Identification of critical lncRNAs for milk fat metabolism in dairy cows using WGCNA and the construction of a ceRNAs network

Abstract

As key regulators, long non-coding RNAs (lncRNAs) play a crucial role in the ruminant mammary gland. However, the function of lncRNAs in milk fat synthesis from dairy cows is largely unknown. In this study, we used the weighted gene co-expression network analysis (WGCNA) to comprehensive analyze the expression profile data of lncRNAs from the group's previous Illumina PE150 sequencing results based on bovine mammary epithelial cells from high-and low-milk-fat-percentage (MFP) cows, and identify core_ lncRNAs significantly associated with MFP by module membership (MM) and gene significance (GS). Functional enrichment analysis (Gene Ontology, Kyoto Encyclopedia of Genes and Genomes) of core_lncRNA target genes (co-localization and co-expression) was performed to screen potential lncRNAs regulating milk fat metabolism and further construct an interactive regulatory network of lipid metabolism-related competing endogenous RNAs (ceRNAs). A total of 4876 lncRNAs were used to construct the WGCNA. The MEdarkturquoise module among the 19 modules obtained was significantly associated with MFP (r = 0.78, p-value <0.05) and contained 64 core_lncRNAs (MM > 0.8, GS > 0.4). Twenty-four lipid metabolism-related lncRNAs were identified by core_lncRNA target gene enrichment analysis. TCONS_00054233, TCONS_00152292, TCONS_00048619, TCONS_00033839, TCONS_00153791 and TCONS_00074642 were key candidate lncRNAs for regulating milk fat synthesis. The 22 ceRNAs most likely to be involved in milk fat metabolism were constructed by interaction network analysis, and TCONS_00133813 and bta-miR-2454-5p were located at the network's core. TCONS_00133813_bta-miR-2454-5p_TNFAIP3, TCONS_00133813_bta-miR-2454-5p_ARRB1 and TCONS_00133813_bta-miR-2454 are key candidate ceRNAs associated with milk fat metabolism. This study provides a framework for the co-expression module of MFP-related lncRNAs in ruminants, identifies several major lncRNAs and ceRNAs that influence milk fat synthesis, and provides a new understanding of the complex biology of milk fat synthesis in dairy cows.

Research Progress on the Mechanism of Milk Fat Synthesis in Cows and the Effect of Conjugated Linoleic Acid on Milk Fat Metabolism and Its Underlying Mechanism: A Review

“…These findings indicate that ELOVL6 not only catalyzes the biosynthesis of LCFAs in BMECs but also indirectly regulates the expression of genes associated with milk fat biosynthesis to increase milk fat production in cattle. With the identification of genes associated with milk fat synthesis in cattle, new candidate genes for dairy cow milk fat synthesis include phosphatidylinositol 4-kinase type 2 alpha (PI4K2A), solute carrier family 16 member 1 (SLC16A1), ATPase phospholipid transporting 8A2 (ATP8A2), vascular endothelial growth factor D (VEGFD), inhibitor of DNA binding 1 (ID1) [143], and arachidonate 12-lipoxygenase (ALXO12) [144].…”