{"title":"镉暴露引起太平洋南美白对虾RNA m6A动态修饰和外转录组调控","authors":"","doi":"10.1016/j.cbd.2024.101307","DOIUrl":null,"url":null,"abstract":"<div><p>N6-methyladenosine (m<sup>6</sup>A) methylation is the most prevalent post-transcriptional RNA modification in eukaryotic organisms, but its roles in the regulation of physiological resistance of marine crustaceans to heavy metal pollutants are poorly understood. In this study, the transcriptome-wide m<sup>6</sup>A RNA methylation profiles and dynamic m<sup>6</sup>A changes induced by acute Cd<sup>2+</sup> exposure in the the pacific whiteleg shrimp <em>Litopenaeus vannamei</em> were comprehensively analyzed. Cd<sup>2+</sup> toxicity caused a significant reduction in global RNA m<sup>6</sup>A methylation level, with major m<sup>6</sup>A regulators including the m<sup>6</sup>A methyltransferase <em>METTL3</em> and the m<sup>6</sup>A binding protein <em>YTHDF2</em> showing declined expression. Totally, 11,467 m<sup>6</sup>A methylation peaks from 6415 genes and 17,291 peaks within 7855 genes were identified from the Cd<sup>2+</sup> exposure group and the control group, respectively. These m<sup>6</sup>A peaks were predominantly enriched in the 3′ untranslated region (UTR) and around the start codon region of the transcripts. 7132 differentially expressed genes (DEGs) and 7382 differentially m<sup>6</sup>A-methylated genes (DMGs) were identified. 3186 genes showed significant changes in both gene expression and m<sup>6</sup>A methylation levels upon cadmium exposure, and they were related to a variety of biological processes and gene pathways. Notably, an array of genes associated with antioxidation homeostasis, transmembrane transporter activity and intracellular detoxification processes were significantly enriched, demonstrating that m<sup>6</sup>A modification may mediate the physiological responses of shrimp to cadmium toxicity via regulating ROS balance, Cd<sup>2+</sup> transport and toxicity mitigation. The study would contribute to a deeper understanding of the evolutionary and functional significance of m<sup>6</sup>A methylation to the physiological resilience of decapod crustaceans to heavy metal toxicants.</p></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":null,"pages":null},"PeriodicalIF":2.2000,"publicationDate":"2024-08-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"Cadmium exposure elicited dynamic RNA m6A modification and epi-transcriptomic regulation in the Pacific whiteleg shrimp Litopenaeus vannamei\",\"authors\":\"\",\"doi\":\"10.1016/j.cbd.2024.101307\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<div><p>N6-methyladenosine (m<sup>6</sup>A) methylation is the most prevalent post-transcriptional RNA modification in eukaryotic organisms, but its roles in the regulation of physiological resistance of marine crustaceans to heavy metal pollutants are poorly understood. In this study, the transcriptome-wide m<sup>6</sup>A RNA methylation profiles and dynamic m<sup>6</sup>A changes induced by acute Cd<sup>2+</sup> exposure in the the pacific whiteleg shrimp <em>Litopenaeus vannamei</em> were comprehensively analyzed. Cd<sup>2+</sup> toxicity caused a significant reduction in global RNA m<sup>6</sup>A methylation level, with major m<sup>6</sup>A regulators including the m<sup>6</sup>A methyltransferase <em>METTL3</em> and the m<sup>6</sup>A binding protein <em>YTHDF2</em> showing declined expression. Totally, 11,467 m<sup>6</sup>A methylation peaks from 6415 genes and 17,291 peaks within 7855 genes were identified from the Cd<sup>2+</sup> exposure group and the control group, respectively. These m<sup>6</sup>A peaks were predominantly enriched in the 3′ untranslated region (UTR) and around the start codon region of the transcripts. 7132 differentially expressed genes (DEGs) and 7382 differentially m<sup>6</sup>A-methylated genes (DMGs) were identified. 3186 genes showed significant changes in both gene expression and m<sup>6</sup>A methylation levels upon cadmium exposure, and they were related to a variety of biological processes and gene pathways. Notably, an array of genes associated with antioxidation homeostasis, transmembrane transporter activity and intracellular detoxification processes were significantly enriched, demonstrating that m<sup>6</sup>A modification may mediate the physiological responses of shrimp to cadmium toxicity via regulating ROS balance, Cd<sup>2+</sup> transport and toxicity mitigation. The study would contribute to a deeper understanding of the evolutionary and functional significance of m<sup>6</sup>A methylation to the physiological resilience of decapod crustaceans to heavy metal toxicants.</p></div>\",\"PeriodicalId\":55235,\"journal\":{\"name\":\"Comparative Biochemistry and Physiology D-Genomics & Proteomics\",\"volume\":null,\"pages\":null},\"PeriodicalIF\":2.2000,\"publicationDate\":\"2024-08-06\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Comparative Biochemistry and Physiology D-Genomics & Proteomics\",\"FirstCategoryId\":\"99\",\"ListUrlMain\":\"https://www.sciencedirect.com/science/article/pii/S1744117X24001205\",\"RegionNum\":2,\"RegionCategory\":\"生物学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q4\",\"JCRName\":\"BIOCHEMISTRY & MOLECULAR BIOLOGY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","FirstCategoryId":"99","ListUrlMain":"https://www.sciencedirect.com/science/article/pii/S1744117X24001205","RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q4","JCRName":"BIOCHEMISTRY & MOLECULAR BIOLOGY","Score":null,"Total":0}
Cadmium exposure elicited dynamic RNA m6A modification and epi-transcriptomic regulation in the Pacific whiteleg shrimp Litopenaeus vannamei
N6-methyladenosine (m6A) methylation is the most prevalent post-transcriptional RNA modification in eukaryotic organisms, but its roles in the regulation of physiological resistance of marine crustaceans to heavy metal pollutants are poorly understood. In this study, the transcriptome-wide m6A RNA methylation profiles and dynamic m6A changes induced by acute Cd2+ exposure in the the pacific whiteleg shrimp Litopenaeus vannamei were comprehensively analyzed. Cd2+ toxicity caused a significant reduction in global RNA m6A methylation level, with major m6A regulators including the m6A methyltransferase METTL3 and the m6A binding protein YTHDF2 showing declined expression. Totally, 11,467 m6A methylation peaks from 6415 genes and 17,291 peaks within 7855 genes were identified from the Cd2+ exposure group and the control group, respectively. These m6A peaks were predominantly enriched in the 3′ untranslated region (UTR) and around the start codon region of the transcripts. 7132 differentially expressed genes (DEGs) and 7382 differentially m6A-methylated genes (DMGs) were identified. 3186 genes showed significant changes in both gene expression and m6A methylation levels upon cadmium exposure, and they were related to a variety of biological processes and gene pathways. Notably, an array of genes associated with antioxidation homeostasis, transmembrane transporter activity and intracellular detoxification processes were significantly enriched, demonstrating that m6A modification may mediate the physiological responses of shrimp to cadmium toxicity via regulating ROS balance, Cd2+ transport and toxicity mitigation. The study would contribute to a deeper understanding of the evolutionary and functional significance of m6A methylation to the physiological resilience of decapod crustaceans to heavy metal toxicants.
期刊介绍:
Comparative Biochemistry & Physiology (CBP) publishes papers in comparative, environmental and evolutionary physiology.
Part D: Genomics and Proteomics (CBPD), focuses on “omics” approaches to physiology, including comparative and functional genomics, metagenomics, transcriptomics, proteomics, metabolomics, and lipidomics. Most studies employ “omics” and/or system biology to test specific hypotheses about molecular and biochemical mechanisms underlying physiological responses to the environment. We encourage papers that address fundamental questions in comparative physiology and biochemistry rather than studies with a focus that is purely technical, methodological or descriptive in nature.