IRLnc: a novel functional noncoding RNA contributes to intramuscular fat deposition

Abstract

Background Intramuscular fat (IMF) is associated with meat quality and insulin resistance in animals. Research on genetic mechanism of IMF decomposition has positive meaning to pork quality and diseases such as obesity and type 2 diabetes treatment. In this study, an IMF trait segregation population was used to perform RNA sequencing and to analyze the joint or independent effects of genes and long intergenic non-coding RNAs (lincRNAs) on IMF. Results A total of 26 genes including six lincRNA genes show significantly different expression between high- and low-IMF pigs. Interesting, one lincRNA gene, named IMF related lincRNA (IRLnc) not only has a 292-bp conserved region in 100 vertebrates but also has conserved up and down stream genes (< 10 kb) in pig and humans. Real-time quantitative polymerase chain reaction (RT-qPCR) validation study indicated that nuclear receptor subfamily 4 group A member 3 (NR4A3) which located at the downstream of IRLnc has similar expression pattern with IRLnc. RNAi-mediated loss of function screens identified that IRLnc silencing could inhibit both of the RNA and protein expression of NR4A3. And the in-situ hybridization co-expression experiment indicates that IRLnc may directly binding to NR4A3. As the NR4A3 could regulate the catecholamine catabolism, which could affect insulin sensitivity, we inferred that IRLnc influence IMF decomposition by regulating the expression of NR4A3. Conclusions In conclusion, a novel functional noncoding variation named IRLnc has been found contribute to IMF by regulating the expression of NR4A3. These findings suggest novel mechanistic approach for treatment of insulin resistance in human beings and meat quality improvement in animal.

Comprehensive Analysis of Differentially Expressed mRNAs, lncRNAs and circRNAs Related to Intramuscular Fat Deposition in Laiwu Pigs

“…For instance, IncIMF2 acts as a molecular sponge for microRNA-217, which has been found associated with adipogenesis, thereby affecting the expression of the miR-217 target gene [ 11 ]. LncRNA IRLnc influence IMF decomposition by regulating the expression of nuclear receptor subfamily 4 group A member 3 [ 12 ]. In addition, lnc-ORA regulates adipogenesis through the phosphatidylinositol-3-kinase/protein kinase B/mechanistic target of rapamycin (PI3K/AKT/mTOR) signaling pathway in mice [ 13 ].…”

Genome-wide characterization of lncRNAs and mRNAs in muscles with differential intramuscular fat contents

“…Owing to its importance in improving meat quality, many studies have focused on revealing the mechanisms underlying IMF content, and some lncRNAs have been implicated in IMF content in recent years, namely, LncIMF4 ( 20 ), IMFNCR ( 21 ), IRLnc ( 22 ), IMFlnc1 ( 23 ), etc. Efforts were also made to characterize lncRNAs involved in IMF deposition at the genome-wide level in pigs ( 24 – 26 ).…”

Integrative Analysis of Nanopore and Illumina Sequencing Reveals Alternative Splicing Complexity in Pig Longissimus Dorsi Muscle

“…The animal materials used in this study were all from the F2 generation resource population of large white pig × Min pig at the Changping Experimental Base of the Institute of Animal Sciences, Chinese Academy of Agricultural Sciences. The pig raising and slaughtering environment, tissue collection, and IMF measuring methods were as described in our previous study ( Wang et al, 2021 ). Thirty samples were screened for full-length transcript sequencing based on IMF content: fifteen samples with high IMF content and fifteen samples with low IMF content.…”