Abstract
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.
Highlights
Milk and dairy products are an excellent source of rich nutrients for humans, providing protein, fatty acids, minerals, and vitamins[1]
After removing reads containing adapters, reads containing poly-N/A, and low quality reads from raw data, we obtained 97.56 gigabases (Gb) and 5.27 Gb high-quality clean data for the mRNAs/long non-coding RNAs (lncRNAs) and miRNAs, respectively
We calculated the correlation coefficient (r2) of the sequencing data among the three individual cows in each period based on the FPKM and TPM values, and found that the r2 values were 0.860–0.995, 0.973–0.998, and 0.883–0.983 for the mRNAs, miRNAs, and lncRNAs, respectively, indicating that the similarity of the three biological replicates was sufficiently high
Summary
Milk and dairy products are an excellent source of rich nutrients for humans, providing protein, fatty acids, minerals, and vitamins[1]. Several RNA-seq studies of bovine transcriptomes in embryos, liver, mammary glands, and milk have been reported so far[7,8,9,10,11,12,13,14,15]. Liver is a complex digestive gland in ruminant animals including dairy cattle, plays an important role in the metabolism of carbohydrates, fats, proteins, vitamins, hormones, and other substances. Dorland et al reported the period of transition from late gestation to early lactation involved considerable metabolic adaptation in dairy cows and the liver, as a key role in adaptation, and supported pregnancy and lactation through coordination and interconversion of nutrients[39]. We built ceRNA regulatory networks via miRNAs to reveal the potential regulatory mechanisms controlling milk fat formation in liver of dairy cattle
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