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Li M, Yin Y, Qin D. Treadmill training impacts the skeletal muscle molecular clock after ischemia stroke in rats. Heliyon 2024; 10:e27430. [PMID: 38509905 PMCID: PMC10951531 DOI: 10.1016/j.heliyon.2024.e27430] [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: 05/14/2023] [Revised: 02/27/2024] [Accepted: 02/28/2024] [Indexed: 03/22/2024] Open
Abstract
Objective Stroke is frequently associated with muscle mass loss. Treadmill training is considered the most effective treatment for sarcopenia. Circadian rhythms are closely related to exercise and have been extensively studied. The skeletal muscle has its molecular clock genes. Exercise may regulate skeletal muscle clock genes. This study evaluated the effects of early treadmill training on the skeletal muscle molecular clock machinery in rats with stroke and determined the relationship of these changes with exercise-induced improvements in skeletal muscle health. Materials and methods Overall, 168 Sprague-Dawley rats were included in this study. We established an ischemic stroke rat model of sarcopenia. Finally, 144 rats were randomly allocated to four groups (36 per group): normal, sham, middle cerebral artery occlusion, and training. Neurological scores, rotating rod test, body weight, muscle circumference, wet weight, and hematoxylin-eosin staining were assessed. Twenty-four rats were used for transcriptome sequencing. Gene and protein expressions of skeletal muscles, such as brain muscle arnt-like 1, period 1, and period 2, were measured by quantitative real-time polymerase chain reaction and enzyme-linked immunosorbent assays. Results Neurological function scores and rotating rod test results improved after treadmill training. Nine differentially expressed genes were identified by comparing the sham group with the hemiplegic side of the model group. Seventeen differentially expressed genes were identified between the hemiplegic and non-hemiplegic sides. BMAL1, PER1, and PER2 mRNA levels increased on both sides after treadmill training. BMAL1 expression increased, and PER1 expression decreased on both sides, whereas PER2 expression decreased on the hemiplegic side but increased on the non-hemiplegic side. Conclusion Treadmill training can mitigate muscle loss and regulate skeletal muscle clock gene expression following ischemic stroke. Exercise affects the hemiplegic side and has a positive regulatory effect on the non-hemiplegic side.
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Affiliation(s)
- Mai Li
- Department of Rehabilitation Medicine, The Second Affiliated Hospital of Kunming Medical University, No. 374, Fengning Street, Dianmian Road, 650101, Kunming, China
| | - Yong Yin
- Department of Rehabilitation Medicine, The Affiliated Hospital of Yunnan University, No. 176, Qingnian Road, 650021, Kunming, China
| | - Dongdong Qin
- School of Basic Medical Sciences, Yunnan University of Chinese Medicine, No. 1076 Yuhua Road, Chenggong District, 650500, Kunming, China
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Xue Z, Gao B, Chen G, Liu J, Ouyang W, Foda MF, Zhang Q, Zhang X, Zhang W, Guo M, Li X, Yi B. Diurnal oscillations of epigenetic modifications are associated with variation in rhythmic expression of homoeologous genes in Brassica napus. BMC Biol 2023; 21:241. [PMID: 37907908 PMCID: PMC10617162 DOI: 10.1186/s12915-023-01735-7] [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: 05/18/2023] [Accepted: 10/12/2023] [Indexed: 11/02/2023] Open
Abstract
BACKGROUND Epigenetic modifications that exhibit circadian oscillations also promote circadian oscillations of gene expression. Brassica napus is a heterozygous polyploid species that has undergone distant hybridization and genome doubling events and has a young and distinct species origin. Studies incorporating circadian rhythm analysis of epigenetic modifications can offer new insights into differences in diurnal oscillation behavior among subgenomes and the regulation of diverse expressions of homologous gene rhythms in biological clocks. RESULTS In this study, we created a high-resolution and multioscillatory gene expression dataset, active histone modification (H3K4me3, H3K9ac), and RNAPII recruitment in Brassica napus. We also conducted the pioneering characterization of the diurnal rhythm of transcription and epigenetic modifications in an allopolyploid species. We compared the evolution of diurnal rhythms between subgenomes and observed that the Cn subgenome had higher diurnal oscillation activity in both transcription and active histone modifications than the An subgenome. Compared to the A subgenome in Brassica rapa, the An subgenome of Brassica napus displayed significant changes in diurnal oscillation characteristics of transcription. Homologous gene pairs exhibited a higher proportion of diurnal oscillation in transcription than subgenome-specific genes, attributed to higher chromatin accessibility and abundance of active epigenetic modification types. We found that the diurnal expression of homologous genes displayed diversity, and the redundancy of the circadian system resulted in extensive changes in the diurnal rhythm characteristics of clock genes after distant hybridization and genome duplication events. Epigenetic modifications influenced the differences in the diurnal rhythm of homologous gene expression, and the diurnal oscillation of homologous gene expression was affected by the combination of multiple histone modifications. CONCLUSIONS Herein, we presented, for the first time, a characterization of the diurnal rhythm characteristics of gene expression and its epigenetic modifications in an allopolyploid species. Our discoveries shed light on the epigenetic factors responsible for the diurnal oscillation activity imbalance between subgenomes and homologous genes' rhythmic expression differences. The comprehensive time-series dataset we generated for gene expression and epigenetic modifications provides a valuable resource for future investigations into the regulatory mechanisms of protein-coding genes in Brassica napus.
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Affiliation(s)
- Zhifei Xue
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Baibai Gao
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Guoting Chen
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Jie Liu
- Lushan Botanical Garden Jiangxi Province and Chinese Academy of Sciences, Jiujiang, 332900, Jiangxi, China
| | - Weizhi Ouyang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Mohamed Frahat Foda
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
- Department of Biochemistry, Faculty of Agriculture, Benha University, Toukh, 13736, Qalyubiyya, Egypt
| | - Qing Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Xiwen Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Wei Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Mingyue Guo
- College of Informatics, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Xingwang Li
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.
| | - Bin Yi
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.
- National Engineering Research Center of Rapeseed, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.
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3
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Salminen A. Aryl hydrocarbon receptor (AhR) impairs circadian regulation: impact on the aging process. Ageing Res Rev 2023; 87:101928. [PMID: 37031728 DOI: 10.1016/j.arr.2023.101928] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 03/23/2023] [Accepted: 04/06/2023] [Indexed: 04/11/2023]
Abstract
Circadian clocks control the internal sleep-wake rhythmicity of 24hours which is synchronized by the solar cycle. Circadian regulation of metabolism evolved about 2.5 billion years ago, i.e., the rhythmicity has been conserved from cyanobacteria and Archaea through to mammals although the mechanisms utilized have developed with evolution. While the aryl hydrocarbon receptor (AhR) is an evolutionarily conserved defence mechanism against environmental threats, it has gained many novel functions during evolution, such as the regulation of cell cycle, proteostasis, and many immune functions. There is robust evidence that AhR signaling impairs circadian rhythmicity, e.g., by interacting with the core BMAL1/CLOCK complex and disturbing the epigenetic regulation of clock genes. The maintenance of circadian rhythms is impaired with aging, disturbing metabolism and many important functions in aged organisms. Interestingly, it is known that AhR signaling promotes an age-related tissue degeneration, e.g., it is able to inhibit autophagy, enhance cellular senescence, and disrupt extracellular matrix. These alterations are rather similar to those induced by a long-term impairment of circadian rhythms. However, it is not known whether AhR signaling enhances the aging process by impairing circadian homeostasis. I will examine the experimental evidence indicating that AhR signaling is able to promote the age-related degeneration via a disruption of circadian rhythmicity.
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Affiliation(s)
- Antero Salminen
- Department of Neurology, Institute of Clinical Medicine, University of Eastern Finland, P.O. Box 1627, FI-70211 Kuopio, Finland.
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4
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Qin Y, Chen ZH, Wu JJ, Zhang ZY, Yuan ZD, Guo DY, Chen MN, Li X, Yuan FL. Circadian clock genes as promising therapeutic targets for bone loss. Biomed Pharmacother 2023; 157:114019. [PMID: 36423544 DOI: 10.1016/j.biopha.2022.114019] [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: 09/21/2022] [Revised: 11/11/2022] [Accepted: 11/13/2022] [Indexed: 11/22/2022] Open
Abstract
The circadian clock regulates many key physiological processes such as the sleep-wake cycle, hormone release, cardiovascular health, glucose metabolism and body temperature. Recent evidence has suggested a critical role of the circadian system in controlling bone metabolism. Here we review the connection between bone metabolism and the biological clock, and the roles of these mechanisms in bone loss. We also analyze the regulatory effects of clock-related genes on signaling pathways and transcription factors in osteoblasts and osteoclasts. Additionally, osteocytes and endothelial cells (ECs) regulated by the circadian clock are also discussed in our review. Furthermore, we also summarize the regulation of circadian clock genes by some novel modulators, which provides us with a new insight into a potential strategy to prevent and treat bone diseases such as osteoporosis by targeting circadian genes.
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Affiliation(s)
- Yi Qin
- Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Zhong-Hua Chen
- Institute of Integrated Chinese and Western Medicine, The Hospital Affiliated to Jiangnan University, Wuxi, Jiangsu 214041, China
| | - Jun-Jie Wu
- Institute of Integrated Chinese and Western Medicine, The Hospital Affiliated to Jiangnan University, Wuxi, Jiangsu 214041, China
| | - Zhen-Yu Zhang
- Institute of Integrated Chinese and Western Medicine, The Hospital Affiliated to Jiangnan University, Wuxi, Jiangsu 214041, China
| | - Zheng-Dong Yuan
- Institute of Integrated Chinese and Western Medicine, The Hospital Affiliated to Jiangnan University, Wuxi, Jiangsu 214041, China
| | - Dan-Yang Guo
- Institute of Integrated Chinese and Western Medicine, The Hospital Affiliated to Jiangnan University, Wuxi, Jiangsu 214041, China
| | - Meng-Nan Chen
- Institute of Integrated Chinese and Western Medicine, The Hospital Affiliated to Jiangnan University, Wuxi, Jiangsu 214041, China
| | - Xia Li
- Institute of Integrated Chinese and Western Medicine, The Hospital Affiliated to Jiangnan University, Wuxi, Jiangsu 214041, China.
| | - Feng-Lai Yuan
- Institute of Integrated Chinese and Western Medicine, The Hospital Affiliated to Jiangnan University, Wuxi, Jiangsu 214041, China.
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5
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Davis W, Endo M, Locke JCW. Spatially specific mechanisms and functions of the plant circadian clock. PLANT PHYSIOLOGY 2022; 190:938-951. [PMID: 35640123 PMCID: PMC9516738 DOI: 10.1093/plphys/kiac236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 04/22/2022] [Indexed: 06/15/2023]
Abstract
Like many organisms, plants have evolved a genetic network, the circadian clock, to coordinate processes with day/night cycles. In plants, the clock is a pervasive regulator of development and modulates many aspects of physiology. Clock-regulated processes range from the correct timing of growth and cell division to interactions with the root microbiome. Recently developed techniques, such as single-cell time-lapse microscopy and single-cell RNA-seq, are beginning to revolutionize our understanding of this clock regulation, revealing a surprising degree of organ, tissue, and cell-type specificity. In this review, we highlight recent advances in our spatial view of the clock across the plant, both in terms of how it is regulated and how it regulates a diversity of output processes. We outline how understanding these spatially specific functions will help reveal the range of ways that the clock provides a fitness benefit for the plant.
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Affiliation(s)
- William Davis
- Sainsbury Laboratory, University of Cambridge, Cambridge, UK
| | - Motomu Endo
- Authors for correspondence: (M.E.); (J.C.W.L.)
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6
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Sun C, Liu S, He C, Zhong C, Liu H, Luo X, Li K, Zhang K, Wang Q, Chen C, Tang Y, Yang B, Chen X, Xu P, Zou T, Li S, Qin P, Wang P, Chu C, Deng X. Crosstalk between the Circadian Clock and Histone Methylation. Int J Mol Sci 2022; 23:ijms23126465. [PMID: 35742907 PMCID: PMC9224359 DOI: 10.3390/ijms23126465] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 06/02/2022] [Accepted: 06/08/2022] [Indexed: 02/05/2023] Open
Abstract
The circadian clock and histone modifications could form a feedback loop in Arabidopsis; whether a similar regulatory mechanism exists in rice is still unknown. Previously, we reported that SDG724 and OsLHY are two rice heading date regulators in rice. SDG724 encodes a histone H3K36 methyltransferase, and OsLHY is a vital circadian rhythm transcription factor. Both could be involved in transcription regulatory mechanisms and could affect gene expression in various pathways. To explore the crosstalk between the circadian clock and histone methylation in rice, we studied the relationship between OsLHY and SDG724 via the transcriptome analysis of their single and double mutants, oslhy, sdg724, and oslhysdg724. Screening of overlapped DEGs and KEGG pathways between OsLHY and SDG724 revealed that they could control many overlapped pathways indirectly. Furthermore, we identified three candidate targets (OsGI, OsCCT38, and OsPRR95) of OsLHY and one candidate target (OsCRY1a) of SDG724 in the clock pathway. Our results showed a regulatory relationship between OsLHY and SDG724, which paved the way for revealing the interaction between the circadian clock and histone H3K36 methylation.
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Affiliation(s)
- Changhui Sun
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (S.L.); (C.H.); (C.Z.); (H.L.); (X.L.); (K.L.); (K.Z.); (Q.W.); (C.C.); (Y.T.); (B.Y.); (X.C.); (P.X.); (T.Z.); (S.L.); (P.Q.); (P.W.)
- Correspondence: (C.S.); (X.D.)
| | - Shihang Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (S.L.); (C.H.); (C.Z.); (H.L.); (X.L.); (K.L.); (K.Z.); (Q.W.); (C.C.); (Y.T.); (B.Y.); (X.C.); (P.X.); (T.Z.); (S.L.); (P.Q.); (P.W.)
| | - Changcai He
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (S.L.); (C.H.); (C.Z.); (H.L.); (X.L.); (K.L.); (K.Z.); (Q.W.); (C.C.); (Y.T.); (B.Y.); (X.C.); (P.X.); (T.Z.); (S.L.); (P.Q.); (P.W.)
| | - Chao Zhong
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (S.L.); (C.H.); (C.Z.); (H.L.); (X.L.); (K.L.); (K.Z.); (Q.W.); (C.C.); (Y.T.); (B.Y.); (X.C.); (P.X.); (T.Z.); (S.L.); (P.Q.); (P.W.)
| | - Hongying Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (S.L.); (C.H.); (C.Z.); (H.L.); (X.L.); (K.L.); (K.Z.); (Q.W.); (C.C.); (Y.T.); (B.Y.); (X.C.); (P.X.); (T.Z.); (S.L.); (P.Q.); (P.W.)
| | - Xu Luo
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (S.L.); (C.H.); (C.Z.); (H.L.); (X.L.); (K.L.); (K.Z.); (Q.W.); (C.C.); (Y.T.); (B.Y.); (X.C.); (P.X.); (T.Z.); (S.L.); (P.Q.); (P.W.)
| | - Ke Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (S.L.); (C.H.); (C.Z.); (H.L.); (X.L.); (K.L.); (K.Z.); (Q.W.); (C.C.); (Y.T.); (B.Y.); (X.C.); (P.X.); (T.Z.); (S.L.); (P.Q.); (P.W.)
| | - Kuan Zhang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (S.L.); (C.H.); (C.Z.); (H.L.); (X.L.); (K.L.); (K.Z.); (Q.W.); (C.C.); (Y.T.); (B.Y.); (X.C.); (P.X.); (T.Z.); (S.L.); (P.Q.); (P.W.)
| | - Qian Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (S.L.); (C.H.); (C.Z.); (H.L.); (X.L.); (K.L.); (K.Z.); (Q.W.); (C.C.); (Y.T.); (B.Y.); (X.C.); (P.X.); (T.Z.); (S.L.); (P.Q.); (P.W.)
| | - Congping Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (S.L.); (C.H.); (C.Z.); (H.L.); (X.L.); (K.L.); (K.Z.); (Q.W.); (C.C.); (Y.T.); (B.Y.); (X.C.); (P.X.); (T.Z.); (S.L.); (P.Q.); (P.W.)
| | - Yulin Tang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (S.L.); (C.H.); (C.Z.); (H.L.); (X.L.); (K.L.); (K.Z.); (Q.W.); (C.C.); (Y.T.); (B.Y.); (X.C.); (P.X.); (T.Z.); (S.L.); (P.Q.); (P.W.)
| | - Bin Yang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (S.L.); (C.H.); (C.Z.); (H.L.); (X.L.); (K.L.); (K.Z.); (Q.W.); (C.C.); (Y.T.); (B.Y.); (X.C.); (P.X.); (T.Z.); (S.L.); (P.Q.); (P.W.)
| | - Xiaoqiong Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (S.L.); (C.H.); (C.Z.); (H.L.); (X.L.); (K.L.); (K.Z.); (Q.W.); (C.C.); (Y.T.); (B.Y.); (X.C.); (P.X.); (T.Z.); (S.L.); (P.Q.); (P.W.)
| | - Peizhou Xu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (S.L.); (C.H.); (C.Z.); (H.L.); (X.L.); (K.L.); (K.Z.); (Q.W.); (C.C.); (Y.T.); (B.Y.); (X.C.); (P.X.); (T.Z.); (S.L.); (P.Q.); (P.W.)
| | - Ting Zou
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (S.L.); (C.H.); (C.Z.); (H.L.); (X.L.); (K.L.); (K.Z.); (Q.W.); (C.C.); (Y.T.); (B.Y.); (X.C.); (P.X.); (T.Z.); (S.L.); (P.Q.); (P.W.)
| | - Shuangcheng Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (S.L.); (C.H.); (C.Z.); (H.L.); (X.L.); (K.L.); (K.Z.); (Q.W.); (C.C.); (Y.T.); (B.Y.); (X.C.); (P.X.); (T.Z.); (S.L.); (P.Q.); (P.W.)
| | - Peng Qin
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (S.L.); (C.H.); (C.Z.); (H.L.); (X.L.); (K.L.); (K.Z.); (Q.W.); (C.C.); (Y.T.); (B.Y.); (X.C.); (P.X.); (T.Z.); (S.L.); (P.Q.); (P.W.)
| | - Pingrong Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (S.L.); (C.H.); (C.Z.); (H.L.); (X.L.); (K.L.); (K.Z.); (Q.W.); (C.C.); (Y.T.); (B.Y.); (X.C.); (P.X.); (T.Z.); (S.L.); (P.Q.); (P.W.)
| | - Chengcai Chu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, South China Agricultural University, Guangzhou 510642, China;
| | - Xiaojian Deng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (S.L.); (C.H.); (C.Z.); (H.L.); (X.L.); (K.L.); (K.Z.); (Q.W.); (C.C.); (Y.T.); (B.Y.); (X.C.); (P.X.); (T.Z.); (S.L.); (P.Q.); (P.W.)
- Correspondence: (C.S.); (X.D.)
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Xu X, Yuan L, Yang X, Zhang X, Wang L, Xie Q. Circadian clock in plants: Linking timing to fitness. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2022; 64:792-811. [PMID: 35088570 DOI: 10.1111/jipb.13230] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 01/25/2022] [Indexed: 05/12/2023]
Abstract
Endogenous circadian clock integrates cyclic signals of environment and daily and seasonal behaviors of organisms to achieve spatiotemporal synchronization, which greatly improves genetic diversity and fitness of species. This review addresses recent studies on the plant circadian system in the field of chronobiology, covering topics on molecular mechanisms, internal and external Zeitgebers, and hierarchical regulation of physiological outputs. The architecture of the circadian clock involves the autoregulatory transcriptional feedback loops, post-translational modifications of core oscillators, and epigenetic modifications of DNA and histones. Here, light, temperature, humidity, and internal elemental nutrients are summarized to illustrate the sensitivity of the circadian clock to timing cues. In addition, the circadian clock runs cell-autonomously, driving independent circadian rhythms in various tissues. The core oscillators responds to each other with biochemical factors including calcium ions, mineral nutrients, photosynthetic products, and hormones. We describe clock components sequentially expressed during a 24-h day that regulate rhythmic growth, aging, immune response, and resistance to biotic and abiotic stresses. Notably, more data have suggested the circadian clock links chrono-culture to key agronomic traits in crops.
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Affiliation(s)
- Xiaodong Xu
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Li Yuan
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Xin Yang
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Xiao Zhang
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Lei Wang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China
| | - Qiguang Xie
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
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Lopez L, Fasano C, Perrella G, Facella P. Cryptochromes and the Circadian Clock: The Story of a Very Complex Relationship in a Spinning World. Genes (Basel) 2021; 12:672. [PMID: 33946956 PMCID: PMC8145066 DOI: 10.3390/genes12050672] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 04/19/2021] [Accepted: 04/27/2021] [Indexed: 01/16/2023] Open
Abstract
Cryptochromes are flavin-containing blue light photoreceptors, present in most kingdoms, including archaea, bacteria, plants, animals and fungi. They are structurally similar to photolyases, a class of flavoproteins involved in light-dependent repair of UV-damaged DNA. Cryptochromes were first discovered in Arabidopsis thaliana in which they control many light-regulated physiological processes like seed germination, de-etiolation, photoperiodic control of the flowering time, cotyledon opening and expansion, anthocyanin accumulation, chloroplast development and root growth. They also regulate the entrainment of plant circadian clock to the phase of light-dark daily cycles. Here, we review the molecular mechanisms by which plant cryptochromes control the synchronisation of the clock with the environmental light. Furthermore, we summarise the circadian clock-mediated changes in cell cycle regulation and chromatin organisation and, finally, we discuss a putative role for plant cryptochromes in the epigenetic regulation of genes.
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Affiliation(s)
| | | | | | - Paolo Facella
- Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), TERIN-BBC-BBE, Trisaia Research Center, 75026 Rotondella, Matera, Italy; (L.L.); (C.F.); (G.P.)
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Sedley L. Advances in Nutritional Epigenetics-A Fresh Perspective for an Old Idea. Lessons Learned, Limitations, and Future Directions. Epigenet Insights 2020; 13:2516865720981924. [PMID: 33415317 PMCID: PMC7750768 DOI: 10.1177/2516865720981924] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Accepted: 11/25/2020] [Indexed: 12/11/2022] Open
Abstract
Nutritional epigenetics is a rapidly expanding field of research, and the natural modulation of the genome is a non-invasive, sustainable, and personalized alternative to gene-editing for chronic disease management. Genetic differences and epigenetic inflexibility resulting in abnormal gene expression, differential or aberrant methylation patterns account for the vast majority of diseases. The expanding understanding of biological evolution and the environmental influence on epigenetics and natural selection requires relearning of once thought to be well-understood concepts. This research explores the potential for natural modulation by the less understood epigenetic modifications such as ubiquitination, nitrosylation, glycosylation, phosphorylation, and serotonylation concluding that the under-appreciated acetylation and mitochondrial dependant downstream epigenetic post-translational modifications may be the pinnacle of the epigenomic hierarchy, essential for optimal health, including sustainable cellular energy production. With an emphasis on lessons learned, this conceptional exploration provides a fresh perspective on methylation, demonstrating how increases in environmental methane drive an evolutionary down regulation of endogenous methyl groups synthesis and demonstrates how epigenetic mechanisms are cell-specific, making supplementation with methyl cofactors throughout differentiation unpredictable. Interference with the epigenomic hierarchy may result in epigenetic inflexibility, symptom relief and disease concomitantly and may be responsible for the increased incidence of neurological disease such as autism spectrum disorder.
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Affiliation(s)
- Lynda Sedley
- Bachelor of Health Science (Nutritional Medicine),
GC Biomedical Science (Genomics), The Research and Educational Institute of
Environmental and Nutritional Epigenetics, Queensland, Australia
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Plant Volatile Organic Compounds Evolution: Transcriptional Regulation, Epigenetics and Polyploidy. Int J Mol Sci 2020; 21:ijms21238956. [PMID: 33255749 PMCID: PMC7728353 DOI: 10.3390/ijms21238956] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 11/18/2020] [Accepted: 11/23/2020] [Indexed: 12/15/2022] Open
Abstract
Volatile organic compounds (VOCs) are emitted by plants as a consequence of their interaction with biotic and abiotic factors, and have a very important role in plant evolution. Floral VOCs are often involved in defense and pollinator attraction. These interactions often change rapidly over time, so a quick response to those changes is required. Epigenetic factors, such as DNA methylation and histone modification, which regulate both genes and transcription factors, might trigger adaptive responses to these evolutionary pressures as well as regulating the rhythmic emission of VOCs through circadian clock regulation. In addition, transgenerational epigenetic effects and whole genome polyploidy could modify the generation of VOCs’ profiles of offspring, contributing to long-term evolutionary shifts. In this article, we review the available knowledge about the mechanisms that may act as epigenetic regulators of the main VOC biosynthetic pathways, and their importance in plant evolution.
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11
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Li MW, Lam HM. The Modification of Circadian Clock Components in Soybean During Domestication and Improvement. Front Genet 2020; 11:571188. [PMID: 33193673 PMCID: PMC7554537 DOI: 10.3389/fgene.2020.571188] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 08/19/2020] [Indexed: 12/19/2022] Open
Abstract
Agricultural production is greatly dependent on daylength, which is determined by latitude. Living organisms align their physiology to daylength through the circadian clock, which is made up of input sensors, core and peripheral clock components, and output. The light/dark cycle is the major input signal, moderated by temperature fluctuations and metabolic changes. The core clock in plants functions mainly through a number of transcription feedback loops. It is known that the circadian clock is not essential for survival. However, alterations in the clock components can lead to substantial changes in physiology. Thus, these clock components have become the de facto targets of artificial selection for crop improvement during domestication. Soybean was domesticated around 5,000 years ago. Although the circadian clock itself is not of particular interest to soybean breeders, specific alleles of the circadian clock components that affect agronomic traits, such as plant architecture, sensitivity to light/dark cycle, flowering time, maturation time, and yield, are. Consequently, compared to their wild relatives, cultivated soybeans have been bred to be more adaptive and productive at different latitudes and habitats for acreage expansion, even though the selection processes were made without any prior knowledge of the circadian clock. Now with the advances in comparative genomics, known modifications in the circadian clock component genes in cultivated soybean have been found, supporting the hypothesis that modifications of the clock are important for crop improvement. In this review, we will summarize the known modifications in soybean circadian clock components as a result of domestication and improvement. In addition to the well-studied effects on developmental timing, we will also discuss the potential of circadian clock modifications for improving other aspects of soybean productivity.
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Affiliation(s)
- Man-Wah Li
- Center for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Hon-Ming Lam
- Center for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China.,Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
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12
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Qi F, Jiang Z, Hou W, Peng B, Cheng S, Zhang X, Luo Z, Dai Z, Wang Y, Liu Y, Wang Y, Wang Z. The Clock-Controlled lncRNA-AK028245 Participates in the Immune Response via Immune Response Factors OTUD7B and A20. J Biol Rhythms 2020; 35:542-554. [PMID: 32748687 DOI: 10.1177/0748730420944328] [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: 11/15/2022]
Abstract
Emerging evidence has demonstrated that long noncoding RNAs (lncRNAs) play critical roles in the epigenetic and transcriptional regulation of mammalian circadian systems. Circadian rhythmicity regulates many aspects of our immune system, and perturbation of the circadian clock can augment the inflammatory response. However, knowledge of the precise functions of lncRNAs in the regulation of immune functions within the circadian system is relatively limited. In this study, differentially expressed lncRNAs induced by Clock knockdown were screened via mRNA/lncRNA microarray and bioinformatic prediction analysis. We identified a Clock-regulated lncRNA, AK028245, which was correlated with the activation of the immune response. The expression levels of AK028245 were decreased in the spleen of immunosuppressed mice and elevated in immune-activated mice treated with lipopolysaccharide (LPS). Further, Clock knockdown decreased the expression of OTUD7B and A20, 2 early immune response factors acting on the NF-κB signaling pathway. Interestingly, inhibition of AK028245 increased their expression, mitigating the effects of Clock knockdown. In addition, inhibition of AK028245 downregulated the expression of tumor necrosis factor-α and interleukin-6 in the late stages of LPS stimulation and the expression of interferon-γ and Cxcl12 in the peak stages. We conclude that this newly identified lncRNA plays a role in the crosstalk between Clock and immune response regulators, likely resulting in a proinflammatory response targeting OTUD7B and A20. The lncRNA AK028245 has revealed a new mechanism of the immune response and provided new targets for the treatment of immune disorders.
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Affiliation(s)
- Fang Qi
- NHC Key Laboratory of Chronobiology (Sichuan University), West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, Sichuan, P.R. China
| | - Zhou Jiang
- NHC Key Laboratory of Chronobiology (Sichuan University), West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, Sichuan, P.R. China
| | - Wang Hou
- NHC Key Laboratory of Chronobiology (Sichuan University), West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, Sichuan, P.R. China
| | - Bo Peng
- NHC Key Laboratory of Chronobiology (Sichuan University), West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, Sichuan, P.R. China
| | - Shuting Cheng
- NHC Key Laboratory of Chronobiology (Sichuan University), West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, Sichuan, P.R. China
| | - Xiaolong Zhang
- NHC Key Laboratory of Chronobiology (Sichuan University), West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, Sichuan, P.R. China
| | - Zhihan Luo
- NHC Key Laboratory of Chronobiology (Sichuan University), West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, Sichuan, P.R. China
| | - Zeyong Dai
- NHC Key Laboratory of Chronobiology (Sichuan University), West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, Sichuan, P.R. China
| | - Yumeng Wang
- NHC Key Laboratory of Chronobiology (Sichuan University), West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, Sichuan, P.R. China
| | - Yanyou Liu
- NHC Key Laboratory of Chronobiology (Sichuan University), West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, Sichuan, P.R. China
| | - Yuhui Wang
- NHC Key Laboratory of Chronobiology (Sichuan University), West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, Sichuan, P.R. China
| | - Zhengrong Wang
- NHC Key Laboratory of Chronobiology (Sichuan University), West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, Sichuan, P.R. China
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Light and Circadian Signaling Pathway in Pregnancy: Programming of Adult Health and Disease. Int J Mol Sci 2020; 21:ijms21062232. [PMID: 32210175 PMCID: PMC7139376 DOI: 10.3390/ijms21062232] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 03/22/2020] [Accepted: 03/22/2020] [Indexed: 12/12/2022] Open
Abstract
Light is a crucial environmental signal that affects elements of human health, including the entrainment of circadian rhythms. A suboptimal environment during pregnancy can increase the risk of offspring developing a wide range of chronic diseases in later life. Circadian rhythm disruption in pregnant women may have deleterious consequences for their progeny. In the modern world, maternal chronodisruption can be caused by shift work, jet travel across time zones, mistimed eating, and excessive artificial light exposure at night. However, the impact of maternal chronodisruption on the developmental programming of various chronic diseases remains largely unknown. In this review, we outline the impact of light, the circadian clock, and circadian signaling pathways in pregnancy and fetal development. Additionally, we show how to induce maternal chronodisruption in animal models, examine emerging research demonstrating long-term negative implications for offspring health following maternal chronodisruption, and summarize current evidence related to light and circadian signaling pathway targeted therapies in pregnancy to prevent the development of chronic diseases in offspring.
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