Whole transcriptome analysis of RNA expression profiles reveals the potential regulating action of long noncoding RNA in lactating cows fed a high concentrate diet

Abstract

Subacute ruminal acidosis (SARA) is a common metabolic disease in the dairy farming industry which is usually caused by an excessive amount of high concentrate diet. SARA not only threatens animal welfare but also leads to economic losses in the farming industry. The liver plays an important role in the distribution of nutritional substances and metabolism; however, a high concentrate diet can cause hepatic metabolic disorders and liver injury. Recently, noncoding RNA has been considered as a critical regulator of hepatic disease, however, its role in the bovine liver is limited. In this study, 12 mid-lactating dairy cows were randomly assigned to a control (CON) group (40% concentrate of dry matter, n = 6) and a SARA group (60% concentrate of dry matter, n = 6). After 21 d of treatment, all cows were sacrificed, and liver tissue samples were collected. Three dairy cows were randomly selected from the CON and SARA groups respectively to perform whole transcriptome analysis. More than 20,000 messenger RNA (mRNA), 10,000 long noncoding RNA (lncRNA), 3,500 circular RNA (circRNA) and 1,000 micro RNA (miRNA) were identified. Furthermore, 43 mRNA, 121 lncRNA and 3 miRNA were differentially expressed, whereas no obvious differentially expressed circRNA were detected between the 2 groups. Gene Ontology (GO) annotation revealed that the differentially expressed genes were mainly enriched in oxidoreductase activity, stress, metabolism, the immune response, cell apoptosis, and cell proliferation. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that the deferentially expressed genes were highly enriched in the phosphatidylinositol 3 kinase ( PI3K ) - serine/threonine kinase ( AKT ) signaling pathway ( P < 0.05). According to KEGG pathway analysis, the differentially expressed lncRNA (DElncRNA) target genes were mainly related to proteasomes, peroxisomes, and the hypoxia-inducible factor-1 signaling pathway ( P < 0.005). Further bioinformatics and integrative analyses revealed that the lncRNA were strongly correlated with mRNA; therefore, it is reasonable to speculate that lncRNA potentially play important roles in the liver dysfunction induced by SARA. Our study provides a valuable resource for future investigations on the mechanisms of SARA to facilitate an understanding of the importance of lncRNA, and offer functional RNA information.

Weighted Gene Co-expression Network Analysis Identifies Specific Modules and Hub Genes Related to Subacute Ruminal Acidosis

“…Because the liver is an important organ of blood circulation, translocated LPS and LPS binding protein (LBP) eventually enter the liver, leading to liver disease (47). However, in recent years, in-depth studies on the inflammatory response of SARA have found that when dairy cows suffer from SARA, stress is induced and calcium, non-esterified fatty acids, and glucose concentrations are reduced, and glucocorticoid receptor protein in the liver is significantly downregulated, which is consistent with the enrichment results of this experiment (48). Although LPS translocation eventually leads to liver inflammation, liver inflammation after a series of reactions has rarely been explored.…”

Integration of Non-Coding RNA and mRNA Profiles Reveals the Mechanisms of Rumen Development Induced by Different Types of Diet in Calves

“…On the 80th day, before morning feeding, 5 mL of calf blood was collected by vacuuming the caudal vein with heparin sodium anticoagulant, and after standing for 30 min and centrifuging at 3000 r for 10 min to collect serum, it was stored at −80 • C in a refrigerator to determine serum indexes [15]. Serum samples were taken for IgG, α-amylase, ceruloplasmin, trypsin and lysozyme testing.…”

“…The transcriptome is considered as the simplified research means for studying the genome, that is, the collection of all transcripts [13,14]. Therefore, RNA-seq is widely used to study the molecular mechanism of feed and to study the genes related to rumen growth and the development of ruminants, which play an important role in promoting rumen morphology and functional development [15,16]. miRNAs regulate the expression of target genes to maintain normal cellular homeostasis, digestion and nutrient absorption in the gastrointestinal tract [15,17].…”

“…Therefore, RNA-seq is widely used to study the molecular mechanism of feed and to study the genes related to rumen growth and the development of ruminants, which play an important role in promoting rumen morphology and functional development [15,16]. miRNAs regulate the expression of target genes to maintain normal cellular homeostasis, digestion and nutrient absorption in the gastrointestinal tract [15,17]. lncRNA not only plays an important role in epigenetic inheritance, genomic imprinting and tissue cell formation, but also influences mRNA expression as an enhancer, promoter and transcriptional activator [18].…”

“…lncRNA not only plays an important role in epigenetic inheritance, genomic imprinting and tissue cell formation, but also influences mRNA expression as an enhancer, promoter and transcriptional activator [18]. Studies have reported that being fed a high proportion of concentrate led to lncRNAs target genes activating PI3K-AKT, proteasome and HIF-1 signaling pathways, causing liver tissue inflammation and cell apoptosis, and aggravating SARA in dairy cows [15,19]. circRNA has a ring structure, is more stable than linear RNA and is rich in multiple binding sites of miRNA.…”