1
|
Zhao H, Huang Y, Shu S, Wang G, Fu C, Huang R, Zhang J, Su H, He Y, Lei C, Du L, Zhao J, Peng W. Transcriptomics and metabolomics of blood, urine and ovarian follicular fluid of yak at induced estrus stage. BMC Genomics 2024; 25:201. [PMID: 38383305 PMCID: PMC10882836 DOI: 10.1186/s12864-024-10079-7] [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: 04/22/2023] [Accepted: 02/01/2024] [Indexed: 02/23/2024] Open
Abstract
To gain a deeper understanding of the metabolic differences within and outside the body, as well as changes in transcription levels following estrus in yaks, we conducted transcriptome and metabolome analyses on female yaks in both estrus and non-estrus states. The metabolome analysis identified 114, 13, and 91 distinct metabolites in urine, blood, and follicular fluid, respectively. The Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis highlighted an enrichment of pathways related to amino acid and lipid metabolism across all three body fluids. Our transcriptome analysis revealed 122 differentially expressed genes within microRNA (miRNA) and 640 within long non-coding RNA (lncRNA). Functional enrichment analysis of lncRNA and miRNA indicated their involvement in cell signaling, disease resistance, and immunity pathways. We constructed a regulatory network composed of 10 lncRNAs, 4 miRNAs, and 30 mRNAs, based on the targeted regulation relationships of the differentially expressed genes. In conclusion, the accumulation of metabolites such as amino acids, steroids, and organic acids, along with the expression changes of key genes like miR-129 during yak estrus, provide initial insights into the estrus mechanism in yaks.
Collapse
Affiliation(s)
- Huangqing Zhao
- Qinghai University, Xining, China
- Northwest A&F University, Yangling, Shaanxi, China
| | | | - Shi Shu
- Qinghai University, Xining, China
| | | | | | | | | | - Huawei Su
- China Agricultural University, Beijing, China
| | - Yang He
- China Agricultural University, Beijing, China
| | - Chuzhao Lei
- Northwest A&F University, Yangling, Shaanxi, China
| | - Lei Du
- Northwest A&F University, Yangling, Shaanxi, China
| | - Jiahao Zhao
- Northwest A&F University, Yangling, Shaanxi, China
| | - Wei Peng
- Qinghai University, Xining, China.
| |
Collapse
|
2
|
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.
Collapse
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,
| |
Collapse
|
3
|
Lu Z, Yuan C, Li J, Guo T, Yue Y, Niu C, Liu J, Yang B. Comprehensive Analysis of Long Non-coding RNA and mRNA Transcriptomes Related to Hypoxia Adaptation in Tibetan Sheep. Front Vet Sci 2022; 8:801278. [PMID: 35141308 PMCID: PMC8818989 DOI: 10.3389/fvets.2021.801278] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 12/20/2021] [Indexed: 11/24/2022] Open
Abstract
Tibetan sheep have lived on the Qinghai-Tibet Plateau for a long time, and after long-term natural selection, they have shown stable genetic adaptability to high-altitude environments. However, little is known about the molecular mechanisms of the long non-coding (lnc)RNAs involved in the adaptation of Tibetan sheep to hypoxia. Here, we collected lung tissues from high-altitude Tibetan sheep and low-altitude Hu sheep for RNA sequencing to study the regulatory mechanisms of the lncRNAs and mRNAs in the adaptation of Tibetan sheep to hypoxia. We identified 254 differentially expressed lncRNAs and 1,502 differentially expressed mRNAs. We found 20 pairs of cis-regulatory relationships between 15 differentially expressed lncRNAs and 14 protein-coding genes and two pairs of trans-regulatory relationships between two differentially expressed lncRNAs and two protein-coding genes. These differentially expressed mRNAs and lncRNA target genes were mainly enriched in pathways related to lipid metabolism and immune function. Interaction network analysis showed that 17 differentially expressed lncRNAs and 15 differentially expressed mRNAs had an interactive relationship. Additionally, we used six differentially expressed lncRNAs and mRNAs to verify the accuracy of the sequencing data via qRT-PCR. Our results provide a comprehensive overview of the expression patterns of the lncRNAs and mRNAs involved in the adaptation of Tibetan sheep to hypoxia, laying a foundation for further analysis of the adaptations of plateau animals.
Collapse
Affiliation(s)
- Zengkui Lu
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Chao Yuan
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Jianye Li
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Tingting Guo
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Yaojing Yue
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Chune Niu
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Jianbin Liu
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Lanzhou, China
- *Correspondence: Jianbin Liu
| | - Bohui Yang
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Lanzhou, China
- Bohui Yang
| |
Collapse
|
4
|
Zheng J, Du M, Zhang J, Liang Z, Ahmad AA, Shen J, Salekdeh GH, Ding X. Transcriptomic and Metabolomic Analyses Reveal Inhibition of Hepatic Adipogenesis and Fat Catabolism in Yak for Adaptation to Forage Shortage During Cold Season. Front Cell Dev Biol 2022; 9:759521. [PMID: 35111749 PMCID: PMC8802892 DOI: 10.3389/fcell.2021.759521] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 12/02/2021] [Indexed: 12/20/2022] Open
Abstract
Animals have adapted behavioral and physiological strategies to conserve energy during periods of adverse conditions. Hepatic glucose is one such adaptation used by grazing animals. While large vertebrates have been shown to have feed utilization and deposition of nutrients—fluctuations in metabolic rate—little is known about the regulating mechanism that controls hepatic metabolism in yaks under grazing conditions in the cold season. Hence, the objective of this research was to integrate transcriptomic and metabolomic data to better understand how the hepatic responds to chronic nutrient stress. Our analyses indicated that the blood parameters related to energy metabolism (glucose, total cholesterol, low-density lipoprotein cholesterol, high-density lipoprotein cholesterol, lipoprotein lipase, insulin, and insulin-like growth factor 1) were significantly (p < 0.05) lower in the cold season. The RNA-Seq results showed that malnutrition inhibited lipid synthesis (particularly fatty acid, cholesterol, and steroid synthesis), fatty acid oxidation, and lipid catabolism and promoted gluconeogenesis by inhibiting the peroxisome proliferator-activated receptor (PPAR) and PI3K-Akt signaling pathways. For metabolite profiles, 359 metabolites were significantly altered in two groups. Interestingly, the cold season group remarkably decreased glutathione and phosphatidylcholine (18:2 (2E, 4E)/0:0). Moreover, integrative analysis of the transcriptome and metabolome demonstrated that glycolysis or gluconeogenesis, PPAR signaling pathway, fatty acid biosynthesis, steroid biosynthesis, and glutathione metabolism play an important role in the potential relationship between differential expression genes and metabolites. The reduced lipid synthesis, fatty acid oxidation, and fat catabolism facilitated gluconeogenesis by inhibiting the PPAR and PI3K-Akt signaling pathways to maintain the energy homeostasis of the whole body in the yak, thereby coping with the shortage of forages and adapting to the extreme environment of the Qinghai-Tibetan Plateau (QTP).
Collapse
Affiliation(s)
- Juanshan Zheng
- Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agricultural and Rural Affairs & Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Mei Du
- Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agricultural and Rural Affairs & Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Jianbo Zhang
- Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agricultural and Rural Affairs & Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Zeyi Liang
- Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agricultural and Rural Affairs & Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Anum Ali Ahmad
- State Key Laboratory of Grassland Agro-Ecosystems, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Jiahao Shen
- Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agricultural and Rural Affairs & Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Ghasem Hosseini Salekdeh
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education, and Extension Organization, Karaj, Iran
- *Correspondence: Ghasem Hosseini Salekdeh, ; Xuezhi Ding,
| | - Xuezhi Ding
- Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agricultural and Rural Affairs & Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agricultural and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
- *Correspondence: Ghasem Hosseini Salekdeh, ; Xuezhi Ding,
| |
Collapse
|
5
|
Ma J, Zhang T, Wang W, Chen Y, Cai W, Zhu B, Xu L, Gao H, Zhang L, Li J, Gao X. Comparative Transcriptome Analyses of Gayal (Bos frontalis), Yak (Bos grunniens), and Cattle (Bos taurus) Reveal the High-Altitude Adaptation. Front Genet 2022; 12:778788. [PMID: 35087567 PMCID: PMC8789257 DOI: 10.3389/fgene.2021.778788] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 12/06/2021] [Indexed: 11/13/2022] Open
Abstract
Gayal and yak are well adapted to their local high-altitude environments, yet the transcriptional regulation difference of the plateau environment among them remains obscure. Herein, cross-tissue and cross-species comparative transcriptome analyses were performed for the six hypoxia-sensitive tissues from gayal, yak, and cattle. Gene expression profiles for all single-copy orthologous genes showed tissue-specific expression patterns. By differential expression analysis, we identified 3,020 and 1,995 differentially expressed genes (DEGs) in at least one tissue of gayal vs. cattle and yak vs. cattle, respectively. Notably, we found that the adaptability of the gayal to the alpine canyon environment is highly similar to the yak living in the Qinghai-Tibet Plateau, such as promoting red blood cell development, angiogenesis, reducing blood coagulation, immune system activation, and energy metabolism shifts from fatty acid β-oxidation to glycolysis. By further analyzing the common and unique DEGs in the six tissues, we also found that numerous expressed regulatory genes related to these functions are unique in the gayal and yak, which may play important roles in adapting to the corresponding high-altitude environment. Combined with WGCNA analysis, we found that UQCRC1 and COX5A are the shared differentially expressed hub genes related to the energy supply of myocardial contraction in the heart-related modules of gayal and yak, and CAPS is a shared differential hub gene among the hub genes of the lung-related module, which is related to pulmonary artery smooth muscle contraction. Additionally, EDN3 is the unique differentially expressed hub gene related to the tracheal epithelium and pulmonary vasoconstriction in the lung of gayal. CHRM2 is a unique differentially expressed hub gene that was identified in the heart of yak, which has an important role in the autonomous regulation of the heart. These results provide a basis for further understanding the complex transcriptome expression pattern and the regulatory mechanism of high-altitude domestication of gayal and yak.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | - Junya Li
- *Correspondence: Junya Li, ; Xue Gao,
| | - Xue Gao
- *Correspondence: Junya Li, ; Xue Gao,
| |
Collapse
|
6
|
Miretti S, Lecchi C, Ceciliani F, Baratta M. MicroRNAs as Biomarkers for Animal Health and Welfare in Livestock. Front Vet Sci 2020; 7:578193. [PMID: 33392281 PMCID: PMC7775535 DOI: 10.3389/fvets.2020.578193] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 10/30/2020] [Indexed: 12/11/2022] Open
Abstract
MicroRNAs (miRNAs) are small and highly conserved non-coding RNA molecules that orchestrate a wide range of biological processes through the post-transcriptional regulation of gene expression. An intriguing aspect in identifying these molecules as biomarkers is derived from their role in cell-to-cell communication, their active secretion from cells into the extracellular environment, their high stability in body fluids, and their ease of collection. All these features confer on miRNAs the potential to become a non-invasive tool to score animal welfare. There is growing interest in the importance of miRNAs as biomarkers for assessing the welfare of livestock during metabolic, environmental, and management stress, particularly in ruminants, pigs, and poultry. This review provides an overview of the current knowledge regarding the potential use of tissue and/or circulating miRNAs as biomarkers for the assessment of the health and welfare status in these livestock species.
Collapse
Affiliation(s)
- Silvia Miretti
- Department of Veterinary Sciences, University of Torino, Grugliasco, Italy
| | - Cristina Lecchi
- Department of Veterinary Medicine, Università degli Studi di Milano, Milan, Italy
| | - Fabrizio Ceciliani
- Department of Veterinary Medicine, Università degli Studi di Milano, Milan, Italy
| | - Mario Baratta
- Department of Veterinary Sciences, University of Torino, Grugliasco, Italy
| |
Collapse
|