Genome-Wide Analysis of mRNAs and lncRNAs of Intramuscular Fat Related to Lipid Metabolism in Two Pig Breeds

Abstract

Background/Aims: Long non-coding RNAs (lncRNAs) can regulate adipogenesis and lipid accumulation. Intramuscular fat deposition appears to vary in different pig breeds, and the regulation mechanism has not yet been fully elucidated at molecular level. Moreover, little is known about the function and profile of lncRNAs in intramuscular fat deposition and metabolism in pig. The aim of this study was thus to explore the regulatory functions of lncRNAs in intramuscular fat deposition. Methods: In this study, Laiwu (LW) pig and Large White (LY) pig with significant difference in fat deposition were selected for use. RNA-seq technology and bioinformatics methods were used to comparatively analyze the gene expression profiles of intramuscular fat between LW and LY pigs to identify key mRNAs and lncRNAs associated with lipid metabolism and adipogenesis. Real-time fluorescence-based quantitative PCR was applied to verify the expression level of the differentially expressed mRNAs and lncRNAs. Results: A total of 513 mRNAs and 55 lncRNAs were differentially expressed between two pig breeds. By co-expression network construction as well as cis- and trans-regulated target gene analysis, 31 key lncRNAs were identified. Gene Ontology and KEGG pathway analyses revealed that differentially expressed genes and lncRNAs were mainly involved in the biological processes and pathways related to adipogenesis and lipid metabolism. Conclusion: XLOC_046142, XLOC_004398 and XLOC_015408 may target MAPKAPK2, NR1D2 and AKR1C4, respectively, and play critical regulatory roles in intramuscular adipogenesis and lipid accumulation in pig. XLOC_064871 and XLOC_011001 may play a role in lipid metabolism-related disease via regulating TRIB3 and BRCA1. This study provides a valuable resource for lncRNA study and improves our understanding of the biological roles of lipid metabolism- related genes and molecular mechanism of intramuscular fat metabolism and deposition.

Screening of lncRNA Profiles During Intramuscular Adipogenic Differentiation Inlongissimus Dorsi and Semitendinosus Muscles in Pigs

“…In terms of conservation between species, lncRNAs were also far less conserved than mRNAs. The lncRNAs obtained through RNA-seq were roughly the same in terms of length, number of exons, and conservation, as those found in previous studies on porcine adipose tissues [19] and intramuscular fat [20]. KEGG analysis showed that the target genes of these lncRNAs were enriched in some classical signaling pathways related to fat formation, in ammation, and growth.…”

Comparative analysis of gene expression profiles in differentiated subcutaneous adipocytes between Jiaxing Black and Large White Pigs

“…Excessive SC fat deposition greatly decreases the growth performance and meat production efficiency, which results in profit reduction [7,8]. However, Chinese indigenous pig breeds often exhibit better fertility, disease resistance and IM fat content than foreign pig breeds [9][10][11]. Understanding the porcine adipocyte regulation network to decrease SC fat deposition is a key issue in genetic improvement of Chinese indigenous pig breeds.…”

“…However, the redundant SC fat deposition decreases the growth efficiency and results in profit reduction. By contrast, Large White pig is the most widely distributed lean-type pig breed with relatively low SC fat deposition [11]. In this study, highthroughput RNA-seq was conducted to compare the gene expression profiles of differentiated SC adipocytes from the two pig breeds.…”

Regulatory Roles of Related Long Non-coding RNAs in the Process of Atherosclerosis

“…Sallam et al found that MeXis can enhance the expression of ABCA1 by regulating the chromatin structure of ABCA1, while suppression of MeXis can accelerate the formation of foam cells and promote AS formation in Apoe −/− mice (Sallam et al, 2018). Using pigs as a model to study fat formation and lipid metabolism, Huang's team found that 55 lncRNAs were differentially expressed between Laiwu and Large White (Large Yorkshire) pigs (Huang et al, 2018). XLOC_046142, XLOC_004398, and XLOC_015408 were hypothesized to play a key role in the regulation of fat formation and lipid accumulation in pig muscle tissues, while LOC_064871 and XLOC_011001 may play a role in diseases related to lipid metabolism.…”