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首页> 外文期刊>BMC Genomics >Integrative analysis of microRNAs and mRNAs revealed regulation of composition and metabolism in Nelore cattle
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Integrative analysis of microRNAs and mRNAs revealed regulation of composition and metabolism in Nelore cattle

机译：microRNA和mRNA的整合分析揭示了内罗尔牛的组成和代谢调控

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The amount of intramuscular fat can influence the sensory characteristics and nutritional value of beef, thus the selection of animals with adequate fat deposition is important to the consumer. There is growing knowledge about the genes and pathways that control the biological processes involved in fat deposition in muscle. MicroRNAs (miRNAs) belong to a well-conserved class of non-coding small RNAs that modulate gene expression across a range of biological functions in animal development and physiology. The aim of this study was to identify differentially expressed (DE) miRNAs, regulatory candidate genes and co-expression networks related to intramuscular fat (IMF) deposition. To achieve this, we used mRNA and miRNA expression data from the Longissimus dorsi muscle of 30 Nelore steers with high (H) and low (L) genomic estimated breeding values (GEBV) for IMF deposition. Differential miRNA expression analysis between animals with extreme GEBV values for IMF identified six DE miRNAs (FDR 10%). Functional annotation of the target genes for these microRNAs indicated that the PPARs signaling pathway is involved with IMF deposition. Candidate regulatory genes such as SDHAF4, FBXO17, ALDOA and PKM were identified by partial correlation with information theory (PCIT), phenotypic impact factor (PIF) and regulatory impact factor (RIF) co-expression approaches from integrated miRNA-mRNA expression data. Two DE miRNAs (FDR 10%), bta-miR-143 and bta-miR-146b, which were upregulated in the Low IMF group, were correlated with regulatory candidate genes, which were functionally enriched for fatty acid oxidation GO terms. Co-expression patterns obtained by weighted correlation network analysis (WGCNA), which showed possible interaction and regulation between mRNAs and miRNAs, identified several modules related to immune system function, protein metabolism, energy metabolism and glucose catabolism according to in silico analysis performed herein. In this study, several genes and miRNAs were identified as candidate regulators of IMF by analyzing DE miRNAs using two different miRNA-mRNA co-expression network methods. This study contributes to the understanding of potential regulatory mechanisms of gene signaling networks involved in fat deposition processes measured in muscle. Glucose metabolism and inflammation processes were the main pathways found in silico to influence intramuscular fat deposition in beef cattle in the integrative mRNA-miRNA co-expression analysis.
机译：肌内脂肪的量会影响牛肉的感官特性和营养价值，因此选择具有足够脂肪沉积的动物对消费者来说很重要。关于控制与肌肉脂肪沉积有关的生物过程的基因和途径的知识越来越多。 MicroRNA（miRNA）属于一类保存良好的非编码小RNA，可在动物发育和生理学中调节多种生物学功能的基因表达。这项研究的目的是确定与肌肉内脂肪（IMF）沉积有关的差异表达（DE）miRNA，调控候选基因和共表达网络。为实现此目的，我们使用了30个Nelore牛的Longissimus dorsi肌肉的mRNA和miRNA表达数据，这些基因具有高（H）和低（L）基因组估计育种值（GEBV）用于IMF沉积。具有极端GEBV值的IMF动物之间的差异性miRNA表达分析确定了六个DE miRNA（FDR 10％）。这些microRNA的目标基因的功能注释表明PPARs信号通路与IMF沉积有关。候选调节基因如SDHAF4，FBXO17，ALDOA和PKM通过与信息理论（PCIT），表型影响因子（PIF）和调节影响因子（RIF）共表达方法的部分相关性从整合的miRNA-mRNA表达数据中鉴定出来。在低IMF组中上调的两个DE miRNA（FDR 10％）bta-miR-143和bta-miR-146b与调节性候选基因相关，后者在功能上富含脂肪酸氧化GO术语。通过加权相关网络分析（WGCNA）获得的共表达模式显示了mRNA和miRNA之间可能的相互作用和调控，根据本文进行的计算机分析，确定了与免疫系统功能，蛋白质代谢，能量代谢和葡萄糖分解代谢有关的几个模块。在这项研究中，通过使用两种不同的miRNA-mRNA共表达网络方法分析DE miRNA，鉴定了几种基因和miRNA作为IMF的候选调控因子。这项研究有助于了解潜在的调控机制的基因信号网络参与肌肉中的脂肪沉积过程。在综合mRNA-miRNA共表达分析中，葡萄糖代谢和炎症过程是影响硅牛肌肉内脂肪沉积的主要途径。

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