol.2021.116775] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 02/03/2021] [Accepted: 02/16/2021] [Indexed: 06/12/2023]
Abstract
Artificial light at night (ALAN) alters the natural light dark patterns in ecosystems. ALAN can have a suite of effects on community structure and is a driver of evolutionary processes that influences a range of behavioral and physiological traits. Our understanding of possible effects of ALAN across species amphibians is lacking and research is warranted as ALAN could contribute to stress and declines of amphibian populations, particularly in urban areas. We tested the hypothesis that exposure to constant light or pulsed ALAN would physiologically stress Rio Grande leopard frog (Rana berlandieri) and Gulf Coast toad (Bufo valliceps) tadpoles. We reared tadpoles under constant or pulsed (on and off again) ALAN for 14 days and measured corticosterone release rates over time using a non-invasive water-borne hormone protocol. ALAN treatments did not affect behavior or growth. Tadpoles of both species had higher corticosterone (cort) release rates after 14 days of constant light exposure. Leopard frog tadpoles had lower cort release rates after exposure to pulsed ALAN while toad tadpoles had higher cort release rates. These results suggest that short-term exposure to constant or pulsed light at night may contribute to stress in tadpoles but that each species differentially modulated their cort response to ALAN exposure and a subsequent stressor. This flexibility in the upregulation and downregulation of hypothalamic-pituitary-interrenal axis response may indicate an alternative mechanism for diminishing the deleterious effects of chronic stress. Nonetheless, ALAN should be considered in management and conservation plans for amphibians.
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Affiliation(s)
- Zachery R Forsburg
- Department of Biology, Texas State University, San Marcos, TX, 78666, USA.
| | - Alex Guzman
- Department of Biology, Texas State University, San Marcos, TX, 78666, USA
| | - Caitlin R Gabor
- Department of Biology, Texas State University, San Marcos, TX, 78666, USA
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50
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Tian W, Wang R, Bo C, Yu Y, Zhang Y, Shin GI, Kim WY, Wang L. SDC mediates DNA methylation-controlled clock pace by interacting with ZTL in Arabidopsis. Nucleic Acids Res 2021; 49:3764-3780. [PMID: 33675668 PMCID: PMC8053106 DOI: 10.1093/nar/gkab128] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 02/13/2021] [Accepted: 02/16/2021] [Indexed: 12/29/2022] Open
Abstract
Molecular bases of eukaryotic circadian clocks mainly rely on transcriptional-translational feedback loops (TTFLs), while epigenetic codes also play critical roles in fine-tuning circadian rhythms. However, unlike histone modification codes that play extensive and well-known roles in the regulation of circadian clocks, whether DNA methylation (5mC) can affect the circadian clock, and the associated underlying molecular mechanisms, remains largely unexplored in many organisms. Here we demonstrate that global genome DNA hypomethylation can significantly lengthen the circadian period of Arabidopsis. Transcriptomic and genetic evidence demonstrate that SUPPRESSOR OF drm1 drm2 cmt3 (SDC), encoding an F-box containing protein, is required for the DNA hypomethylation-tuned circadian clock. Moreover, SDC can physically interact with another F-box containing protein ZEITLUPE (ZTL) to diminish its accumulation. Genetic analysis further revealed that ZTL and its substrate TIMING OF CAB EXPRESSION 1 (TOC1) likely act downstream of DNA methyltransferases to control circadian rhythm. Together, our findings support the notion that DNA methylation is important to maintain proper circadian pace in Arabidopsis, and further established that SDC links DNA hypomethylation with a proteolytic cascade to assist in tuning the circadian clock.
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Affiliation(s)
- Wenwen Tian
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, People's Republic of China.,University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Ruyi Wang
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, People's Republic of China
| | - Cunpei Bo
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, People's Republic of China.,University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Yingjun Yu
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, People's Republic of China.,University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Yuanyuan Zhang
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, People's Republic of China
| | - Gyeong-Im Shin
- Division of Applied Life Science (BK21Plus), Research Institute of Life Sciences (RILS) and Institute of Agricultural and Life Science(IALS), Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Woe-Yeon Kim
- Division of Applied Life Science (BK21Plus), Research Institute of Life Sciences (RILS) and Institute of Agricultural and Life Science(IALS), Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Lei Wang
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, People's Republic of China.,University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
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