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Nikolic B, Trnski-Levak S, Kosic K, Drlje M, Banovac I, Hranilovic D, Jovanov-Milosevic N. Lasting mesothalamic dopamine imbalance and altered exploratory behavior in rats after a mild neonatal hypoxic event. Front Integr Neurosci 2024; 17:1304338. [PMID: 38304737 PMCID: PMC10832065 DOI: 10.3389/fnint.2023.1304338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 12/22/2023] [Indexed: 02/03/2024] Open
Abstract
Introduction Adversities during the perinatal period can decrease oxygen supply to the fetal brain, leading to various hypoxic brain injuries, which can compromise the regularity of brain development in different aspects. To examine the catecholaminergic contribution to the link between an early-life hypoxic insult and adolescent behavioral aberrations, we used a previously established rat model of perinatal hypoxia but altered the hypobaric to normobaric conditions. Methods Exploratory and social behavior and learning abilities were tested in 70 rats of both sexes at adolescent age. Inherent vertical locomotion, sensory-motor functions and spatial learning abilities were explored in a subset of animals to clarify the background of altered exploratory behavior. Finally, the concentrations of dopamine (DA) and noradrenaline in midbrain and pons, and the relative expression of genes for DA receptors D1 and D2, and their down-stream targets (DA- and cAMP-regulated phosphoprotein, Mr 32 kDa, the regulatory subunit of protein kinase A, and inhibitor-5 of protein phosphatase 1) in the hippocampus and thalamus were investigated in 31 rats. Results A lesser extent of alterations in exploratory and cognitive aspects of behavior in the present study suggests that normobaric conditions mitigate the hypoxic injury compared to the one obtained under hypobaric conditions. Increased exploratory rearing was the most prominent consequence, with impaired spatial learning in the background. In affected rats, increased midbrain/pons DA content, as well as mRNA levels for DA receptors and their down-stream elements in the thalamus, but not the hippocampus, were found. Conclusion We can conclude that a mild hypoxic event induced long-lasting disbalances in mesothalamic DA signaling, contributing to the observed behavioral alterations. The thalamus was thereby indicated as another structure, besides the well-established striatum, involved in mediating hypoxic effects on behavior through DA signaling.
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Affiliation(s)
- Barbara Nikolic
- Department of Biology, University of Zagreb Faculty of Science, Zagreb, Croatia
| | - Sara Trnski-Levak
- Croatian Institute for Brain Research, University of Zagreb School of Medicine, Zagreb, Croatia
| | - Kristina Kosic
- Department of Biology, University of Zagreb Faculty of Science, Zagreb, Croatia
| | - Matea Drlje
- Croatian Institute for Brain Research, University of Zagreb School of Medicine, Zagreb, Croatia
| | - Ivan Banovac
- Department of Biology, University of Zagreb School of Medicine, Zagreb, Croatia
- Department for Anatomy and Clinical Anatomy, University of Zagreb School of Medicine, Zagreb, Croatia
| | - Dubravka Hranilovic
- Department of Biology, University of Zagreb Faculty of Science, Zagreb, Croatia
| | - Natasa Jovanov-Milosevic
- Croatian Institute for Brain Research, University of Zagreb School of Medicine, Zagreb, Croatia
- Department of Biology, University of Zagreb School of Medicine, Zagreb, Croatia
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Chen J, Zhang H, Yang M, Wang R, Zhang H, Ren Z, Wang Q, Liu Y, Chen J, Ji J, Zhao J, He G, Guo J, Zhu K, Yang X, Ma H, Wang CC, Huang J. Genomic formation of Tibeto-Burman speaking populations in Guizhou, Southwest China. BMC Genomics 2023; 24:672. [PMID: 37936086 PMCID: PMC10630991 DOI: 10.1186/s12864-023-09767-7] [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: 05/27/2023] [Accepted: 10/25/2023] [Indexed: 11/09/2023] Open
Abstract
Sino-Tibetan is the most prominent language family in East Asia. Previous genetic studies mainly focused on the Tibetan and Han Chinese populations. However, due to the sparse sampling, the genetic structure and admixture history of Tibeto-Burman-speaking populations in the low-altitude region of Southwest China still need to be clarified. We collected DNA from 157 individuals from four Tibeto-Burman-speaking groups from the Guizhou province in Southwest China. We genotyped the samples at about 700,000 genome-wide single nucleotide polymorphisms. Our results indicate that the genetic variation of the four Tibeto-Burman-speaking groups in Guizhou is at the intermediate position in the modern Tibetan-Tai-Kadai/Austronesian genetic cline. This suggests that the formation of Tibetan-Burman groups involved a large-scale gene flow from lowland southern Chinese. The southern ancestry could be further modelled as deriving from Vietnam's Late Neolithic-related inland Southeast Asia agricultural populations and Taiwan's Iron Age-related coastal rice-farming populations. Compared to the Tibeto-Burman speakers in the Tibetan-Yi Corridor reported previously, the Tibeto-Burman groups in the Guizhou region received additional gene flow from the southeast coastal area of China. We show a difference between the genetic profiles of the Tibeto-Burman speakers of the Tibetan-Yi Corridor and the Guizhou province. Vast mountain ranges and rivers in Southwest China may have decelerated the westward expansion of the southeast coastal East Asians. Our results demonstrate the complex genetic profile in the Guizhou region in Southwest China and support the multiple waves of human migration in the southern area of East Asia.
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Affiliation(s)
- Jinwen Chen
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, 361102, China
| | - Han Zhang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, Shanghai, 200063, China
| | - Meiqing Yang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Rui Wang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, 361102, China
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, Xiamen University, Xiamen, 361005, China
| | - Hongling Zhang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Zheng Ren
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Qiyan Wang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Yubo Liu
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Jing Chen
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Jingyan Ji
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Jing Zhao
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, 361102, China
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, Xiamen University, Xiamen, 361005, China
| | - Guanglin He
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, 361102, China
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, Xiamen University, Xiamen, 361005, China
| | - Jianxin Guo
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, 361102, China
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, Xiamen University, Xiamen, 361005, China
| | - Kongyang Zhu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, 361102, China
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, Xiamen University, Xiamen, 361005, China
| | - Xiaomin Yang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, 361102, China
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, Xiamen University, Xiamen, 361005, China
| | - Hao Ma
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, 361102, China
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, Xiamen University, Xiamen, 361005, China
| | - Chuan-Chao Wang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, 361102, China.
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, Xiamen University, Xiamen, 361005, China.
- Department of Anthropology and Human Genetics, Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China.
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, 361102, China.
- Institute of Artificial Intelligence, Xiamen University, Xiamen, 361005, Fujian, China.
| | - Jiang Huang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China.
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Chang X, Xiao Y, Cheng L, Gu X, Yang L, Chamba Y, Zhang J, Geng F. Quantitative Proteomic Analysis of Yorkshire Pig Liver Reveals Its Response to High Altitude. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:7618-7629. [PMID: 37140090 DOI: 10.1021/acs.jafc.3c01724] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
In this study, the protein profiles in the livers of Shannan Yorkshire pigs (SNY), Linzhi Yorkshire pigs (LZY), and Jiuzhaigou Yorkshire pigs (JZY) were comparatively analyzed using quantitative proteomics. A total of 6804 proteins were identified, of which 6471 were quantified and 774 differentially expressed proteins (DEPs) were screened. The higher level of energy metabolism in LZY livers was in response to the critical altitude environment compared to that in JZY, while the high-altitude environment suppressed energy output in SNY livers. Several key antioxidant enzymes were locally regulated in Yorkshire pig liver to balance antioxidant levels in a high-altitude, low-oxygen environment. In addition, ribosomal proteins were differentially expressed in Yorkshire pig livers in response to different altitudinal environments. These findings provide clues to the adaptation of the Yorkshire pig liver to the three altitudinal environments and the molecular links that exist between them.
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Affiliation(s)
- Xinping Chang
- Meat Processing Key Laboratory of Sichuan Province, School of Food and Biological Engineering, Chengdu University, Chengdu 610106, China
| | - Yu Xiao
- Meat Processing Key Laboratory of Sichuan Province, School of Food and Biological Engineering, Chengdu University, Chengdu 610106, China
| | - Lei Cheng
- School of Food and Health, Beijing Technology & Business University (BTBU), Beijing 100048, China
| | - Xuedong Gu
- College of Food Science, Tibet Agriculture and Animal Husbandry University, Linzhi 860000, China
- Provincial and Ministerial Co-Founded Collaborative Innovation Center for R & D in Tibet Characteristic Agricultural and Animal Husbandry Resources, Tibet Agricultural and Animal Husbandry University, Linzhi 860000, China
| | - Lin Yang
- Provincial and Ministerial Co-Founded Collaborative Innovation Center for R & D in Tibet Characteristic Agricultural and Animal Husbandry Resources, Tibet Agricultural and Animal Husbandry University, Linzhi 860000, China
| | - Yangzom Chamba
- College of Food Science, Tibet Agriculture and Animal Husbandry University, Linzhi 860000, China
- Provincial and Ministerial Co-Founded Collaborative Innovation Center for R & D in Tibet Characteristic Agricultural and Animal Husbandry Resources, Tibet Agricultural and Animal Husbandry University, Linzhi 860000, China
| | - Jiamin Zhang
- Meat Processing Key Laboratory of Sichuan Province, School of Food and Biological Engineering, Chengdu University, Chengdu 610106, China
| | - Fang Geng
- Meat Processing Key Laboratory of Sichuan Province, School of Food and Biological Engineering, Chengdu University, Chengdu 610106, China
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Luo W, Xu Y, Gu X, Zhang J, Wang J, Geng F. Divergence of Liver Lipidomes in Tibetan and Yorkshire Pigs Living at Different Altitudes. Molecules 2023; 28:molecules28072991. [PMID: 37049754 PMCID: PMC10095695 DOI: 10.3390/molecules28072991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 03/24/2023] [Accepted: 03/24/2023] [Indexed: 03/30/2023] Open
Abstract
The Tibetan pig is a characteristic breed of the Qinghai-Tibet Plateau with distinct physiological and meat quality attributes. The liver lipid profile can offer an important perspective to explore the uniqueness of Tibetan pigs. A quantitative comparison of liver lipidomes revealed significant differences in the lipid profiles between Tibetan and Yorkshire pigs raised at different altitudes. The abundance of lipids in the livers of pigs raised at a high altitude was higher than that of pigs raised at a lower altitude, whereas the abundance of lipids in the livers of Yorkshire pigs was higher than that of Tibetan pigs raised at the same altitude. Of the 1101 lipids identified, 323 and 193 differentially abundant lipids (DALs) were identified in the pairwise comparisons of Tibetan and Yorkshire pigs raised at different altitudes, respectively. The DALs of Tibetan pigs consisted mainly of 161 triglycerides, along with several acylcarnitines, represented by carnitine C2:0, and significant changes in the abundance of some phospholipids. The DALs of Yorkshire pigs were more complex, with significant increases in the abundance of triglycerides, cholesteryl esters, and free fatty acids, and decreases in the abundance of some phospholipids. This research provides strong theoretical and data support for the high-quality development of the highland livestock industry.
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Affiliation(s)
- Wei Luo
- Meat Processing Key Laboratory of Sichuan Province, School of Food and Biological Engineering, Chengdu University, Chengdu 610106, China
| | - Yisha Xu
- Meat Processing Key Laboratory of Sichuan Province, School of Food and Biological Engineering, Chengdu University, Chengdu 610106, China
| | - Xuedong Gu
- College of Food Science, Tibet Agriculture and Animal Husbandry University, Linzhi 860000, China
| | - Jiamin Zhang
- Meat Processing Key Laboratory of Sichuan Province, School of Food and Biological Engineering, Chengdu University, Chengdu 610106, China
| | - Jinqiu Wang
- Meat Processing Key Laboratory of Sichuan Province, School of Food and Biological Engineering, Chengdu University, Chengdu 610106, China
| | - Fang Geng
- Meat Processing Key Laboratory of Sichuan Province, School of Food and Biological Engineering, Chengdu University, Chengdu 610106, China
- Correspondence:
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Liu L, Zhang Y, Ma H, Cao H, Liu W. Integrating genome-wide methylation and transcriptome-wide analyses to reveal the genetic mechanism of milk traits in Kazakh horses. Gene 2023; 856:147143. [PMID: 36574934 DOI: 10.1016/j.gene.2022.147143] [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: 07/28/2022] [Revised: 12/06/2022] [Accepted: 12/21/2022] [Indexed: 12/25/2022]
Abstract
Horse Milk has important quantitative characteristics and high economic value. However, the DNA methylation regulators involved in horse milk traits have not been clarified. To explore the important role of genome-wide DNA methylation in regulating equine milk yield, this study systematically investigated the genome-wide DNA methylation profiles of Kazakh horse blood by comparing a high-production group (HP, average daily milk yield of 7.5 kg) and low-production group (LP, average daily milk yield of 3.2 kg) using deep whole-genome bisulfite sequencing. First, both groups showed similar proportions of methylation at CpG sites. Subsequently, we identified 26,677 differential methylated regions (DMRs) of CG, 15 DMRs of CHG, 480 DMRs of CHH and 8268 DMR-related genes (DMGs). GO and KEGG analyses revealed that some DMGs were involved in regulating milk and milk component formation. By combining the WGBS-seq and the previous RNA-seq data, a total of 94 overlapping genes were obtained. Finally, we found that 9 DMGs are likely involved in milk production by Kazakh horses.
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Affiliation(s)
- Lingling Liu
- College of Animal Science, Xinjiang Agricultural University, Urumqi 830052, China
| | - Yunting Zhang
- College of Animal Science, Xinjiang Agricultural University, Urumqi 830052, China
| | - Haiyu Ma
- College of Animal Science, Xinjiang Agricultural University, Urumqi 830052, China
| | - Hang Cao
- College of Animal Science, Xinjiang Agricultural University, Urumqi 830052, China
| | - Wujun Liu
- College of Animal Science, Xinjiang Agricultural University, Urumqi 830052, China.
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Quantitative Proteomic Analysis of Tibetan Pig Livers at Different Altitudes. Molecules 2023; 28:molecules28041694. [PMID: 36838681 PMCID: PMC9960092 DOI: 10.3390/molecules28041694] [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: 11/30/2022] [Revised: 02/01/2023] [Accepted: 02/07/2023] [Indexed: 02/12/2023] Open
Abstract
In this study, the differences in protein profiles between the livers of Shannan Tibetan pigs (SNT), Linzhi Tibetan pigs (LZT) and Jiuzhaigou Tibetan pigs (JZT) were comparatively analyzed by tandem mass spectrometry-labeling quantitative proteomics. A total of 6804 proteins were identified: 6471 were quantified and 1095 were screened as differentially expressed proteins (DEPs). Bioinformatics analysis results show that, compared with JZT livers, up-regulated DEPs in SNT and LZT livers mainly promoted hepatic detoxification through steroid hormone biosynthesis and participated in lipid metabolism to maintain body energy homeostasis, immune response and immune regulation, while down-regulated DEPs were mainly involved in lipid metabolism and immune regulation. Three proteases closely related to hepatic fatty acid oxidation were down-regulated in enzymatic activity, indicating higher levels of lipid oxidation in SNT and LZT livers than in JZT livers. Down-regulation of the expression of ten immunoglobulins suggests that JZT are more susceptible to autoimmune diseases. It is highly likely that these differences in lipid metabolism and immune-related proteins are in response to the ecological environment at different altitudes, and the findings contribute to the understanding of the potential molecular link between Tibetan pig livers and the environment.
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7
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Cai S, Hu B, Wang X, Liu T, Lin Z, Tong X, Xu R, Chen M, Duo T, Zhu Q, Liang Z, Li E, Chen Y, Li J, Liu X, Mo D. Integrative single-cell RNA-seq and ATAC-seq analysis of myogenic differentiation in pig. BMC Biol 2023; 21:19. [PMID: 36726129 PMCID: PMC9893630 DOI: 10.1186/s12915-023-01519-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 01/18/2023] [Indexed: 02/03/2023] Open
Abstract
BACKGROUND Skeletal muscle development is a multistep process whose understanding is central in a broad range of fields and applications, from the potential medical value to human society, to its economic value associated with improvement of agricultural animals. Skeletal muscle initiates in the somites, with muscle precursor cells generated in the dermomyotome and dermomyotome-derived myotome before muscle differentiation ensues, a developmentally regulated process that is well characterized in model organisms. However, the regulation of skeletal muscle ontogeny during embryonic development remains poorly defined in farm animals, for instance in pig. Here, we profiled gene expression and chromatin accessibility in developing pig somites and myotomes at single-cell resolution. RESULTS We identified myogenic cells and other cell types and constructed a differentiation trajectory of pig skeletal muscle ontogeny. Along this trajectory, the dynamic changes in gene expression and chromatin accessibility coincided with the activities of distinct cell type-specific transcription factors. Some novel genes upregulated along the differentiation trajectory showed higher expression levels in muscular dystrophy mice than that in healthy mice, suggesting their involvement in myogenesis. Integrative analysis of chromatin accessibility, gene expression data, and in vitro experiments identified EGR1 and RHOB as critical regulators of pig embryonic myogenesis. CONCLUSIONS Collectively, our results enhance our understanding of the molecular and cellular dynamics in pig embryonic myogenesis and offer a high-quality resource for the further study of pig skeletal muscle development and human muscle disease.
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Affiliation(s)
- Shufang Cai
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510006 Guangdong China
- Guangdong Key Laboratory of Animal Breeding and Nutrition, State Key Laboratory of Livestock and Poultry Breeding, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 Guangdong China
| | - Bin Hu
- Guangdong Key Laboratory of Animal Breeding and Nutrition, State Key Laboratory of Livestock and Poultry Breeding, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 Guangdong China
| | - Xiaoyu Wang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510006 Guangdong China
| | - Tongni Liu
- Faculty of Forestry, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
| | - Zhuhu Lin
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510006 Guangdong China
| | - Xian Tong
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510006 Guangdong China
| | - Rong Xu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510006 Guangdong China
| | - Meilin Chen
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510006 Guangdong China
| | - Tianqi Duo
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510006 Guangdong China
| | - Qi Zhu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510006 Guangdong China
| | - Ziyun Liang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510006 Guangdong China
| | - Enru Li
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510006 Guangdong China
| | - Yaosheng Chen
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510006 Guangdong China
| | - Jianhao Li
- Guangdong Key Laboratory of Animal Breeding and Nutrition, State Key Laboratory of Livestock and Poultry Breeding, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 Guangdong China
| | - Xiaohong Liu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510006 Guangdong China
| | - Delin Mo
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510006 Guangdong China
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He L, Liang X, Wang Q, Yang C, Li Y, Liao L, Zhu Z, Wang Y. Genome-wide DNA methylation reveals potential epigenetic mechanism of age-dependent viral susceptibility in grass carp. Immun Ageing 2022; 19:28. [PMID: 35655223 PMCID: PMC9161582 DOI: 10.1186/s12979-022-00285-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 05/14/2022] [Indexed: 11/10/2022]
Abstract
Background Grass carp are an important farmed fish in China that are infected by many pathogens, especially grass carp reovirus (GCRV). Notably, grass carp showed age-dependent susceptibility to GCRV; that is, grass carp not older than one year were sensitive to GCRV, while those over three years old were resistant to this virus. However, the underlying mechanism remains unclear. Herein, whole genome-wide DNA methylation and gene expression variations between susceptible five-month-old (FMO) and resistant three-year-old (TYO) grass carp were investigated aiming to uncover potential epigenetic mechanisms. Results Colorimetric quantification revealed that the global methylation level in TYO fish was higher than that in FMO fish. Whole-genome bisulfite sequencing (WGBS) of the two groups revealed 6214 differentially methylated regions (DMRs) and 4052 differentially methylated genes (DMGs), with most DMRs and DMGs showing hypermethylation patterns in TYO fish. Correlation analysis revealed that DNA hypomethylation in promoter regions and DNA hypermethylation in gene body regions were associated with gene expression. Enrichment analysis revealed that promoter hypo-DMGs in TYO fish were significantly enriched in typical immune response pathways, whereas gene body hyper-DMGs in TYO fish were significantly enriched in terms related to RNA transcription, biosynthesis, and energy production. RNA-seq analysis of the corresponding samples indicated that most of the genes in the above terms were upregulated in TYO fish. Moreover, gene function analysis revealed that the two genes involved in energy metabolism displayed antiviral effects. Conclusions Collectively, these results revealed genome-wide variations in DNA methylation between grass carp of different ages. DNA methylation and gene expression variations in genes involved in immune response, biosynthesis, and energy production may contribute to age-dependent susceptibility to GCRV in grass carp. Our results provide important information for disease-resistant breeding programs for grass carp and may also benefit research on age-dependent diseases in humans. Supplementary Information The online version contains supplementary material available at 10.1186/s12979-022-00285-w.
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Hou J, Wen X, Long P, Xiong S, Liu H, Cai L, Deng H, Zhang Z. The role of post-translational modifications in driving abnormal cardiovascular complications at high altitude. Front Cardiovasc Med 2022; 9:886300. [PMID: 36186970 PMCID: PMC9515308 DOI: 10.3389/fcvm.2022.886300] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 06/16/2022] [Indexed: 11/13/2022] Open
Abstract
The high-altitude environment is characterized by hypobaric hypoxia, low temperatures, low humidity, and high radiation, which is a natural challenge for lowland residents entering. Previous studies have confirmed the acute and chronic effects of high altitude on the cardiovascular systems of lowlanders. Abnormal cardiovascular complications, including pulmonary edema, cardiac hypertrophy and pulmonary arterial hypertension were commonly explored. Effective evaluation of cardiovascular adaptive response in high altitude can provide a basis for early warning, prevention, diagnosis, and treatment of altitude diseases. At present, post-translational modifications (PTMs) of proteins are a key step to regulate their biological functions and dynamic interactions with other molecules. This process is regulated by countless enzymes called “writer, reader, and eraser,” and the performance is precisely controlled. Mutations and abnormal expression of these enzymes or their substrates have been implicated in the pathogenesis of cardiovascular diseases associated with high altitude. Although PTMs play an important regulatory role in key processes such as oxidative stress, apoptosis, proliferation, and hypoxia response, little attention has been paid to abnormal cardiovascular response at high altitude. Here, we reviewed the roles of PTMs in driving abnormal cardiovascular complications at high altitude.
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Affiliation(s)
- Jun Hou
- Department of Cardiology, Chengdu Third People’s Hospital, Cardiovascular Disease Research Institute of Chengdu, Affiliated Hospital of Southwest Jiaotong University, Chengdu, China
- School of Material Science and Engineering, Southwest Jiaotong University, Chengdu, China
| | - Xudong Wen
- Department of Gastroenterology and Hepatology, Chengdu First People’s Hospital, Chengdu, China
| | - Pan Long
- School of Material Science and Engineering, Southwest Jiaotong University, Chengdu, China
| | - Shiqiang Xiong
- Department of Cardiology, Chengdu Third People’s Hospital, Cardiovascular Disease Research Institute of Chengdu, Affiliated Hospital of Southwest Jiaotong University, Chengdu, China
| | - Hanxiong Liu
- Department of Cardiology, Chengdu Third People’s Hospital, Cardiovascular Disease Research Institute of Chengdu, Affiliated Hospital of Southwest Jiaotong University, Chengdu, China
| | - Lin Cai
- Department of Cardiology, Chengdu Third People’s Hospital, Cardiovascular Disease Research Institute of Chengdu, Affiliated Hospital of Southwest Jiaotong University, Chengdu, China
- *Correspondence: Lin Cai,
| | - Haoyu Deng
- Department of Medicine, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
- Center for Heart and Lung Innovation, St. Paul’s Hospital, University of British Columbia, Vancouver, BC, Canada
- Department of Vascular Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Haoyu Deng,
| | - Zhen Zhang
- Department of Cardiology, Chengdu Third People’s Hospital, Cardiovascular Disease Research Institute of Chengdu, Affiliated Hospital of Southwest Jiaotong University, Chengdu, China
- Zhen Zhang,
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Chen P, Liu Y, Liu W, Wang Y, Liu Z, Rong M. Impact of High-Altitude Hypoxia on Bone Defect Repair: A Review of Molecular Mechanisms and Therapeutic Implications. Front Med (Lausanne) 2022; 9:842800. [PMID: 35620712 PMCID: PMC9127390 DOI: 10.3389/fmed.2022.842800] [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: 12/24/2021] [Accepted: 04/15/2022] [Indexed: 11/23/2022] Open
Abstract
Reaching areas at altitudes over 2,500–3,000 m above sea level has become increasingly common due to commerce, military deployment, tourism, and entertainment. The high-altitude environment exerts systemic effects on humans that represent a series of compensatory reactions and affects the activity of bone cells. Cellular structures closely related to oxygen-sensing produce corresponding functional changes, resulting in decreased tissue vascularization, declined repair ability of bone defects, and longer healing time. This review focuses on the impact of high-altitude hypoxia on bone defect repair and discusses the possible mechanisms related to ion channels, reactive oxygen species production, mitochondrial function, autophagy, and epigenetics. Based on the key pathogenic mechanisms, potential therapeutic strategies have also been suggested. This review contributes novel insights into the mechanisms of abnormal bone defect repair in hypoxic environments, along with therapeutic applications. We aim to provide a foundation for future targeted, personalized, and precise bone regeneration therapies according to the adaptation of patients to high altitudes.
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Affiliation(s)
- Pei Chen
- Department of Periodontology and Implantology, Stomatological Hospital, Southern Medical University, Guangzhou, China
| | - Yushan Liu
- Department of Periodontology and Implantology, Stomatological Hospital, Southern Medical University, Guangzhou, China
| | - Wenjing Liu
- Department of Prosthodontics, Stomatological Hospital, Southern Medical University, Guangzhou, China
| | - Yarong Wang
- Department of Periodontology and Implantology, Stomatological Hospital, Southern Medical University, Guangzhou, China
| | - Ziyi Liu
- Department of Periodontology and Implantology, Stomatological Hospital, Southern Medical University, Guangzhou, China
| | - Mingdeng Rong
- Department of Periodontology and Implantology, Stomatological Hospital, Southern Medical University, Guangzhou, China
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11
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Mammalian eIF4E2-GSK3β maintains basal phosphorylation of p53 to resist senescence under hypoxia. Cell Death Dis 2022; 13:459. [PMID: 35568694 PMCID: PMC9107480 DOI: 10.1038/s41419-022-04897-4] [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: 09/01/2021] [Revised: 04/25/2022] [Accepted: 04/29/2022] [Indexed: 12/14/2022]
Abstract
Hypoxia modulates senescence, but their physiological link remains unclear. Here, we found that eIF4E2, a hypoxia-activated translation initiation factor, interacted with GSK3β to maintain phosphorylation of p53, thus resisting senescence under hypoxia. RNA-binding protein RBM38 interacted with eIF4E to inhibit the translation of p53, but GSK3β-mediated Ser195 phosphorylation disrupted the RBM38-eIF4E interaction. Through investigation of RBM38 phosphorylation, we found that the eIF4E2-GSK3β pathway specifically regulated proline-directed serine/threonine phosphorylation (S/T-P). Importantly, peptides e2-I or G3-I that blocking eIF4E2-GSK3β interaction can inhibit the basal S/T-P phosphorylation of p53 at multiple sites, therby inducing senescence through transcriptional inhibition. Additionally, a nanobody was screened via the domain where eIF4E2 bound to GSK3β, and this nanobody inhibited S/T-P phosphorylation to promote senescence. Furthermore, hypoxia inhibited eIF4E2-GSK3β pathway by mediating S-Nitrosylation of GSK3β. Blocking eIF4E2-GSK3β interaction promoted liver senescence under hypoxia, thus leading to liver fibrosis, eventually accelerating N, N-diethylnitrosamine (DEN)-induced tumorigenesis. Interestingly, eIF4E2 isoforms with GSK3β-binding motif exclusively exist in mammals, which protect zebrafish heart against hypoxia. Together, this study reveals a mammalian eIF4E2-GSK3β pathway that prevents senescence by maintaining basal S/T-P phosphorylation of p53, which underlies hypoxia adaptation of tissues.
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12
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Hu H, Li Y, Yang Y, Xu K, Yang L, Qiao S, Pan H. Effect of a Plateau Environment on the Oxidation State of the Heart and Liver through AMPK/p38 MAPK/Nrf2-ARE Signaling Pathways in Tibetan and DLY Pigs. Animals (Basel) 2022; 12:1219. [PMID: 35565644 PMCID: PMC9104009 DOI: 10.3390/ani12091219] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 04/28/2022] [Accepted: 05/07/2022] [Indexed: 12/13/2022] Open
Abstract
This study evaluated the effect of a plateau environment on the heart and liver oxidation state of Tibetan pigs (TPs) and DLY pigs through analyzing AMPK, p38 MAPK, and Nrf2 signaling pathways. Twelve 120-day-old TPs and twelve 120-day-old DLY pigs were randomly divided into two groups in a plateau environment for three weeks. Exposed to a plateau environment, TPs exhibited a lower (p < 0.05) malondialdehyde level but higher (p < 0.05) glutathione, superoxide dismutase (SOD), glutathione peroxidase (GSH-Px), and total antioxidant capacity (T-AOC) activities in the liver and heart than those observed in DLY pigs. TPs also showed higher (p < 0.05) mRNA levels of SOD and GSH-Px in the liver and heart compared with those of DLY pigs. The TPs showed higher (p < 0.05) mRNA and protein levels of AMPK and Nrf2 in the liver and heart compared with those of DLY pigs. Furthermore, TPs showed higher (p < 0.05) mRNA and protein levels of p38 MAPK in the heart and higher mRNA levels of p38 MAPK in the liver compared with those of DLY pigs under a plateau environment. In summary, TPs possess a stronger antioxidant capacity in the heart and liver than that of DLY pigs in a plateau environment through AMPK/p38 MAPK/Nrf2-ARE signaling pathways.
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Affiliation(s)
- Hong Hu
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed Science, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (H.H.); (Y.L.)
| | - Yongxiang Li
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed Science, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (H.H.); (Y.L.)
| | - Yuting Yang
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (Y.Y.); (L.Y.)
| | - Kexing Xu
- College of Animal Science, Anhui Science and Technology University, Chuzhou 233100, China;
| | - Lijie Yang
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (Y.Y.); (L.Y.)
| | - Shiyan Qiao
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (Y.Y.); (L.Y.)
| | - Hongbin Pan
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed Science, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (H.H.); (Y.L.)
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13
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Yang Y, Yuan H, Yang Q, Cai Y, Ren Y, Li Y, Gao C, Zhao S. Post-transcriptional regulation through alternative splicing in the lungs of Tibetan pigs under hypoxia. Gene 2022; 819:146268. [PMID: 35124151 DOI: 10.1016/j.gene.2022.146268] [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: 08/31/2021] [Revised: 01/22/2022] [Accepted: 01/28/2022] [Indexed: 11/15/2022]
Abstract
In multicellular organisms, alternative splicing (AS) is central to the regulation of multiple biological processes. To further elucidate the adaptive strategy of AS in the lungs of Tibetan pigs in response to hypoxia, we identified and analyzed five basic AS types and 59,930 AS events in 18,179 genes. We found that approximately 65.10% of the total expressed genes underwent AS in the lungs of Tibetan pigs at a high altitude (TH). The frequencies of AS events were similar among the different groups (5.06-5.30 events in each gene on average). Skipped exons (SEs) were the predominant type of AS event, followed by mutually exclusive exons (MXEs), alternative 3' splice sites (A3SSs) and alternative 5' splice sites (A5SSs). Retained introns (RIs), the remaining type of AS event, showed lower frequencies. Further comparison analysis of differentially expressed genes (DEGs) and differentially spliced genes (DSGs) identified 2,209 differential splicing events in the above 18,000 expressed genes, including 918 increased and 1,291 decreased splicing events between the TH and Tibetan pigs at a low altitude (TL) groups. We identified 227 hypoxia-related genes involved in lung development that were differentially regulated through AS. Gene Ontology (GO) annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis clearly identified many DEGs and DSGs at high or low altitude. Seven pathways in the top 20 enriched KEGG terms overlapped for the DEGs and DSGs, including the chemokine signaling pathway, B cell receptor signaling pathway, and cytokine-cytokine receptor interaction, which exert many immunoregulatory and inflammatory actions critical to the lung under hypoxia. Twelve pathways overlapped in hypoxic DEGs and DSGs and included antigen processing, presentation and biosynthesis. GO analysis of the DEGs and DSGs among the four groups showed that numerous GO terms were enriched in the biological category, and the proportion of genes with downregulated expression was greater among 227 hypoxic genes than that of all genes. The results suggest that AS plays an essential role in the regulation of gene expression during hypoxia and that numerous genes involved in lung development are differentially regulated through AS.
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Affiliation(s)
- Yanan Yang
- College of Animal Science & Technology, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Haonan Yuan
- College of Animal Science & Technology, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Qiaoli Yang
- College of Animal Science & Technology, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Yuan Cai
- College of Animal Science & Technology, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Yue Ren
- Academy of Agriculture and Animal Husbandry Sciences, Institute of Animal Husbandry and Veterinary Medicine, Lhasa, Xizang, China
| | - Yongqing Li
- Xinjiang Academy of Animal Sciences, Urumqi, Xinjiang, China
| | - Caixia Gao
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, Heilongjiang, China
| | - Shengguo Zhao
- College of Animal Science & Technology, Gansu Agricultural University, Lanzhou, Gansu, China.
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14
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Du H, Yao W, Kulyar MFEA, Ding Y, Zhu H, Pan H, Li K, Bhutta ZA, Liu S, Li J. Effects of Bacillus amyloliquefaciens TL106 Isolated from Tibetan Pigs on Probiotic Potential and Intestinal Microbes in Weaned Piglets. Microbiol Spectr 2022; 10:e0120521. [PMID: 35080439 PMCID: PMC8791190 DOI: 10.1128/spectrum.01205-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Accepted: 12/16/2021] [Indexed: 11/20/2022] Open
Abstract
Bacillus amyloliquefaciens is a nonpathogenic microorganism whose highly active amylase is widely isolated from soil and plants. TL106 is an isolate of Bacillus amyloliquefaciens isolated from cold- and disease-resistant Tibetan pigs in Linzhi, Tibet. Here, we report that TL106 not only could survive in acidic environments, high bile salt concentrations, and high-temperature conditions but also was resistant to antibiotics. It significantly improved the growth performance of weaned piglets, especially in the prevention of diarrhea. The crude fiber and crude ash digestibility in weaned piglets after TL106 administration was considerably higher than that in other groups. The results of 16S rRNA sequencing conveyed that TL106 stabilized gut microbiota that was disturbed by the weaning process with an increased level of Lachnospiraceae, Peptococcaceae.rc4_4, Erysipelotrichaceae.L7A_E11, and Mollicutes.RF39. Hence, this study proved that Bacillus amyloliquefaciens TL106 might be a candidate for antibiotics in Duroc×Landrace×Yorkshire weaned piglets. IMPORTANCE Antibiotics are often used to promote animal growth and prevent diarrhea in weanling piglets. Nevertheless, intestinal pathogenic bacterial resistance and drug residues caused by antibiotic overuse are worthy of concern and demand an urgent solution. Bacillus amyloliquefaciens TL106 has been isolated from cold- and disease-resistant Tibetan pigs in Linzhi, Tibet. It significantly improved the growth performance, decreased diarrhea, increased the absorption of crude substances, and regulated the gut flora homeostasis in Duroc×Landrace×Yorkshire weaned piglets. As an antibiotic candidate, TL106 perfectly displayed its probiotic potential and pollution-free properties.
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Affiliation(s)
- Haitao Du
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, People’s Republic of China
- Guangxi Yangxiang co., LTD, Guigang City, Guangxi, People’s Republic of China
| | - Wangyuan Yao
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, People’s Republic of China
| | | | - Yanmei Ding
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, People’s Republic of China
| | - Huaisen Zhu
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, People’s Republic of China
| | - Huachun Pan
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, People’s Republic of China
| | - Kewei Li
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, People’s Republic of China
| | - Zeeshan Ahmad Bhutta
- The Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, Scotland, United Kingdom
| | - Suozhu Liu
- College of Animals Husbandry and Veterinary Medicine, Tibet Agricultural and Animal Husbandry University, Linzhi, Tibet, People’s Republic China
| | - Jiakui Li
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, People’s Republic of China
- College of Animals Husbandry and Veterinary Medicine, Tibet Agricultural and Animal Husbandry University, Linzhi, Tibet, People’s Republic China
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15
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Ibeagha-Awemu EM, Yu Y. Consequence of epigenetic processes on animal health and productivity: is additional level of regulation of relevance? Anim Front 2021; 11:7-18. [PMID: 34934525 PMCID: PMC8683131 DOI: 10.1093/af/vfab057] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Affiliation(s)
- Eveline M Ibeagha-Awemu
- Sherbrooke Research and Development Centre, Agriculture and Agri-Food Canada, Sherbrooke, Quebec, Canada
| | - Ying Yu
- Department of Animal Breeding and Genetics, College of Animal Sciences and Technology, China Agricultural University, Beijing, China
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16
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Yang Y, Yuan H, Yang T, Li Y, Gao C, Jiao T, Cai Y, Zhao S. The Expression Regulatory Network in the Lung Tissue of Tibetan Pigs Provides Insight Into Hypoxia-Sensitive Pathways in High-Altitude Hypoxia. Front Genet 2021; 12:691592. [PMID: 34691141 PMCID: PMC8529057 DOI: 10.3389/fgene.2021.691592] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 08/31/2021] [Indexed: 12/31/2022] Open
Abstract
To adapt to a low-oxygen environment, Tibetan pigs have developed a series of unique characteristics and can transport oxygen more effectively; however, the regulation of the associated processes in high-altitude animals remains elusive. We performed mRNA-seq and miRNA-seq, and we constructed coexpression regulatory networks of the lung tissues of Tibetan and Landrace pigs. HBB, AGT, COL1A2, and EPHX1 were identified as major regulators of hypoxia-induced genes that regulate blood pressure and circulation, and they were enriched in pathways related to signal transduction and angiogenesis, such as HIF-1, PI3K-Akt, mTOR, and AMPK. HBB may promote the combination of hemoglobin and oxygen as well as angiogenesis for high-altitude adaptation in Tibetan pigs. The expression of MMP2 showed a similar tendency of alveolar septum thickness among the four groups. These results indicated that MMP2 activity may lead to widening of the alveolar wall and septum, alveolar structure damage, and collapse of alveolar space with remarkable fibrosis. These findings provide a perspective on hypoxia-adaptive genes in the lungs in addition to insights into potential candidate genes in Tibetan pigs for further research in the field of high-altitude adaptation.
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Affiliation(s)
- Yanan Yang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Haonan Yuan
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Tianliang Yang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Yongqing Li
- Research on Quality Standard of Animal Husbandry, Xinjiang Academy of Animal Sciences, Xinjiang, China
| | - Caixia Gao
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Ting Jiao
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China.,College of Grassland Science, Gansu Agricultural University, Lanzhou, China
| | - Yuan Cai
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Shengguo Zhao
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
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17
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Tian Y, Yang X, Du J, Zeng W, Wu W, Di J, Huang X, Tian K. Differential Methylation and Transcriptome Integration Analysis Identified Differential Methylation Annotation Genes and Functional Research Related to Hair Follicle Development in Sheep. Front Genet 2021; 12:735827. [PMID: 34659357 PMCID: PMC8515899 DOI: 10.3389/fgene.2021.735827] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Accepted: 08/30/2021] [Indexed: 11/13/2022] Open
Abstract
Hair follicle growth and development are a complex and long-term physiological process, which is regulated by a variety of physical factors and signal pathways. Increasing the understanding of the epigenetic regulation and function of candidate genes related to hair follicle development will help to better understand the molecular regulatory mechanisms of hair follicle development. In this study, the methylated DNA immunoprecipitation sequencing (MeDIP-seq) was used to obtain the genome-wide methylation map of the hair follicular development of Super Merino sheep in six stages (fetal skin tissue at 65d, 85d, 105d, 135d, 7d, and 30d after birth). Combined with the results of previous RNA-sequencing, 65 genes were screened out that were both differential methylation and differential expression, including EDN1, LAMC2, NR1D1, RORB, MyOZ3, and WNT2 gene. Differential methylation genes were enriched in Wnt, TNF, TGF-beta, and other signaling pathways related to hair follicle development. The bisulfite sequencing PCR results and MeDIP-seq were basically consistent, indicating that the sequencing results were accurate. As a key gene in the Wnt signaling pathway, both differential methylation and expression gene identified by MeDIP-seq and RNA-seq, further exploration of the function of WNT2 gene revealed that the DNA methylation of exon 5 (CpG11 site) promoted the expression of WNT2 gene. The overexpression vector of lentivirus pLEX-MCS-WNT2 was constructed, and WNT2 gene effectively promoted the proliferation of sheep skin fibroblasts. The results showed that WNT2 gene could promote the growth and development of skin and hair follicles. The results of this study will provide a theoretical basis for further research on sheep hair follicle development and gene regulation mechanisms.
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Affiliation(s)
- Yuezhen Tian
- The Key Laboratory for Genetics Breeding and Reproduction of Xinjiang Cashmere and Wool Sheep, Institute of Animal Science, Xinjiang Academy of Animal Sciences, Urumqi, China
| | - Xuemei Yang
- College of Animal Science, Xinjiang Agricultural University, Urumqi, China
| | - Jianwen Du
- College of Animal Science, Xinjiang Agricultural University, Urumqi, China
| | - Weidan Zeng
- College of Animal Science, Xinjiang Agricultural University, Urumqi, China
| | - Weiwei Wu
- The Key Laboratory for Genetics Breeding and Reproduction of Xinjiang Cashmere and Wool Sheep, Institute of Animal Science, Xinjiang Academy of Animal Sciences, Urumqi, China
| | - Jiang Di
- The Key Laboratory for Genetics Breeding and Reproduction of Xinjiang Cashmere and Wool Sheep, Institute of Animal Science, Xinjiang Academy of Animal Sciences, Urumqi, China
| | - Xixia Huang
- College of Animal Science, Xinjiang Agricultural University, Urumqi, China
| | - Kechuan Tian
- The Key Laboratory for Genetics Breeding and Reproduction of Xinjiang Cashmere and Wool Sheep, Institute of Animal Science, Xinjiang Academy of Animal Sciences, Urumqi, China
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18
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Yang Y, Gao C, Yang T, Sha Y, Cai Y, Wang X, Yang Q, Liu C, Wang B, Zhao S. Vascular characteristics and expression of hypoxia genes in Tibetan pigs' hearts. Vet Med Sci 2021; 8:177-186. [PMID: 34561963 PMCID: PMC8788992 DOI: 10.1002/vms3.639] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Background Tibetan pigs have exhibited unique characteristics from low‐altitudes pigs and adapted well to the Qinghai‐Tibet Plateau. Objectives The current study was undertaken to investigate the hypoxic adaptation of heart in Tibetan pigs. Methods The hearts of Tibetan pigs and Landrace pigs raised at high or low altitudes were compared using 3D casting technology, scanning electron microscopy and real‐time quantitative PCR (qRT‐PCR). Results We found that the ratio of the major axis to the minor axis and the density of the heart were significantly higher in Tibetan pigs than in Landrace pigs (p < 0.05). Tibetan pigs had larger diameters and higher densities of arterioles than Landrace pigs (p < 0.05), and these features have a similar variation with the expression of vascular endothelial growth factor (VEGF). The cardiac expression levels of hypoxia‐inducible factor‐1α (HIF‐1α) and endothelial nitric oxide synthase (eNOS) were significantly higher in pigs reared at high altitudes than in those reared at low altitudes (p < 0.05). In contrast, Egl nine homolog 1 (EGLN1) had the opposite trend with respect to HIF‐1α and eNOS and was related to red blood cell (RBC) counts. Notably, the expressions of erythropoietin (EPO) and endothelial PAS domain‐containing protein 1 (EPAS1) were significantly higher in Landrace pigs kept at high altitudes than in the others (p < 0.05) and were associated with haemoglobin. Conclusions These findings show that the regulation of the heart function of Tibetan pigs in a hypoxic environment is manifested at various levels to ensure the circulation of blood under extreme environmental conditions.
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Affiliation(s)
- Yanan Yang
- College of Animal Science & Technology, Gansu Agricultural University, Lanzhou, P.R. China
| | - Caixia Gao
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, P.R. China
| | - Tianliang Yang
- College of Animal Science & Technology, Gansu Agricultural University, Lanzhou, P.R. China
| | - Yuzhu Sha
- College of Animal Science & Technology, Gansu Agricultural University, Lanzhou, P.R. China
| | - Yuan Cai
- College of Animal Science & Technology, Gansu Agricultural University, Lanzhou, P.R. China
| | - Xinrong Wang
- College of Animal Science & Technology, Gansu Agricultural University, Lanzhou, P.R. China
| | - Qiaoli Yang
- College of Animal Science & Technology, Gansu Agricultural University, Lanzhou, P.R. China
| | - Chengze Liu
- College of Animal Science & Technology, Gansu Agricultural University, Lanzhou, P.R. China
| | - Biao Wang
- College of Animal Science & Technology, Gansu Agricultural University, Lanzhou, P.R. China
| | - Shengguo Zhao
- College of Animal Science & Technology, Gansu Agricultural University, Lanzhou, P.R. China
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19
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Padmasekar M, Savai R, Seeger W, Pullamsetti SS. Exposomes to Exosomes: Exosomes as Tools to Study Epigenetic Adaptive Mechanisms in High-Altitude Humans. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:8280. [PMID: 34444030 PMCID: PMC8392481 DOI: 10.3390/ijerph18168280] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 07/30/2021] [Accepted: 07/31/2021] [Indexed: 12/29/2022]
Abstract
Humans on earth inhabit a wide range of environmental conditions and some environments are more challenging for human survival than others. However, many living beings, including humans, have developed adaptive mechanisms to live in such inhospitable, harsh environments. Among different difficult environments, high-altitude living is especially demanding because of diminished partial pressure of oxygen and resulting chronic hypobaric hypoxia. This results in poor blood oxygenation and reduces aerobic oxidative respiration in the mitochondria, leading to increased reactive oxygen species generation and activation of hypoxia-inducible gene expression. Genetic mechanisms in the adaptation to high altitude is well-studied, but there are only limited studies regarding the role of epigenetic mechanisms. The purpose of this review is to understand the epigenetic mechanisms behind high-altitude adaptive and maladaptive phenotypes. Hypobaric hypoxia is a form of cellular hypoxia, which is similar to the one suffered by critically-ill hypoxemia patients. Thus, understanding the adaptive epigenetic signals operating in in high-altitude adjusted indigenous populations may help in therapeutically modulating signaling pathways in hypoxemia patients by copying the most successful epigenotype. In addition, we have summarized the current information about exosomes in hypoxia research and prospects to use them as diagnostic tools to study the epigenome of high-altitude adapted healthy or maladapted individuals.
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Affiliation(s)
- Manju Padmasekar
- Max-Planck Institute for Heart and Lung Research, Member of the German Center for Lung Research (DZL), Member of the Cardio-Pulmonary Institute (CPI), 61231 Bad Nauheim, Germany; (M.P.); (R.S.); (W.S.)
| | - Rajkumar Savai
- Max-Planck Institute for Heart and Lung Research, Member of the German Center for Lung Research (DZL), Member of the Cardio-Pulmonary Institute (CPI), 61231 Bad Nauheim, Germany; (M.P.); (R.S.); (W.S.)
- Institute for Lung Health (ILH), Justus Liebig University, 35392 Giessen, Germany
- Department of Internal Medicine, Justus-Liebig University Giessen, Member of the DZL, Member of CPI, 35392 Giessen, Germany
- Frankfurt Cancer Institute (FCI), Goethe University, 60438 Frankfurt am Main, Germany
| | - Werner Seeger
- Max-Planck Institute for Heart and Lung Research, Member of the German Center for Lung Research (DZL), Member of the Cardio-Pulmonary Institute (CPI), 61231 Bad Nauheim, Germany; (M.P.); (R.S.); (W.S.)
- Institute for Lung Health (ILH), Justus Liebig University, 35392 Giessen, Germany
- Department of Internal Medicine, Justus-Liebig University Giessen, Member of the DZL, Member of CPI, 35392 Giessen, Germany
| | - Soni Savai Pullamsetti
- Max-Planck Institute for Heart and Lung Research, Member of the German Center for Lung Research (DZL), Member of the Cardio-Pulmonary Institute (CPI), 61231 Bad Nauheim, Germany; (M.P.); (R.S.); (W.S.)
- Institute for Lung Health (ILH), Justus Liebig University, 35392 Giessen, Germany
- Department of Internal Medicine, Justus-Liebig University Giessen, Member of the DZL, Member of CPI, 35392 Giessen, Germany
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20
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Wang K, Wu P, Wang S, Ji X, Chen D, Xiao W, Gu Y, Zeng Y, Xu X, Tang G. Differential DNA methylation analysis reveals key genes in Chinese Qingyu and Landrace pigs. Genome 2021; 65:1-8. [PMID: 34242523 DOI: 10.1139/gen-2021-0006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The Chinese Qingyu pig is a typical domestic fatty pig breed and an invaluable indigenous genetic resource in China. Compared with the Landrace pig, the Qingyu pig has unique meat characteristics, including muscle development, intramuscular fat, and other meat quality traits. At present, few studies have explored epigenetic differences due to DNA methylation between the Qingyu pig and the Landrace pig. In this study, 30 Qingyu pigs and 31 Landrace pigs were subjected to reduced representation bisulfite sequencing (RRBS). Genome-wide differential DNA methylation analysis was conducted. Six genomic regions, including regions on Sus scrofa chromosome (SSC) 1: 266.09-274.23 Mb, SSC5: 0.88-10.68 Mb, SSC8: 41.23-48.51 Mb, SSC12: 45.43-54.38 Mb, SSC13: 202.15-207.95 Mb, and SSC14: 126.43-139.85 Mb, were regarded as key regions that may be associated with phenotypic differences between the Qingyu pig and the Landrace pig. Furthermore, according to further analysis, five differentially methylated genes (ADCY1, FUBP3, GRIN2B, KIT, and PIK3R6) were identified as key candidate genes that might be associated with meat characteristics. Our findings provide new insights into the differences in DNA methylation between the Qingyu pig and the Landrace pig. These results enrich the epigenetic research of the Chinese Qingyu pig.
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Affiliation(s)
- Kai Wang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Pingxian Wu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Shujie Wang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Xiang Ji
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Dong Chen
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Weihang Xiao
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Yiren Gu
- Sichuan Animal Science Academy, Chengdu, 610066, Sichuan, China
| | - Yangshuang Zeng
- Sichuan Animal Husbandry Station, Chengdu, 610041, Sichuan, China
| | - Xu Xu
- Sichuan Animal Husbandry Station, Chengdu, 610041, Sichuan, China
| | - Guoqing Tang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
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21
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Wang K, Wu P, Wang S, Ji X, Chen D, Jiang A, Xiao W, Gu Y, Jiang Y, Zeng Y, Xu X, Li X, Tang G. Genome-wide DNA methylation analysis in Chinese Chenghua and Yorkshire pigs. BMC Genom Data 2021; 22:21. [PMID: 34134626 PMCID: PMC8207654 DOI: 10.1186/s12863-021-00977-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 06/07/2021] [Indexed: 11/10/2022] Open
Abstract
Background The Chinese Chenghua pig (CHP) is a typical Chinese domestic fatty pig breed with superior meat quality characteristics, while the Yorkshire pig (YP) has the characteristics of fast growth and a high rate of lean meat. Long term natural selection and artificial selection resulted in great phenotypic differences between the two breeds, including growth, development, production performance, meat quality, and coat color. However, genome-wide DNA methylation differences between CHP and YP remain unclear. Results DNA methylation data were generated for muscle tissues of CHP and YP using reduced representation bisulfite sequencing (RRBS). In this study, a total of 2,416,211 CpG sites were identified. Besides, the genome-wide DNA methylation analysis revealed 722 differentially methylated regions (DMRs) and 466 differentially methylated genes (DMGs) in pairwise CHP vs. YP comparison. Six key genomic regions (Sus scrofa chromosome (SSC)1:253.47–274.23 Mb, SSC6:148.71–169.49 Mb, SSC7:0.25–9.86 Mb, SSC12:43.06–61.49 Mb, SSC14:126.43–140.95 Mb, and SSC18:49.17–54.54 Mb) containing multiple DMRs were identified, and differences of methylation patterns in these regions may be related to phenotypic differences between CHP and YP. Based on the functional analysis of DMGs, 8 DMGs (ADCY1, AGBL4, EXOC2, FUBP3, PAPPA2, PIK3R1, MGMT and MYH8) were considered as important candidate genes associated with muscle development and meat quality traits in pigs. Conclusions This study explored the difference in meat quality between CHP and YP from the epigenetic point of view, which has important reference significance for the local pork industry and pork food processing. Supplementary Information The online version contains supplementary material available at 10.1186/s12863-021-00977-0.
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Affiliation(s)
- Kai Wang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Pingxian Wu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Shujie Wang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Xiang Ji
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Dong Chen
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Anan Jiang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Weihang Xiao
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Yiren Gu
- Sichuan Animal Science Academy, Chengdu, 610066, China
| | - Yanzhi Jiang
- College of Life Science, Sichuan Agricultural University, Yaan, China
| | | | - Xu Xu
- Sichuan Animal Husbandry Station, Chengdu, 610041, China
| | - Xuewei Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Guoqing Tang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China.
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22
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Wang M, Ibeagha-Awemu EM. Impacts of Epigenetic Processes on the Health and Productivity of Livestock. Front Genet 2021; 11:613636. [PMID: 33708235 PMCID: PMC7942785 DOI: 10.3389/fgene.2020.613636] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 12/21/2020] [Indexed: 12/23/2022] Open
Abstract
The dynamic changes in the epigenome resulting from the intricate interactions of genetic and environmental factors play crucial roles in individual growth and development. Numerous studies in plants, rodents, and humans have provided evidence of the regulatory roles of epigenetic processes in health and disease. There is increasing pressure to increase livestock production in light of increasing food needs of an expanding human population and environment challenges, but there is limited related epigenetic data on livestock to complement genomic information and support advances in improvement breeding and health management. This review examines the recent discoveries on epigenetic processes due to DNA methylation, histone modification, and chromatin remodeling and their impacts on health and production traits in farm animals, including bovine, swine, sheep, goat, and poultry species. Most of the reports focused on epigenome profiling at the genome-wide or specific genic regions in response to developmental processes, environmental stressors, nutrition, and disease pathogens. The bulk of available data mainly characterized the epigenetic markers in tissues/organs or in relation to traits and detection of epigenetic regulatory mechanisms underlying livestock phenotype diversity. However, available data is inadequate to support gainful exploitation of epigenetic processes for improved animal health and productivity management. Increased research effort, which is vital to elucidate how epigenetic mechanisms affect the health and productivity of livestock, is currently limited due to several factors including lack of adequate analytical tools. In this review, we (1) summarize available evidence of the impacts of epigenetic processes on livestock production and health traits, (2) discuss the application of epigenetics data in livestock production, and (3) present gaps in livestock epigenetics research. Knowledge of the epigenetic factors influencing livestock health and productivity is vital for the management and improvement of livestock productivity.
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Affiliation(s)
- Mengqi Wang
- Agriculture and Agri-Food Canada, Sherbrooke Research and Development Centre, Sherbrooke, QC, Canada
- Department of Animal Science, Laval University, Quebec, QC, Canada
| | - Eveline M. Ibeagha-Awemu
- Agriculture and Agri-Food Canada, Sherbrooke Research and Development Centre, Sherbrooke, QC, Canada
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23
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Tandem mass tag-labeled quantitative proteomic analysis of tenderloins between Tibetan and Yorkshire pigs. Meat Sci 2021; 172:108343. [DOI: 10.1016/j.meatsci.2020.108343] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 08/12/2020] [Accepted: 10/12/2020] [Indexed: 12/15/2022]
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24
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Bao CL, Liu SZ, Shang ZD, Liu YJ, Wang J, Zhang WX, Dong B, Cao YH. Bacillus amyloliquefaciens TL106 protects mice against enterohaemorrhagic Escherichia coli O157:H7-induced intestinal disease through improving immune response, intestinal barrier function and gut microbiota. J Appl Microbiol 2020; 131:470-484. [PMID: 33289241 DOI: 10.1111/jam.14952] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 11/24/2020] [Accepted: 11/26/2020] [Indexed: 01/20/2023]
Abstract
AIMS This study evaluated the effects of Bacillus amyloliquefaciens TL106, isolated from Tibetan pigs' faeces, on the growth performance, immune response, intestinal barrier function, morphology of jejunum, caecum and colon, and gut microbiota in the mice with enterohaemorrhagic Escherichia coli (EHEC)-induced intestinal diseases. METHODS AND RESULTS In all, 40 female C57BL/6J mice were randomly divided into four groups: mice fed a normal diet (Control), mice oral administration of TL106 daily (Ba), mice challenged with EHEC O157:H7 on day 15 (O157) and mice oral administration of TL106 daily and challenged with EHEC O157:H7 on day 15 (Ba+O157). The TL106 was administrated to mice for 14 days, and mice were infected with O157:H7 at day 15. We found that TL106 could prevent the weight loss caused by O157:H7 infection and alleviated the associated increase in pro-inflammatory factors (TNF-α, IL-1β, IL-6 and IL-8) and decrease in anti-inflammatory factor (IL-10) in serum and intestinal tissues of mice caused by O157:H7 infection (P < 0·05). Additionally, TL106 could prevent disruption of gut morphology caused by O157:H7 infection, and alleviate the associated decrease in expression of tight junction proteins (ZO-1, occludin and claudin-1) in jejunum and colon (P < 0·05). In caecum and colon, the alpha diversity for bacterial community analysis of Chao and ACE index in Ba+O157 group were higher than O157 group. The TL106 stabilized gut microbiota disturbed by O157:H7, including increasing Lachnospiraceae, Prevotellaceae, Muribaculaceae and Akkermansiaceae, and reducing Lactobacillaceae. CONCLUSIONS We indicated the B. amyloliquefaciens TL106 can effectively protect mice against EHEC O157:H7 infection by relieving inflammation, improving intestinal barrier function, mitigating permeability disruption and stabilizing the gut microbiota. SIGNIFICANCE AND IMPACT OF THE STUDY Bacillus amyloliquefaciens TL106 can prevent and treat intestinal disease induced by EHEC O157:H7 in mice, which may be a promising probiotic for disease prevention in animals.
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Affiliation(s)
- C L Bao
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, People's Republic of China
| | - S Z Liu
- College of Animal Science, Tibet Agricultural and Animal Husbandry University, Linzhi, People's Republic of China
| | - Z D Shang
- College of Animal Science, Tibet Agricultural and Animal Husbandry University, Linzhi, People's Republic of China
| | - Y J Liu
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, People's Republic of China
| | - J Wang
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, People's Republic of China
| | - W X Zhang
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, People's Republic of China
| | - B Dong
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, People's Republic of China
| | - Y H Cao
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, People's Republic of China
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25
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Wang Q, Li D, Guo A, Li M, Li L, Zhou J, Mishra SK, Li G, Duan Y, Li Q. Whole-genome resequencing of Dulong Chicken reveal signatures of selection. Br Poult Sci 2020; 61:624-631. [PMID: 32627575 DOI: 10.1080/00071668.2020.1792832] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
1. Dulong Chickens (DLCs) live at high altitude (~3000 m) and humidity (~90%), are endemic to the Yunnan province, and have gradually developed unique physiological characteristics, but their genetic basis is still unclear. Using the fixation index (FST ) approach, based on whole-genome resequencing, DLCs were analysed to uncover the genomic architecture of the population and candidate genes involved in selection during domestication. 2. A total of 469 candidate genes were obtained to be putatively under selection in DLCs. Further investigations revealed the genic footprint for local adaptation (high-altitude and high-humidity) as the genic signatures that are involved in economic traits (related to egg production). 3. Candidate genes were identified that may be associated with disease resistance, aggressiveness, small body size and positive selection of vision in DLCs. 4. These data revealed loci of selective signals that operate during selection for production at high altitude and humidity.
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Affiliation(s)
- Q Wang
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China (Southwest Forestry University), Ministry of Education , Kunming, China.,Life Science College, Southwest Forestry University , Kunming, China
| | - D Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University , Chengdu, China
| | - A Guo
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China (Southwest Forestry University), Ministry of Education , Kunming, China.,Life Science College, Southwest Forestry University , Kunming, China
| | - M Li
- School of Mathematics and Computer Science, Yunnan Nationalities University , Kunming, China
| | - L Li
- Life Science College, Southwest Forestry University , Kunming, China
| | - J Zhou
- Life Science College, Southwest Forestry University , Kunming, China
| | - S K Mishra
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University , Chengdu, China
| | - G Li
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China (Southwest Forestry University), Ministry of Education , Kunming, China.,Life Science College, Southwest Forestry University , Kunming, China
| | - Y Duan
- Technology Center, China Tobacco Yunnan Industrial Co., Ltd ., Kunming, China
| | - Q Li
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China (Southwest Forestry University), Ministry of Education , Kunming, China.,Life Science College, Southwest Forestry University , Kunming, China.,Kunming Xianghao Technology Co. Ltd ., Kunming, China
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26
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Gu X, Gao Y, Luo Z, Yang L, Chi F, Xiao J, Wang W, Geng F. In-depth mapping of the proteome of Tibetan pig tenderloin (longissimus dorsi) using offline high-pH reversed-phase fractionation and LC-MS/MS. J Food Biochem 2019; 43:e13015. [PMID: 31429109 DOI: 10.1111/jfbc.13015] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2019] [Revised: 07/29/2019] [Accepted: 08/02/2019] [Indexed: 12/11/2022]
Abstract
In recent years, Tibetan pig breeding and meat processing have developed rapidly. However, the basic physiological and biochemical characteristics of Tibetan pork have not been systematically explored. The present study conducted a high-throughput analysis of the tenderloin (longissimus dorsi) proteome of the Tibetan pigs and performed a functional annotation and bioinformatics analysis of the identified proteins. Based on offline two-dimensional liquid chromatography fractionation and MS/MS identification, a total of 1,723 proteins were identified in the tenderloin of Tibetan pigs. Gene ontology analysis and pathway enrichment analysis revealed that the proteins involved in respiration (oxidative phosphorylation, glycolysis/gluconeogenesis, citric acid cycle, and pyruvate metabolism) and protein synthesis and metabolism (proteasome, amino acid biosynthesis, endoplasmic reticulum protein processing, and ribosomes) were significantly enriched, indicating that the energy production and protein metabolism are the most important physiological processes in Tibetan pig tenderloin. Practical applications The in-depth mapping of the tenderloin (longissimus dorsi) proteome of the Tibetan pigs gives a panoramic perspective at the protein molecular level and provides important information on the mechanisms of postmortem muscle physiology and meat quality formation. Furthermore, the development of Tibetan pork storage and processing technologies would also benefit from the characterization of the biochemical properties of Tibetan pork.
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Affiliation(s)
- Xuedong Gu
- College of Food Science, Tibet Agriculture and Animal Husbandry University, Linzhi, China
| | - Yuling Gao
- College of Food Science, Tibet Agriculture and Animal Husbandry University, Linzhi, China
| | - Zhang Luo
- College of Food Science, Tibet Agriculture and Animal Husbandry University, Linzhi, China
| | - Lin Yang
- College of Food Science, Tibet Agriculture and Animal Husbandry University, Linzhi, China
| | - Fumin Chi
- College of Food Science, Tibet Agriculture and Animal Husbandry University, Linzhi, China
| | - Jing Xiao
- Meat Processing Key Laboratory of Sichuan Province, College of Pharmacy and Biological Engineering, Chengdu University, Chengdu, China
| | - Wei Wang
- Meat Processing Key Laboratory of Sichuan Province, College of Pharmacy and Biological Engineering, Chengdu University, Chengdu, China
| | - Fang Geng
- Meat Processing Key Laboratory of Sichuan Province, College of Pharmacy and Biological Engineering, Chengdu University, Chengdu, China
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