慢性缺氧对三体虹鳟肝脏lncRNA和mRNA表达的影响

IF 2.2 2区生物学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY

Comparative Biochemistry and Physiology D-Genomics & Proteomics Pub Date : 2025-02-09 DOI:10.1016/j.cbd.2025.101442

Jun Sun , Yan Han , Jiao Li , Huizhen Li , Yuqiong Meng , Guoliang Sun , Changzhong Li , Rui Ma

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引用次数: 0

摘要

长链非编码rna （lncRNAs）在三倍体虹鳟鱼对环境胁迫（如缺氧）的响应中起着至关重要的作用。然而，三倍体虹鳟鱼肝脏中lncrna在慢性缺氧中的作用机制尚不完全清楚。因此，本研究采用高通量RNA测序和生物信息学分析的方法，研究了三倍体虹鳟鱼lncRNA及其靶基因对慢性缺氧的响应机制。结果显示，与常氧组相比，低氧组差异表达的lncrna （delncrna）有37个，差异表达的mrna （demrna）有780个。DElncRNAs的靶基因主要富集于叶酸、糖异生和视黄醇代谢途径下的Ferroptosis、One carbon pool中。GSEA富集的DEmRNA对视黄醇代谢和类固醇激素的生物合成有显著的富集作用。上述途径中有9个关键蛋白组成了蛋白-蛋白相互作用（PPI）网络。由于DElncRNAs与demrna共表达，筛选了9个关键demrna和13个DElncRNAs。基于Pearson相关系数>；0.99和DElncRNAs与demmrnas共表达关系，筛选出3对关键靶基因对（MSTRG.5664.2-pck1、XR_002475125.2-pck1和XR_005052355.1-pck1）。最后通过qRT-PCR验证关键基因的表达。这些结果为虹鳟鱼应对慢性缺氧提供了基础数据，为开发适应缺氧环境的虹鳟鱼饲料提供了技术支持。

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Comprehensive analysis of lncRNA and mRNA expression in triploid rainbow trout (Oncorhynchus mykiss) liver in response to chronic hypoxia

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Comprehensive analysis of lncRNA and mRNA expression in triploid rainbow trout (Oncorhynchus mykiss) liver in response to chronic hypoxia

Long non-coding RNAs (lncRNAs) play a crucial role in response to environmental stresses (e.g. hypoxia) in triploid rainbow trout. However, the action mechanism of lncRNAs in triploid rainbow trout liver in chronic hypoxia is still not fully understood. Therefore, we investigated the mechanism of lncRNA and its target genes in response to chronic hypoxia in triploid rainbow trout using high-throughput RNA sequencing and bioinformatics analysis in this study. Results showed that 37 differentially expressed lncRNAs (DElncRNAs) and 780 differentially expressed mRNAs (DEmRNAs) were found in hypoxic group compared to normoxic group. Target genes of DElncRNAs were mainly enriched in Ferroptosis, One carbon pool by folate, Gluconeogenesis and Retinol metabolism pathways. GSEA enrichment of DEmRNA showed significant enrichment for retinol metabolism and steroid hormone biosynthesis. There were 9 key proteins in above pathways forming a protein-protein interaction (PPI) network. As a result of co-expression of DElncRNAs with DEmRNAs, 9 key DEmRNAs and 13 DElncRNAs were screened. Based on the Pearson correlation coefficient > 0.99 and the co-expression relationship between DElncRNAs and DEmRNAs, 3 pairs (MSTRG.5664.2-pck1, XR_002475125.2-pck1, and XR_005052355.1-pck1) of key target gene pairs were screened. Finally, qRT-PCR verified the expression of critical genes. These results provide basic data for rainbow trout to cope with chronic hypoxia and technical support for the development of rainbow trout feeds adapted to hypoxic environments.

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来源期刊

Comparative Biochemistry and Physiology D-Genomics & Proteomics 生物-生化与分子生物学

CiteScore

5.10

自引率

3.30%

发文量

审稿时长

33 days

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.