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

Abstract

Long noncoding RNAs (lncRNAs) and circular RNAs (circRNAs) are important classes of small noncoding RNAs that can regulate numerous biological processes. To understand the role of message RNA (mRNAs, lncRNAs and circRNAs) in the regulation of intramuscular fat (IMF) deposition, in this study the expression profiles of longissimus dorsi (LD) muscle from six Laiwu pigs (three with extremely high and three with extremely low IMF content) were sequenced based on rRNA-depleted library construction. In total, 323 differentially expressed protein-coding genes (DEGs), 180 lncRNAs (DELs) and 105 circRNAs (DECs) were detected between the high IMF and low IMF groups. Functional analysis indicated that most DEGs, and some target genes of DELs, were enriched into GO terms and pathways related to adipogenesis, suggesting their important roles in regulating IMF deposition. In addition, 12 DELs were observed to exhibit a positive relationship with stearoyl-CoA desaturase (SCD), phosphoenolpyruvate carboxykinase 1(PCK1), and adiponectin (ADIPOQ), suggesting they are highly likely to be the target genes of DELs. Finally, we constructed a source gene-circRNA-miRNA connective network, and some of miRNA of the network have been reported to affect lipid metabolism or adipogenesis. Overall, this work provides a valuable resource for further research and helps to understand the potential functions of lncRNAs and circRNAs in IMF deposition.

Genome-wide identification of antisense lncRNAs and their association with susceptibility to Flavobacterium psychrophilum in rainbow trout

“…CPAT Protein-coding potentials scores for lncNATs and lincRNAs averaged 0.02 compared to 0.97 in protein-coding genes ( Figure 2F ). The number of exons, GC content, the median size of ORF, and coding scores in all three types of transcripts showed a similar pattern to other species, suggesting evolutionarily conserved genome structures ( 13 , 74 , 76 – 80 ). A large fraction of the lncNATs (83.6%) had at least 50% of their sequence length overlapped with protein-coding genes.…”

Differential deposition of intramuscular and abdominal fat in chicken

“…Especially the TF L3MBTL1 and the TF co-factors TNIP1, HAT1, and BEND6, which were identified as significantly positively related to the high IMF and significantly negatively related to the low AFW could be relevant biomarkers for chicken breeding. RT-q-PCR of the four TFs/TFCFs in breast muscle of the Jingxing-Huang chickens and Cobb chickens in a large number of individuals, showed that the expression of TNIP1 and HAT1 in the high IMF group is significantly higher than in the low IMF group (Li et al, 2020).…”