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. 2021 Mar 4:12:579393.
doi: 10.3389/fgene.2021.579393. eCollection 2021.

Metabolic Regulations by lncRNA, miRNA, and ceRNA Under Grass-Fed and Grain-Fed Regimens in Angus Beef Cattle

Cunling Jia  1   2 , Ying Bai  2 , Jianan Liu  2 , Wentao Cai  2 , Lei Liu  2   3 , Yanghua He  4 , Jiuzhou Song  2
Affiliations

Metabolic Regulations by lncRNA, miRNA, and ceRNA Under Grass-Fed and Grain-Fed Regimens in Angus Beef Cattle

Cunling Jia et al. Front Genet. .

Abstract

Beef cattle raised under grass-fed and grain-fed have many differences, including metabolic efficiency and meat quality. To investigate these two regimens' intrinsic influence on beef cattle, we used high-throughput sequencing and metabolomics analyses to explore differentially expressed genes (DEGs) and metabolimic networks in the liver. A total of 200 DEGs, 76 differentially expressed miRNAs (DEmiRNAs), and two differentially expressed lncRNAs (DElncRNAs) were detected between regimen groups. Metabolic processes and pathways enriched functional genes including target genes of miRNAs and lncRNAs. We found that many genes were involved in energy, retinol and cholesterol metabolism, and bile acid synthesis. Combined with metabolites such as low glucose concentration, high cholesterol concentration, and increased primary bile acid concentration, these genes were mainly responsible for lowering intramuscular fat, low cholesterol, and yellow meat in grass-fed cattle. Additionally, we identified two lncRNAs and eight DEGs as potential competing endogenous RNAs (ceRNAs) to bind miRNAs by the interaction network analysis. These results revealed that the effects of two feeding regimens on beef cattle were mainly induced by gene expression changes in metabolic pathways mediated via lncRNAs, miRNAs, and ceRNAs, and contents of metabolites in the liver. It may provide a clue on feeding regimens inducing the metabolic regulations.

Keywords: beef cattle; ceRNAs; feeding regimens; lncRNAs; metabolic regulations; miRNAs.

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Conflict of interest statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

Figure 1
Figure 1
Top 10 significantly enriched function for differential expression gene in grass-fed vs. grain-fed. Biological process (A), molecular function (B), cellular component (C), and KEGG pathways (D).
Figure 2
Figure 2
Cluster analysis of differential expression miRNAs in grass-fed vs. grain-fed. On the top-right of the figure, the color difference represents the relative abundance.
Figure 3
Figure 3
Significantly enriched function for the target genes of differential expression miRNAs (DEmiRNAs). Blue pillar represented the enrichment from down-regulated target genes and red pillar from up-regulated target genes by DEmiRNAs (A); Biological process (B).
Figure 4
Figure 4
Visualizing regulatory networks of metabolic processes and pathways in liver for grass-fed vs. grain-fed group. Blue represented RNAs up-regulated; green represented RNAs down-regulated; triangle represented miRNAs; circle represented differential expression genes; diamond represented lncRNAs; and red lines represented the edge of lncRNA-miRNA-mRNA network.
Figure 5
Figure 5
Validation of differentially expressed mRNA, miRNA, and lncRNA by RT-qPCR in liver samples. (A) The quantification of mRNA and lncRNA in liver from grass-fed vs. grain-fed groups. (B) The quantification of miRNA in liver from grass-fed vs. grain-fed group.
Figure 6
Figure 6
Retinol metabolism in animal (https://www.genome.jp/kegg-bin/show_pathway?ec00830+1.2.3.1). Red dashed represented differential expression genes in liver from grass-fed cattle.
See this image and copyright information in PMC

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