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低氧胁迫下红鳍东方鲀肝脏全基因组甲基化和基因表达分析
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Abstract:
本研究利用WGBS和RNA-Seq技术，比较分析了常氧和低氧胁迫下红鳍东方鲀肝脏的DNA甲基化和基因表达差异。研究鉴定了差异甲基化区域(DMRs)、差异甲基化基因(DMGs)和差异表达基因(DEGs)，并进行了GO和KEGG富集分析。通过关联甲基化和转录组数据，探索了二者之间的潜在联系，发现甲基化程度升高与转录组表达降低呈负相关趋势，并鉴定了一些在甲基化和转录组数据中同时富集的通路和基因，例如robo2和prkcb。研究旨在揭示低氧胁迫下红鳍东方鲀肝脏的分子机制。
In this study, WGBS and RNA-Seq technology were used to compare and analyze the differences in DNA methylation and gene expression in the liver of Takifugu rubripes under normoxia and hypoxic stress. Differentially methylated regions (DMRs), differentially methylated genes (DMGs) and differentially expressed genes (DEGs) were identified and GO and KEGG enrichment analyses were performed. By correlating methylation and transcriptome data, the potential link between the two was explored, and a negative correlation between increased methylation and decreased transcriptome expression was found, and some pathways and genes enriched in both methylation and transcriptome data were identified, such as robo2 and prkcb. The aim of this study was to reveal the molecular mechanism of the liver of the Takifugu rubripes under hypoxic stress.
| [1] | 崔舒畅, 曾范双, 武琳, 等. 北方海域五种鱼类营养需求的研究进展[J]. 中国饲料, 2023(13): 68-78. |
| [2] | 郝薇薇, 高长富, 仇雪梅, 等. 红鳍东方鲀转录因子GATA4基因的表达[J]. 生物技术通报, 2016, 32(6): 155. |
| [3] | Abdel-Tawwab, M., Monier, M.N., Hoseinifar, S.H. and Faggio, C. (2019) Fish Response to Hypoxia Stress: Growth, Physiological, and Immunological Biomarkers. Fish Physiology and Biochemistry, 45, 997-1013. https://doi.org/10.1007/s10695-019-00614-9 |
| [4] | 梁燕珊. 珍珠龙胆石斑鱼对急性低氧胁迫的转录组响应研究[D]: [硕士学位论文]. 湛江: 广东海洋大学, 2023. |
| [5] | 余家麒. 青海湖裸鲤低氧胁迫的转录组学分析[D]: [硕士学位论文]. 西宁: 青海大学, 2023. |
| [6] | Li, M., Wang, X., Qi, C., Li, E., Du, Z., Qin, J.G., et al. (2018) Metabolic Response of Nile Tilapia (Oreochromis niloticus) to Acute and Chronic Hypoxia Stress. Aquaculture, 495, 187-195. https://doi.org/10.1016/j.aquaculture.2018.05.031 |
| [7] | van der Weele, C.M. and Jeffery, W.R. (2022) Cavefish Cope with Environmental Hypoxia by Developing More Erythrocytes and Overexpression of Hypoxia-Inducible Genes. eLife, 11, e69109. https://doi.org/10.7554/elife.69109 |
| [8] | Ma, Q., Zhang, R., Wei, Y., Liang, M. and Xu, H. (2024) Effects of Intermittent and Chronic Hypoxia on Fish Size and Nutrient Metabolism in Tiger Puffer (Takifugu rubripes). Animals, 14, Article No. 2470. https://doi.org/10.3390/ani14172470 |
| [9] | 宋娜, 黄娜婷, 王舒闻, 等. 肝脏在牦牛对高原环境适应过程中的生物学作用及相关机制研究[J]. 黑龙江畜牧兽医, 2024(20): 117-123+132-134. |
| [10] | 张楠, 黄慈, 王会, 王嘉博, 柴志欣, 岳炳霖, 王吉坤. 牦牛不同发育时期卵巢全基因组甲基化谱分析[J]. 南京农业大学学报, 2024: 1-15. |
| [11] | Goldberg, A.D., Allis, C.D. and Bernstein, E. (2007) Epigenetics: A Landscape Takes Shape. Cell, 128, 635-638. https://doi.org/10.1016/j.cell.2007.02.006 |
| [12] | Gu, Y., Jin, C.X., Tong, Z.H., Jiang, T., Yao, F.C., Zhang, Y., et al. (2024) Expression of Genes Related to Gonadal Development and Construction of Gonadal DNA Methylation Maps of Trachinotus blochii under Hypoxia. Science of the Total Environment, 935, Article ID: 173172. https://doi.org/10.1016/j.scitotenv.2024.173172 |
| [13] | Li, X., Liu, B., Yang, J., Li, G., Wen, H., Zhang, M., et al. (2022) DNA Methylation in Promoter Region of Immune Related Genes STAT3 and VEGFA and Biochemical Parameters Change in Muscle of Japanese Flounder under Acute Hypoxia. Developmental & Comparative Immunology, 129, Article ID: 104295. https://doi.org/10.1016/j.dci.2021.104295 |
| [14] | Gonçalo, S., Paulo, S., et al. (2022) Trimming and Validation of Illumina Short Reads Using Trimmomatic, Trinity Assembly, and Assessment of RNA-Seq Data. Methods in Molecular Biology (Clifton, N.J.), 2443, 211-232. |
| [15] | Krueger, F. and Andrews, S.R. (2011) Bismark: A Flexible Aligner and Methylation Caller for Bisulfite-Seq Applications. Bioinformatics, 27, 1571-1572. https://doi.org/10.1093/bioinformatics/btr167 |
| [16] | Akalin, A., Kormaksson, M., Li, S., Garrett-Bakelman, F.E., Figueroa, M.E., Melnick, A., et al. (2012) Methylkit: A Comprehensive R Package for the Analysis of Genome-Wide DNA Methylation Profiles. Genome Biology, 13, R87. https://doi.org/10.1186/gb-2012-13-10-r87 |
| [17] | 李岩. 长期低氧胁迫下的红鳍东方鲀鳔转录组变化及关键差异基因功能分析[D]: [硕士学位论文]. 大连: 大连海洋大学, 2023. |
| [18] | Kim, S.W. and Kim, K. (2020) Expression of Genes Involved in Axon Guidance: How Much Have We Learned? International Journal of Molecular Sciences, 21, Article No. 3566. https://doi.org/10.3390/ijms21103566 |
| [19] | Koohini, Z., Koohini, Z. and Teimourian, S. (2019) Slit/Robo Signaling Pathway in Cancer; a New Stand Point for Cancer Treatment. Pathology & Oncology Research, 25, 1285-1293. https://doi.org/10.1007/s12253-018-00568-y |
| [20] | Li, X., Ren, Y., Sorokin, V., Poh, K.K., Ho, H.H., Lee, C.N., et al. (2014) Quantitative Profiling of the Rat Heart Myoblast Secretome Reveals Differential Responses to Hypoxia and Re-Oxygenation Stress. Journal of Proteomics, 98, 138-149. https://doi.org/10.1016/j.jprot.2013.12.025 |
| [21] | Hauptman, G., Reichert, M.C., Abdal Rhida, M.A. and Evans, T.A. (2022) Characterization of Enhancer Fragments in drosophila Robo2. Fly, 16, 312-346. https://doi.org/10.1080/19336934.2022.2126259 |
| [22] | Motwani, J., Rodger, E.J., Stockwell, P.A., Baguley, B.C., Macaulay, E.C. and Eccles, M.R. (2021) Genome-Wide DNA Methylation and RNA Expression Differences Correlate with Invasiveness in Melanoma Cell Lines. Epigenomics, 13, 577-598. https://doi.org/10.2217/epi-2020-0440 |
| [23] | Ji, F., Fu, S., Shen, S., Zhang, L., Cao, Q., Li, S., et al. (2015) The Prognostic Value of Combined TGF-β1 and ELF in Hepatocellular Carcinoma. BMC Cancer, 15, Article No. 116. https://doi.org/10.1186/s12885-015-1127-y |
| [24] | Deng, Z., Fan, T., Xiao, C., Tian, H., Zheng, Y., Li, C., et al. (2024) TGF-β Signaling in Health, Disease and Therapeutics. Signal Transduction and Targeted Therapy, 9, Article No. 61. https://doi.org/10.1038/s41392-024-01764-w |
| [25] | Chen, J., Gingold, J.A. and Su, X. (2019) Immunomodulatory TGF-β Signaling in Hepatocellular Carcinoma. Trends in Molecular Medicine, 25, 1010-1023. https://doi.org/10.1016/j.molmed.2019.06.007 |
| [26] | Gao, L., Xing, X., Guo, R., Li, Q., Xu, Y., Pan, H., et al. (2024) Effect of Different Dietary Iron Contents on Liver Transcriptome Characteristics in Wujin Pigs. Animals, 14, Article No. 2399. https://doi.org/10.3390/ani14162399 |
| [27] | Zhang, H., Li, R., Wang, Y., Zhou, J., Xu, H., Gou, M., et al. (2023) Transcriptomic Analysis of Takifugu Obscurus Gills under Acute Hypoxic Stress. Animals, 13, Article No. 1572. https://doi.org/10.3390/ani13101572 |
| [28] | Chen, C., Song, C., Liu, B., Wang, Y., Jia, J., Pang, K., et al. (2024) Activation of BMP4/SMAD Pathway by HIF-1α in Hypoxic Environment Promotes Osteogenic Differentiation of BMSCS and Leads to Ectopic Bone Formation. Tissue and Cell, 88, Article ID: 102376. https://doi.org/10.1016/j.tice.2024.102376 |
| [29] | Brochu-Gaudreau, K., Charbonneau, M., Harper, K. and Dubois, C.M. (2022) Hypoxia Selectively Increases a SMAD3 Signaling Axis to Promote Cancer Cell Invasion. Cancers, 14, Article No. 2751. https://doi.org/10.3390/cancers14112751 |
| [30] | Seifried, H.E., Anderson, D.E., Fisher, E.I. and Milner, J.A. (2007) A Review of the Interaction among Dietary Antioxidants and Reactive Oxygen Species. The Journal of Nutritional Biochemistry, 18, 567-579. https://doi.org/10.1016/j.jnutbio.2006.10.007 |
| [31] | Roffey, J., Rosse, C., Linch, M., Hibbert, A., McDonald, N.Q. and Parker, P.J. (2009) Protein Kinase C Intervention—The State of Play. Current Opinion in Cell Biology, 21, 268-279. https://doi.org/10.1016/j.ceb.2009.01.019 |
| [32] | Feng, D., Wang, Z., Zhao, Y., Li, Y., Liu, D., Chen, Z., et al. (2020) circ-PRKCB Acts as a Cerna to Regulate P66shc-Mediated Oxidative Stress in Intestinal Ischemia/Reperfusion. Theranostics, 10, 10680-10696. https://doi.org/10.7150/thno.44250 |
| [33] | Yang, Y., Fu, Q., Wang, X., Liu, Y., Zeng, Q., Li, Y., et al. (2018) Comparative Transcriptome Analysis of the Swim Bladder Reveals Expression Signatures in Response to Low Oxygen Stress in Channel Catfish, Ictalurus punctatus. Physiological Genomics, 50, 636-647. https://doi.org/10.1152/physiolgenomics.00125.2017 |
| [34] | Li, L., Fei, X., Wang, H., Chen, S., Xu, X., Ke, H., et al. (2024) Genome-Wide DNA Methylation Profiling Reveals a Novel Hypermethylated Biomarker PRKCB in Gastric Cancer. Scientific Reports, 14, Article No. 26605. https://doi.org/10.1038/s41598-024-78135-6 |
