Genome‐wide identification and comparison of mRNAs, lncRNAs and circRNAs in porcine intramuscular, subcutaneous, retroperitoneal and mesenteric adipose tissues

Abstract

SummaryMany types of RNAs, including messenger RNAs (mRNAs), long noncoding RNAs (lncRNAs) and circular RNAs (circRNAs), play crucial roles in regulating fat cell differentiation and tissue development. However, the expression profiles of these RNAs in different adipose tissues are still largely unknown. To shed light on this issue, we performed a transcriptome analysis of mRNAs, lncRNAs and circRNAs obtained from intramuscular adipose tissue, subcutaneous adipose tissue, retroperitoneal adipose tissue and mesenteric adipose tissue of Chinese Erhualian pigs. A number of differentially expressed mRNAs, lncRNAs and circRNAs were identified among the four adipose tissues. Tissue‐specific analysis indicated that circRNAs exhibited the highest tissue specificity among mRNAs, lncRNAs and circRNAs, whereas intramuscular adipose tissue had the most tissue‐specific genes among the four adipose tissues. Gene Ontology analysis showed that differentially expressed mRNAs among groups were involved mainly in lipid metabolism and immune inflammatory response processes. Furthermore, the co‐expression network construction of mRNAs–lncRNAs revealed that several important lncRNAs, such as MSTRG.426159 and MSTRG.604206, might associate with lipid metabolic process. Taken together, these data provide a genome‐wide resource of mRNAs, lncRNAs and circRNAs potentially involved in porcine fat metabolism, thus improving understanding of their function in diverse adipose tissues.

miR‐32‐5p Regulates Lipid Accumulation in Intramuscular Fat of Erhualian Pigs by Suppressing KLF3

“…Thus, we first investigated the expression level of KLF3 in IMF tissues of Erhualian pigs' longissimus dorsi muscle with different IMF content and found that the expression of KLF3 is negatively correlated with IMF content. We then compared KLF3 expression levels between IMF and SCF tissues, which revealed that IMF possesses higher KLF3 level than SCF, which correlates with our previous microarray analysis on gene expression profiles in various fat tissues (Liu et al, 2019). Gene function analysis in vitro further reveals that KLF3 can suppress preadipocyte differentiation, which is in line with earlier studies (Hashmi et al, 2011;Sue et al, 2008).…”

“…Several studies have compared gene expression profiles among different fat tissues using gene expression microarray analysis to identify the genes involved (Kojima et al, 2018;Martínez Del Pino et al, 2017). Our earlier study found that KLF3 expression level differs between IMF and SCF tissues (Liu et al, 2019), and RNA sequencing data by Lim et al also showed KLF3 is one of the differentially expressed genes in longissimus muscle of pigs with high and low IMF content (Lim et al, 2017). We propose that KLF3 expression level is negatively correlated with the fat content in longissimus dorsi muscle and SCF.…”

Myostatin regulates fatty acid desaturation and fat deposition through MEF2C/miR222/SCD5 cascade in pigs

“…MEF2C was also shown to be able to activate carnitine palmitoyltransferase 1 (CPT1β) expression in non-muscle cells, and to specifically bind to PPARα in vitro, implying its involvement in the fatty acid metabolism 29 . In pigs, a few studies had validated MEF2C expression in different fat tissues, including intramuscular, subcutaneous, retroperitoneal, and mesenteric adipose tissues [30][31][32] . In this study, by using in vivo and in vitro assays, we demonstrated that MEF2C is the upstream regulator of miR222 in the adipose tissues of pigs.…”

A Previously Undiscovered Circular RNA, circTNFAIP3, and Its Role in Coronavirus Replication

“…We identified 57,704 circRNA candidates in mock- and PDCoV-infected ST cells; the number was more than that of circRNAs in porcine liver tissues (6,366), adipose tissues (13,746), IPEC-J2 cells (26,670), and ovary tissues (38,722) ( 18 , 54 – 56 ), but less than that in Jinhua and Landrace pig liver tissues (84,864) ( 57 ). It indicates that the circRNA expression in pigs exhibits a complex tissue- or cell-specific characteristic, which is consistent with the circRNA expression pattern in other species ( 1 , 58 , 59 ).…”