Identification and Functional Prediction of Long Non-Coding RNA in Longissimus Dorsi Muscle of Queshan Black and Large White Pigs

Abstract

Long non-coding RNA (lncRNA) participates in the regulation of various biological processes, but its function and characteristics in intramuscular fat (IMF) deposition in different breeds of pigs have not been fully understood. IMF content is one of the important factors affecting pork quality. In the present study, the differentially expressed lncRNAs (DE lncRNAs) and their target genes were screened by comparing Queshan Black (QS) and Large White (LW) pigs based on RNA-seq. The results displayed 55 DE lncRNAs between QS and LW, 29 upregulated and 26 downregulated, with 172 co-located target genes, and 6203 co-expressed target genes. The results of GO and KEGG analysis showed that the target genes of DE lncRNAs were involved in multiple pathways related to lipogenesis and lipid metabolism, such as the lipid biosynthetic process, protein phosphorylation, activation of MAPK activity, and the Jak-STAT signaling pathway. By constructing regulatory networks, lincRNA-ZFP42-ACTC1, lincRNA-AMY2-STAT1, and/or lincRNA-AMY2/miR-204/STAT1 were sieved, and the results indicate that lncRNA could participate in IMF deposition through direct regulation or ceRNA. These findings provide a basis for analyzing the molecular mechanism of IMF deposition in pigs and lay a foundation for developing and utilizing high-quality resources of local pig breeds.

Comprehensive Atlas of Alternative Splicing Reveals NSRP1 Promoting Adipogenesis through CCDC18

“…Specifically, in adipose tissue, we found that the SOX5 , ENSSSCG00000014414 , PPP1R12A , ZNF148 , TNFSF10 , and ROCK1 genes were under selection in Eastern pigs and significantly upregulated in adipose tissue, suggesting their potential influence on adipose deposition. Moreover, previous research has shown that SOX5 , PPP1R12A , ZNF148 , TNFSF10 , and ROCK1 genes regulate adipose deposition processes [ 54 , 55 , 56 , 57 , 58 , 59 ]. In blood, the MACF1 , IL1RL1 , MGA , TTC14 , ANKRD17 , PDLIM7 , FGD3 , NPRL3 , ENSSSCG00000014060 , ENSSSCG00000039214 , CYB5A , and HAGH genes were under selection in Eastern pigs, and the MACF1 , IL1RL1 , MGA , TTC14 , and ANKRD17 genes were significantly upregulated in Eastern pig blood.…”

Expression Profile and Regulatory Properties of m6A-Modified circRNAs in the Longissimus Dorsi of Queshan Black and Large White Pigs

“…Sample Collection, Sequencing, and m6A-circRNA Prediction Analysis Sample collection was described previously. Briefly, the experimental animals were three Queshan Black and three Large White pigs, all of which were castrated boars in this study, and samples were frozen in liquid nitrogen and stored at −80 • C until RNA extraction [17,18]. Total RNA was extracted from the samples using TRIzol reagent (15596026, Thermo Fisher Scientific, Waltham, MA, USA), and its concentration and quality were tested for satisfactory sequencing analysis.…”