Intramuscular fat content is one of the most important factors affecting beef quality. However, the role of alternate polyadenylation (APA) in intramuscular fat deposition remains unclear. We compared APA events in muscle samples from high and low intramuscular fat (IMF) cattle, based on RNA-seq data. A total of 363 significant APAs were identified. Notably, the number of shortened 3′UTR events exceeded the number of lengthened 3′UTR events, and genes associated with shortened 3′UTR events were enriched in fatty acid metabolism-related pathways. Most APA events had alternative 3′UTR (aUTR) lengths of 200-300 bp. As the 3′UTR lengthened, the aUTR also lengthened (R2 = 0.79). These findings indicate that genes with longer 3′UTRs are more likely to be regulated by APA in the muscle of cattle with high IMF. To determine whether the identified APA events drove alterations in the expression of fat deposition-related genes, we analyzed the relationship between APA events and differentially expressed genes and identified several genes critical for fat deposition (e.g., PFKL and SLC1A5). Since miRNAs usually bind to the 3'UTR region of protein-coding genes and affect gene expression, we constructed an miRNA-APA network to detect several key miRNAs that may regulate fat deposition. We identified 10 important miRNAs that affect changes in IMF content, which may be gained (gained miRNA-binding sites) or lost (lost miRNA-binding sites) owing to 187 differential APA events. Our study characterized the APA profiles of cattle with high and low intramuscular fat content and provided further insights into the relationship between APA, miRNA, and fat deposition.

中文翻译：

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牛肌内脂肪含量高和低的背最长肌的替代多腺苷酸化景观


肌内脂肪含量是影响牛肉品质的最重要因素之一。然而，交替聚腺苷酸化 （APA） 在肌内脂肪沉积中的作用仍不清楚。我们根据 RNA-seq 数据比较了高和低肌内脂肪 （IMF） 牛肌肉样本中的 APA 事件。共确定了 363 个重要的 APA。值得注意的是，缩短的 3'UTR 事件的数量超过了延长的 3'UTR 事件的数量，并且与缩短的 3'UTR 事件相关的基因在脂肪酸代谢相关通路中富集。大多数 APA 事件具有 200-300 bp 的替代 3′UTR （aUTR） 长度。随着 3′UTR 的延长，aUTR 也延长 （R2 = 0.79）。这些发现表明，在具有高 IMF 的牛的肌肉中，具有较长 3′UTR 的基因更有可能受到 APA 的调节。为了确定已鉴定的 APA 事件是否驱动脂肪沉积相关基因表达的改变，我们分析了 APA 事件与差异表达基因之间的关系，并确定了几个对脂肪沉积至关重要的基因 （例如，PFKL 和 SLC1A5）。由于 miRNAs 通常与蛋白质编码基因的 3'UTR 区域结合并影响基因表达，因此我们构建了一个 miRNA-APA 网络来检测可能调节脂肪沉积的几个关键 miRNA。我们确定了 10 个影响 IMF 含量变化的重要 miRNA，由于 187 个不同的 APA 事件，这些 miRNA 可能会获得（获得 miRNA 结合位点）或丢失（丢失 miRNA 结合位点）。我们的研究表征了肌内脂肪含量高和低的牛的 APA 谱，并进一步揭示了 APA 、 miRNA 和脂肪沉积之间的关系。