Intramuscular fat (IMF) content and its fatty acid (FA) composition are typically controlled by several genes, each with a small effect. In the current study, to pinpoint candidate genes and putative regulators involved in FA composition, we performed a multivariate integrative analysis between intramuscular FA and transcriptome profiles of porcine longissimus dorsi (LD) muscle. We also carried out a combination of network, regulatory impact factor (RIF), in silico prediction of putative target genes, and functional analyses to better support the biological relevance of our findings. For this purpose, we used LD RNA-Seq and intramuscular FA composition profiles of 129 Iberian × Duroc backcrossed pigs. We identified 378 correlated variables (13 FA and 365 genes), including six FA (C20:4n-6, C18:2n-6, C20:3n-6, C18:1n-9, C18:0, and C16:1n-7) that were among the most interconnected variables in the predicted network. The detected FA-correlated genes include genes involved in lipid and/or carbohydrate metabolism or in regulation of IMF deposition (e.g., ADIPOQ, CHUK, CYCS, CYP4B1, DLD, ELOVL6, FBP1, G0S2, GCLC, HMGCR, IDH3A, LEP, LGALS12, LPIN1, PLIN1, PNPLA8, PPP1R1B, SDR16C5, SFRP5, SOD3, SNW1, and TFRC), meat quality (GALNT15, GOT1, MDH1, NEU3, PDHA1, SDHD, and UNC93A), and transport (e.g., EXOC7 and SLC44A2). Functional analysis highlighted 54 over-represented gene ontology terms, including well-known biological processes and pathways that regulate lipid and carbohydrate metabolism. RIF analysis suggested a pivotal role for six transcription factors (CARHSP1, LBX1, MAFA, PAX7, SIX5, and TADA2A) as putative regulators of gene expression and intramuscular FA composition. Based on in silico prediction, we identified putative target genes for these six regulators. Among these, TADA2A and CARHSP1 had extreme RIF scores and present novel regulators in pigs. In addition, the expression of TADA2A correlated (either positively or negatively) with C20:4n-6, C18:2n-6, C20:3n-6, C18:1n-9, and that of CARHSP1 correlated (positively) with the C16:1n-7 lipokine. We also found that these two transcription factors share target genes that are involved in lipid metabolism (e.g., GOT1, PLIN1, and TFRC). This integrative analysis of muscle transcriptome and intramuscular FA profile revealed valuable information about key candidate genes and potential regulators for FA and lipid metabolism in pigs, among which some transcription factors are proposed to control gene expression and modulate FA composition differences.

中文翻译：

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通过转录组分析鉴定猪肌内脂肪酸组成的候选调控基因


肌内脂肪 (IMF) 含量及其脂肪酸 (FA) 组成通常由多个基因控制，每个基因的影响都很小。在当前的研究中，为了查明参与 FA 组成的候选基因和假定的调节因子，我们对肌内 FA 和猪背最长肌 (LD) 肌肉的转录组谱进行了多变量综合分析。我们还结合了网络、调节影响因子 (RIF)、推定目标基因的计算机预测和功能分析，以更好地支持我们研究结果的生物学相关性。为此，我们使用了 129 头伊比利亚 × 杜洛克回交猪的 LD RNA-Seq 和肌内 FA 组成图谱。我们确定了 378 个相关变量（13 个 FA 和 365 个基因），包括 6 个 FA（C20:4n-6、C18:2n-6、C20:3n-6、C18:1n-9、C18:0 和 C16:1n- 7）它们是预测网络中相互关联性最强的变量之一。检测到的FA相关基因包括参与脂质和/或碳水化合物代谢或IMF沉积调节的基因（例如ADIPOQ、CHUK、CYCS、CYP4B1、DLD、ELOVL6、FBP1、G0S2、GCLC、HMGCR、IDH3A、LEP、LGALS12 、LPIN1、PLIN1、PNPLA8、PPP1R1B、SDR16C5、SFRP5、SOD3、SNW1 和 TFRC）、肉质（GALNT15、GOT1、MDH1、NEU3、PDHA1、SDHD 和 UNC93A）和运输（例如 EXOC7 和 SLC44A2）。功能分析突出显示了 54 个过度代表性的基因本体术语，包括众所周知的调节脂质和碳水化合物代谢的生物过程和途径。 RIF 分析表明，六种转录因子（CARHSP1、LBX1、MAFA、PAX7、SIX5 和 TADA2A）作为基因表达和肌内 FA 组成的假定调节因子发挥着关键作用。基于计算机预测，我们确定了这六个调节因子的假定目标基因。 其中，TADA2A 和 CARHSP1 具有极高的 RIF 评分，并在猪中呈现出新型调节因子。此外，TADA2A 的表达与 C20:4n-6、C18:2n-6、C20:3n-6、C18:1n-9 呈正相关或负相关，CARHSP1 的表达与 C16 呈正相关（正相关）。 ：1n-7脂因子。我们还发现这两个转录因子共享参与脂质代谢的靶基因（例如，GOT1、PLIN1 和 TFRC）。对肌肉转录组和肌内 FA 谱的综合分析揭示了有关猪 FA 和脂质代谢的关键候选基因和潜在调节因子的有价值的信息，其中一些转录因子被提出来控制基因表达和调节 FA 组成差异。