Systematic Identification and Comparison of the Expressed Profiles of lncRNAs, miRNAs, circRNAs, and mRNAs with Associated Co-Expression Networks in Pigs with Low and High Intramuscular Fat

Abstract

Intramuscular fat (IMF) content is a complex trait that affects meat quality and determines pork quality. In order to explore the potential mechanisms that affect the intramuscular fat content of pigs, a Large white × Min pigs F2 resource populations were constructed, then whole-transcriptome profile analysis was carried out for five low-IMF and five high-IMF F2 individuals. In total, 218 messenger RNA (mRNAs), 213 long non-coding RNAs (lncRNAs), 18 microRNAs (miRNAs), and 59 circular RNAs (circRNAs) were found to be differentially expressed in the longissimus dorsi muscle. Gene ontology analysis and Kyoto Encyclopedia of Genes and Genomes annotations revealed that these differentially expressed (DE) genes or potential target genes (PTGs) of DE regulatory RNAs (lncRNAs, miRNAs, and circRNAs) are mainly involved in cell differentiation, fatty acid synthesis, system development, muscle fiber development, and regulating lipid metabolism. In total, 274 PTGs were found to be differentially expressed between low- and high-IMF pigs, which indicated that some DE regulatory RNAs may contribute to the deposition/metabolism of IMF by regulating their PTGs. In addition, we analyzed the quantitative trait loci (QTLs) of DE RNAs co-located in high- and low-IMF groups. A total of 97 DE regulatory RNAs could be found located in the QTLs related to IMF. Co-expression networks among different types of RNA and competing endogenous RNA (ceRNA) regulatory networks were also constructed, and some genes involved in type I diabetes mellitus were found to play an important role in the complex molecular process of intramuscular fat deposition. This study identified and analyzed some differential RNAs, regulatory RNAs, and PTGs related to IMF, and provided new insights into the study of IMF formation at the level of the genome-wide landscape.

Circular RNA Profiling Identifies Novel circPPARA that Promotes Intramuscular Fat Deposition in Pigs

“…Therefore, the present study assessed the circRNA expression patterns in the longissimus dorsi muscle using RNA-seq and identified 336 circRNAs DE between pigs with high and low content of IMF, suggesting their role in porcine IMF deposition. The circRNAs identified in this study and found to be DE between the pigs with different IMF levels are more than those in the previous reports. , This observation suggests that the circRNAs regulating IMF content in pigs has not been comprehensively explored, and thus, additional mechanisms regulating IMF deposition remain elusive.…”

“…The circRNAs identified in this study and found to be DE between the pigs with different IMF levels are more than those in the previous reports. 12,60 This observation suggests that the circRNAs regulating IMF content in pigs has not been comprehensively explored, and thus, additional mechanisms regulating IMF deposition remain elusive. In addition, certain circRNAs function as competitors of their linear RNAs, influencing host gene expression levels.…”

“…Meanwhile, many circRNAs regulate muscle development and muscle fiber formation in pigs. , Liu et al identified 8,623 circRNAs during the development and differentiation of subcutaneous fat in pigs, including 1,760 DE circRNAs probably regulating subcutaneous fat deposition . Recently, Cheng et al identified 59 circRNAs DE between pigs with low and high content of IMF, while Qi et al identified 7608 circRNAs, including 62 DE ones, from the longissimus dorsi muscle of Queshan Black and Large White pigs . However, these studies were incomplete in terms of the mechanisms by which circRNA regulates IMF.…”

“…Over 2 decades of research have identified numerous genes associated with this trait. Components such as mRNAs, miRNAs, long noncoding RNAs (lncRNAs), and circular RNAs (circRNAs) influencing the IMF content have been identified in pigs. Li et al identified 22 long intergenic noncoding RNAs (lincRNAs) differentially expressed (DE) between Wei (fat-type) and Yorkshire (lean-type) pigs .…”

miR-381-3p Inhibits Intramuscular Fat Deposition through Targeting FABP3 by ceRNA Regulatory Network

“…In chickens, lncRNA IMFNCR promotes intramuscular adipocyte differentiation by sponging miR-128-3p and miR-27b-3p [ 81 ]. Generally, ncRNA regulates the expression of targeted mRNAs [ 80 ]; for example, Cheng et al (2021) identified DE lncRNAs, miRNAs, circRNAs, and mRNAs and constructed multiple ceRNAs which play an important role in the complex molecular processes of IMF deposition between large white × Min crossbred pigs [ 82 ]. Previous studies have reported that miR-381-3p plays a positive role in adipogenic differentiation of adipose-derived stem cells [ 83 ], obesity-related diseases (type 2 diabetes) [ 84 ], and sheep muscle growth and development [ 85 ] by regulating target genes.…”