Comparison study of differential expression genes and Cis-NATs of skeletal muscle between lantang and landrace pig

[Objective] This study was designed to analyze the molecular mechanism of pig skeletal muscle development regulated by cis-natural antisense transcripts (cis-NATs) by comparing the differential expression genes and cis-NATs between Lantang and Landrace pig during their skeletal muscle development. [Method] In this study, the following steps were adopted: (i) The differential expression genes (DEGs) and cis-NATs comparing Lantang (LT) and Landrace (LR) pig breeds at 10 time-points distributed from 35 days-post-coitus (dpc) to 180 days-post-natum (dpn) were identified (|log₂FC|>1 and FDR<0.01). (ii) The significant biological process Gene Ontology (GO) terms (P<0.01) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways (P < 0.05) of the DEGs and the sense gene of differential expression cis-NATs were enriched via function enrichment analysis. (iii) Then the significant biological process GO terms and KEGG pathways that cis-NATS participated were filtered by the number of related genes of cis-NATs, and KEGG pathways were integrated by the number of same genes between pathways. Finally, visual analyses was conducted based on fold change of differential expression cis-NATs and their sense gene between breeds within pathways. [Result] A total of 5 350 DEGs and 738 differential expression cis-NATs were identified between LT and LR at 10 time points in this study. GO analysis showed that the expression of differential expression cis-NATs between LT and LR in skeletal muscle was primarily concerned with genes in biological process, including muscle development and energy metabolism. The integrated analysis of KEGG pathways found that energy metabolism pathways were strongly related by DE genes and their correlated cis-NATs. Moreover the expression of genes and their correlated cis-NATs were higher in pig mitochondrial citrate cycle pathway during early stages of birth than adulthood. The visual analyses of KEGG pathways showed that the expression level of energy metabolism pathway involved genes and their correlated cis-NATs were higher in LT than LR at 49 dpc and 77 dpc, which were two critical points for muscle fibers growth. The differences of expression patterns between LT and LR primarily appear at the early postnatal stages of 2 dpn-90 dpn. [Conclusion] In this study, 738 differential expression cis-NATs were identified by comparing between LT and LR at 10 time points of skeletal muscle development. Function enrichment analysis showed that cis-NATs played a role in developmental differences of skeletal muscle fibers between LT and LR by interacting with genes expressed in energy metabolism related pathways.