Identification of Long Non-Coding RNAs Involved in Fat Deposition in Pigs Using Two High-Throughput Sequencing Methods

Abstract

Background: Adipose is an important body tissue in pigs, and fatty traits are critical in pig production. The function of long non-coding RNA (lncRNA) in fat deposition and metabolism has been proven in previous studies. In this study, we focused on lncRNAs associated with fattening traits in pigs. The adipose tissue of six Landrace pigs with either extremely-high or -low backfat thickness ( n high = 3, n low = 3) was collected, after which we performed strand-specific RNA sequencing using biological replicates and pooling methods. Results: A total of 19,631 genes and 2,013 lncRNAs were identified using the coding potential calculator, coding-non-coding index, and Pfam database, including 334 known transcripts and 1,679 novel transcripts. Using edgeR, we determined that 220 lncRNAs and 1,512 genes were differentially expressed (|Fold Change| > 2 and false discovery rate < 0.05) between the two groups in biological replicate RNA sequencing (RNA-seq), and 127 lncRNAs and 2,240 genes were differently expressed in pooling RNA-seq. Further Kyoto Encyclopedia of Genes and Genomes and Gene Ontology enrichment analysis of the differentially expressed genes found that some of the genes were involved in several key pathways related to fat development. After targeting gene prediction, we determined that some cis-target genes of the differentially expressed lncRNAs play an important role in fat deposition. For example, ACSL3 is cis-targeted by lncRNA TCONS-00052400, and it can activate the conversion of long-chain fatty acids. In addition, lncRNA TCONS_00041740 was up-regulated in the high backfat thickness group, and its cis-target gene ACACB was also up-regulated in this group. It has been reported that ACACB is the rate-limiting enzyme in fatty acid oxidation. Conclusions: Since these genes have necessary functions in fat metabolism, the results imply that the lncRNAs detected in our study may affect fat deposition in pigs through regulation of their target genes. In summary, our study explored the regulation of lncRNA and their target genes on fat deposition in pigs and provided new insights for further investigation of the biological functions of lncRNA.