Genome-Wide Expression Profiling of mRNAs, lncRNAs and circRNAs in Skeletal Muscle of Two Different Pig Breeds

Abstract

RNA-Seq technology is widely used to analyze global changes in the transcriptome and investigate the influence on relevant phenotypic traits. Beijing Black pigs show differences in growth rate and meat quality compared to western pig breeds. However, the molecular mechanisms responsible for such phenotypic differences remain unknown. In this study, longissimus dorsi muscles from Beijing Black and Yorkshire pigs were used to construct RNA libraries and perform RNA-seq. Significantly different expressions were observed in 1051 mRNAs, 322 lncRNAs, and 82 circRNAs. GO and KEGG pathway annotation showed that differentially expressed mRNAs participated in skeletal muscle development and fatty acid metabolism, which determined the muscle-related traits. To explore the regulatory role of lncRNAs, the cis and trans-target genes were predicted and these lncRNAswere involved in the biological processes related to skeletal muscle development and fatty acid metabolismvia their target genes. CircRNAs play a ceRNA role by binding to miRNAs. Therefore, the potential miRNAs of differentially expressed circRNAs were predicted and interaction networks among circRNAs, miRNAs, and key regulatory mRNAs were constructed to illustrate the function of circRNAs underlying skeletal muscle development and fatty acid metabolism. This study provides new clues for elucidating muscle phenotypic variation in pigs.

Integrated transcriptome analysis reveals roles of long non-coding RNAs (lncRNAs) in caprine skeletal muscle mass and meat quality

“…Meanwhile, the expression pro les of lncRNAs in skeletal muscle tissues were also investigated and lncRNAs were found to be differentially expressed in samples with different genetic backgrounds. However, these studies in livestock have mainly been focused on sheep [10][11][12], cattle [13][14][15], chicken [16][17][18], and pigs [19][20][21].…”

Comparative Transcriptomic Analysis of mRNAs, miRNAs and lncRNAs in the Longissimus dorsi Muscles between Fat-Type and Lean-Type Pigs

“…In this study, we constructed an mRNA–miRNA–lncRNA regulatory network and found potential pathways that may regulate intramuscular fat deposition and muscle development in pigs. Similarly, a comparison of the expression profiling of mRNAs, lncRNAs and circRNAs in the LD muscle of Beijing Black and Yorkshire pigs at 210 d identified DE mRNAs that are mainly enriched in the ECM–receptor interaction, focal adhesion, AMPK signaling pathway, PI3K-Akt signaling pathway, adipocytokine signaling pathway, fatty acid metabolism, and PPAR signaling pathway [ 92 ].…”

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

“…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. RNA-seq has been widely applied to analyze gene expression patterns and identify new transcripts useful for elucidating the molecular function and regulation mechanisms in various organisms due to its high detection sensitivity and low noise [ 39 , 40 ]. In this study, to identify candidate genes and illustrate the molecular regulatory mechanisms of backfat quality, the systematic expression profiles of mRNAs and lncRNAs in backfat tissue of Beijing Black pigs with high- and low-fat quality have been compared by RNA-sequencing.…”