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

Abstract

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 found in previous studies. In this study, we collected the adipose tissue of six Landrace pigs with contrast backfat thickness (nhigh = 3, nlow = 3), after which we performed strand-specific RNA sequencing (RNA-seq) based on pooling and biological replicate methods. Biological replicate and pooling RNA-seq revealed 1870 and 1618 lncRNAs, respectively. Using edgeR, we determined that 1512 genes and 220 lncRNAs, 2240 genes and 127 lncRNAs were differentially expressed in biological replicate and pooling RNA-seq, respectively. After target gene prediction, we found that ACSL3 was cis-targeted by lncRNA TCONS-00052400 and could activate the conversion of long-chain fatty acids. In addition, lncRNA TCONS_00041740 cis-regulated gene ACACB regulated the rate-limiting enzyme in fatty acid oxidation. Since these genes have necessary functions in fat metabolism, the results imply that the lncRNAs detected in our study may affect backfat deposition in swine through regulation of their target genes. Our study explored the regulation of lncRNA and their target genes in porcine backfat deposition and provided new insights for further investigation of the biological functions of lncRNA.

Transcriptomics-Based Study of Differentially Expressed Genes Related to Fat Deposition in Tibetan and Yorkshire Pigs

“…Back fat thickness of pigs is an important indicator to determine the fat deposition in commercial pigs. Back fat thickness of pigs can directly reflect their body fat content ( 23 ). Investigation on measures to reduce back fat deposition is an important way to effectively promote genetic improvement of pigs.…”

“…The KEGG results showed the pathways were mostly concentrated on glucose metabolism. some of these pathways, such as ‘Glycolysis/Gluconeogenesis', although they are not directly related to lipid synthesis and metabolism, glucose and lipids can change Therefore, the process of glucose metabolism can have an indirect effect on lipid metabolism ( 23 ). Thyroid hormone response protein (THRSP), alias LPGP1, SPOT14, THRP, is induced by thyroid hormone expression and is closely related to lipid deposition in animals.…”

Integrated Analysis of Long Non-Coding RNA and mRNA to Reveal Putative Candidate Genes Associated with Backfat Quality in Beijing Black Pig

“…Therefore, backfat deposition affects not only backfat thickness but also fat quality. Backfat deposition is a complex biological process regulated by multiple genes and epigenetic factors, including lncRNA [ 17 ]. The genetic mechanism of meat quality-related traits has always been a popular area of research, but the molecular mechanism of fat quality has rarely been reported.…”

“…LncRNAs can regulate transcriptional processes via signals and can even interact with other proteins to produce a ribonucleoproten complex as scaffolds. Previous studies have reported that many lncRNAs participate in various biological processes, including fat-related processes, and even play a key regulatory role [ 17 , 66 , 67 ]. However, the lncRNAs associated with backfat quality in pigs have not been studied.…”

“…Additionally, some candidate lncRNAs and lncRNA-mRNA pathways have been defined, and the regulatory effects on some biosynthesis, metabolism, and disease processes have been validated [ 13 , 14 , 15 , 16 ]. Backfat deposition is a complex biological process regulated by multiple genes and epigenetic factors, including lncRNAs [ 17 ]. There have been some reports on lnRNAs related to fat deposition and metabolism in various species [ 18 , 19 , 20 ]; however, the lncRNAs related to fat color and firmness, and their regulatory relation profiles with the corresponding mRNA, remain unclear.…”