Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Key Laboratory of Animal Genetics and Breeding of Ministry of Agriculture, National Engineering Laboratory of Animal Breeding, China Agricultural University, Beijing, 100193, China.
Department of Animal Production and Environmental Control, College of Animal Science and Technology, Hebei Agricultural University, Baoding, 071001, China.
Sci Rep. 2017 Jul 25;7(1):6396. doi: 10.1038/s41598-017-06634-w.
RNA sequencing has been extensively used to study specific gene expression patterns to discover potential key genes related to complex traits of interest in animals. Of note, a new regulatory mechanism builds a large-scale regulatory network among transcriptome, where lncRNAs act as competing endogenous RNAs (ceRNAs) to sponge miRNAs to regulate the expression of miRNA target genes post-transcriptionally. In this study, we sequenced the cDNA and sRNA libraries of nine liver samples from three Holstein cows during dry period, early lactation, and peak of lactation with HiSeq platform. As a result, we identified 665 genes, 57 miRNAs and 33 lncRNAs that displayed differential expression patterns across periods. Subsequently, a total of 41ceRNA pairs (lncRNA-mRNA) sharing 11 miRNAs were constructed including 30 differentially expressed genes. Importantly, 12 among them were presented in our large metabolic networks, and predicted to influence the lipid metabolism through insulin, PI3K-Akt, MAPK, AMPK, mTOR, and PPAR signaling pathways, thus, these genes were considered as the most promising candidates for milk fat formation. To our knowledge, this is first investigation to profile the ceRNA regulatory networks of liver transcriptome that could affect milk fat synthesis in bovine, providing a new view of the regulatory mechanism of RNAs.
RNA 测序已被广泛用于研究特定基因的表达模式，以发现与动物感兴趣的复杂特征相关的潜在关键基因。值得注意的是，一种新的调控机制在转录组中构建了一个大规模的调控网络，其中 lncRNA 作为竞争性内源 RNA（ceRNA）来吸收 miRNA，从而在后转录水平调节 miRNA 靶基因的表达。在这项研究中，我们使用 HiSeq 平台对 3 头荷斯坦奶牛在干奶期、泌乳早期和泌乳高峰期的 9 个肝脏样本的 cDNA 和 sRNA 文库进行了测序。结果，我们鉴定了 665 个基因、57 个 miRNA 和 33 个 lncRNA，它们在不同时期表现出不同的表达模式。随后，构建了总共 41 对（lncRNA-mRNA）ceRNA 对，共享 11 个 miRNA，包括 30 个差异表达基因。重要的是，其中 12 个存在于我们的大型代谢网络中，并预测通过胰岛素、PI3K-Akt、MAPK、AMPK、mTOR 和 PPAR 信号通路影响脂质代谢，因此，这些基因被认为是乳脂形成最有前途的候选基因。据我们所知，这是首次对影响牛乳脂合成的肝脏转录组 ceRNA 调控网络进行分析，为 RNA 的调控机制提供了新的视角。
