Genome-Wide Analysis of mRNAs and lncRNAs of Intramuscular Fat Related to Lipid Metabolism in Two Pig Breeds
Genome-Wide Analysis of mRNAs and lncRNAs of Intramuscular Fat Related to Lipid Metabolism in Two Pig Breeds
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DOI：
10.1159/000495101
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发表时间：
2018-01-01
影响因子：
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通讯作者：
Miao, Xiangyang
中科院分区：
文献类型：
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作者：
Huang, Wanlong;Zhang, Xiuxiu;Miao, Xiangyang
背景/目的：长非编码RNA(Long Non-Coding RNAs，LncRNAs)可调节脂肪生成和脂肪堆积。不同品种猪的肌内脂肪沉积似乎不同，其调控机制在分子水平上尚未完全阐明。此外，关于lncRNAs在猪肌内脂肪沉积和代谢中的功能和分布还知之甚少。因此，本研究的目的是探索lncRNAs在肌肉内脂肪沉积中的调节功能。方法：选用脂肪沉积差异显著的莱芜猪(LW)和大白猪(LY)。本研究利用RNA-SEQ技术和生物信息学方法对LW和LY猪肌内脂肪的基因表达谱进行了比较分析，以寻找与脂肪代谢和脂肪形成相关的关键mRNAs和lncRNAs。采用实时荧光定量聚合酶链式反应检测差异表达的mRNAs和lncRNAs的表达水平。结果：共有513个mRNAs和55个lncRNAs在两个猪品种间存在差异表达。通过共表达网络的构建以及顺式和反式调控靶基因的分析，共鉴定出31个关键的lncRNAs。基因本体论和KEGG途径分析表明，差异表达的基因和lncRNAs主要参与脂肪形成和脂代谢相关的生物学过程和途径。结论：XLOC_046142、XLOC_004398和XLOC_015408可能分别针对MAPKAPK2、NR1D2和AKR1C4，在猪肌内脂肪生成和脂肪积累过程中起着关键的调节作用。XLOC_064871和XLOC_011001可能通过调节TRIB3和BRCA1在脂代谢相关疾病中发挥作用。本研究为LncRNA的研究提供了有价值的资源，加深了我们对脂代谢相关基因的生物学作用以及肌内脂肪代谢和沉积的分子机制的认识。
Background/Aims: Long non-coding RNAs (lncRNAs) can regulate adipogenesis and lipid accumulation. Intramuscular fat deposition appears to vary in different pig breeds, and the regulation mechanism has not yet been fully elucidated at molecular level. Moreover, little is known about the function and profile of lncRNAs in intramuscular fat deposition and metabolism in pig. The aim of this study was thus to explore the regulatory functions of lncRNAs in intramuscular fat deposition. Methods: In this study, Laiwu (LW) pig and Large White (LY) pig with significant difference in fat deposition were selected for use. RNA-seq technology and bioinformatics methods were used to comparatively analyze the gene expression profiles of intramuscular fat between LW and LY pigs to identify key mRNAs and lncRNAs associated with lipid metabolism and adipogenesis. Real-time fluorescence-based quantitative PCR was applied to verify the expression level of the differentially expressed mRNAs and lncRNAs. Results: A total of 513 mRNAs and 55 lncRNAs were differentially expressed between two pig breeds. By co-expression network construction as well as cis- and trans-regulated target gene analysis, 31 key lncRNAs were identified. Gene Ontology and KEGG pathway analyses revealed that differentially expressed genes and lncRNAs were mainly involved in the biological processes and pathways related to adipogenesis and lipid metabolism. Conclusion:XLOC_046142, XLOC_004398 and XLOC_015408 may target MAPKAPK2, NR1D2 and AKR1C4, respectively, and play critical regulatory roles in intramuscular adipogenesis and lipid accumulation in pig. XLOC_064871 and XLOC_011001 may play a role in lipid metabolism-related disease via regulating TRIB3 and BRCA1. This study provides a valuable resource for lncRNA study and improves our understanding of the biological roles of lipid metabolism- related genes and molecular mechanism of intramuscular fat metabolism and deposition.