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Shang F, Lu Y, Li Y, Han B, Wei R, Liu S, Liu Y, Liu Y, Wang X. Transcriptome Analysis Identifies Key Metabolic Changes in the Brain of Takifugu rubripes in Response to Chronic Hypoxia. Genes (Basel) 2022; 13:genes13081347. [PMID: 36011255 PMCID: PMC9407616 DOI: 10.3390/genes13081347] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 07/23/2022] [Accepted: 07/24/2022] [Indexed: 02/04/2023] Open
Abstract
The brain is considered to be an extremely sensitive tissue to hypoxia, and the brain of fish plays an important role in regulating growth and adapting to environmental changes. As an important aquatic organism in northern China, the economic yield of Takifugu rubripes is deeply influenced by the oxygen content of seawater. In this regard, we performed RNA-seq analysis of T. rubripes brains under hypoxia and normoxia to reveal the expression patterns of genes involved in the hypoxic response and their enrichment of metabolic pathways. Studies have shown that carbohydrate, lipid and amino acid metabolism are significant pathways for the enrichment of differentially expressed genes (DEGs) and that DEGs are significantly upregulated in those pathways. In addition, some biological processes such as the immune system and signal transduction, where enrichment is not significant but important, are also discussed. Interestingly, the DEGs associated with those pathways were significantly downregulated or inhibited. The present study reveals the mechanism of hypoxia tolerance in T. rubripes at the transcriptional level and provides a useful resource for studying the energy metabolism mechanism of hypoxia response in this species.
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Affiliation(s)
- Fengqin Shang
- College of Fisheries and Life Science, Dalian Ocean University, Dalian 116023, China; (F.S.); (Y.L.); (Y.L.); (B.H.); (R.W.); (S.L.)
- College of Marine Technology and Environment, Dalian Ocean University, Dalian 116023, China;
| | - Yun Lu
- College of Fisheries and Life Science, Dalian Ocean University, Dalian 116023, China; (F.S.); (Y.L.); (Y.L.); (B.H.); (R.W.); (S.L.)
| | - Yan Li
- College of Fisheries and Life Science, Dalian Ocean University, Dalian 116023, China; (F.S.); (Y.L.); (Y.L.); (B.H.); (R.W.); (S.L.)
| | - Bing Han
- College of Fisheries and Life Science, Dalian Ocean University, Dalian 116023, China; (F.S.); (Y.L.); (Y.L.); (B.H.); (R.W.); (S.L.)
| | - Renjie Wei
- College of Fisheries and Life Science, Dalian Ocean University, Dalian 116023, China; (F.S.); (Y.L.); (Y.L.); (B.H.); (R.W.); (S.L.)
| | - Shengmei Liu
- College of Fisheries and Life Science, Dalian Ocean University, Dalian 116023, China; (F.S.); (Y.L.); (Y.L.); (B.H.); (R.W.); (S.L.)
| | - Ying Liu
- College of Marine Technology and Environment, Dalian Ocean University, Dalian 116023, China;
- Key Laboratory of Environment Controlled Aquaculture, Dalian Ocean University, Ministry of Education, Dalian 116023, China
| | - Yang Liu
- College of Fisheries and Life Science, Dalian Ocean University, Dalian 116023, China; (F.S.); (Y.L.); (Y.L.); (B.H.); (R.W.); (S.L.)
- Correspondence: (Y.L.); (X.W.)
| | - Xiuli Wang
- Key Laboratory of Pufferfish Breeding and Culture in Liaoning Province, Dalian Ocean University, Dalian 116023, China
- Correspondence: (Y.L.); (X.W.)
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Li J, Zhao H, Xing Y, Zhao T, Cai L, Yan Z. A Genome-Wide Analysis of the Gene Expression and Alternative Splicing Events in a Whole-Body Hypoxic Preconditioning Mouse Model. Neurochem Res 2021; 46:1101-1111. [PMID: 33582968 DOI: 10.1007/s11064-021-03241-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 12/07/2020] [Accepted: 01/07/2021] [Indexed: 12/13/2022]
Abstract
Exposure to specific doses of hypoxia can trigger endogenous neuroprotective and neuroplastic mechanisms of the central nervous system. These molecular mechanisms, together referred to as hypoxic preconditioning (HPC), remain poorly understood. In the present study, we applied RNA sequencing and bioinformatics analyses to study HPC in a whole-body HPC mouse model. The preconditioned (H4) and control (H0) groups showed 605 differentially expressed genes (DEGs), of which 263 were upregulated and 342 were downregulated. Gene Ontology enrichment analysis indicated that these DEGs were enriched in several biological processes, including metabolic stress and angiogenesis. The Kyoto Encyclopedia of Genes and Genomes enrichment analysis showed that the FOXO and Notch signaling pathways were involved in hypoxic tolerance and protection during HPC. Furthermore, 117 differential alternative splicing events (DASEs) were identified, with exon skipping being the dominant one (48.51%). Repeated exposure to systemic hypoxia promoted skipping of exon 7 in Edrf1 and exon 9 or 13 in Lrrc45. This study expands the understanding of the endogenous protective mechanisms of HPC and the DASEs that occur during HPC.
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Affiliation(s)
- Jun Li
- College of Science, Inner Mongolia Agricultural University, Hohhot, 010018, People's Republic of China
- School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou, 014010, People's Republic of China
- Inner Mongolia Key Laboratory of Functional Genome Bioinformatics, Inner Mongolia University of Science and Technology, Baotou, 014010, People's Republic of China
| | - Hongyu Zhao
- School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou, 014010, People's Republic of China
- Inner Mongolia Key Laboratory of Functional Genome Bioinformatics, Inner Mongolia University of Science and Technology, Baotou, 014010, People's Republic of China
| | - Yongqiang Xing
- School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou, 014010, People's Republic of China
- Inner Mongolia Key Laboratory of Functional Genome Bioinformatics, Inner Mongolia University of Science and Technology, Baotou, 014010, People's Republic of China
| | - Tongling Zhao
- School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou, 014010, People's Republic of China
- Inner Mongolia Key Laboratory of Functional Genome Bioinformatics, Inner Mongolia University of Science and Technology, Baotou, 014010, People's Republic of China
| | - Lu Cai
- School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou, 014010, People's Republic of China.
- Inner Mongolia Key Laboratory of Functional Genome Bioinformatics, Inner Mongolia University of Science and Technology, Baotou, 014010, People's Republic of China.
| | - Zuwei Yan
- College of Science, Inner Mongolia Agricultural University, Hohhot, 010018, People's Republic of China.
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Xia Z, Zhou X, Li J, Li L, Ma Y, Wu Y, Huang Z, Li X, Xu P, Xue M. Multiple-Omics Techniques Reveal the Role of Glycerophospholipid Metabolic Pathway in the Response of Saccharomyces cerevisiae Against Hypoxic Stress. Front Microbiol 2019; 10:1398. [PMID: 31316482 PMCID: PMC6610297 DOI: 10.3389/fmicb.2019.01398] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 06/04/2019] [Indexed: 11/13/2022] Open
Abstract
Although the biological processes of organism under hypoxic stress had been elucidated, the whole physiological changes of Saccharomyces cerevisiae are still unclear. In this work, we investigated the changes of biological process of S. cerevisiae under hypoxia by the methods of transcriptomics, proteomics, metabolomics, and bioinformatics. The results showed that the expression of a total of 1017 mRNA in transcriptome, 213 proteins in proteome, and 51 metabolites in metabolome had been significantly changed between the hypoxia and normoxia conditions. Moreover, based on the integration of system-omics data, we found that the carbohydrate, amino acids, fatty acid biosynthesis, lipid metabolic pathway, and oxidative phosphorylation were significantly changed in hypoxic stress. Among these pathways, the glycerophospholipid metabolic pathway was remarkably up-regulated from the mRNA, protein, and metabolites levels under hypoxic stress, and the expression of relevant mRNA was also confirmed by the qPCR. The metabolites of glycerophospholipid pathway such as phosphatidylcholine, phosphatidylethanolamine, phosphoinositide, and phosphatidic acids probably maintained the stability of cell membranes against hypoxic stress to relieve the cell injury, and kept S. cerevisiae survive with energy production. These findings in the hypoxic omics and integrated networks provide very useful information for further exploring the molecular mechanism of hypoxic stress.
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Affiliation(s)
- Zhengchao Xia
- Department of Pharmacology, Beijing Laboratory for Biomedical Detection Technology and Instrument, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Xuelin Zhou
- Department of Pharmacology, Beijing Laboratory for Biomedical Detection Technology and Instrument, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Jingyi Li
- Department of Pharmacology, Beijing Laboratory for Biomedical Detection Technology and Instrument, School of Basic Medical Sciences, Capital Medical University, Beijing, China.,Beijing Tropical Medicine Research Institute, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Lei Li
- Central Laboratory, Capital Medical University, Beijing, China
| | - Yi Ma
- Department of Pharmacology, Beijing Laboratory for Biomedical Detection Technology and Instrument, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Yi Wu
- Department of Pharmacology, Beijing Laboratory for Biomedical Detection Technology and Instrument, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Zhong Huang
- Health Branch College, Lanzhou Modern Vocational College, Lanzhou, China
| | - Xiaorong Li
- Department of Pharmacology, Beijing Laboratory for Biomedical Detection Technology and Instrument, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Pingxiang Xu
- Department of Pharmacology, Beijing Laboratory for Biomedical Detection Technology and Instrument, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Ming Xue
- Department of Pharmacology, Beijing Laboratory for Biomedical Detection Technology and Instrument, School of Basic Medical Sciences, Capital Medical University, Beijing, China.,Beijing Engineering Research Center for Nerve System Drugs, Beijing, China
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