The Landscape And Difference Of Chromatin Accessibility In Skeletal Muscle During Embryonic Development In Large White And Min Pigs

The development of skeletal muscle in pigs during the embryonic stage is precisely regulated by transcriptional mechanisms,which depend on chromatin accessibility.However,how chromatin accessibility plays a regulatory role during embryonic skeletal muscle development in pigs has not been reported.To gain insight into the landscape of chromatin accessibility and the associated genome-wide transcriptome during embryonic muscle development,we performed ATAC-seq(Transposase-accessible chromatin with high-through sequencing)and RNA-seq analyses of skeletal muscle from Large White and Min pigs embryos at gestation period of 45,70 and 100 days.Weighted correlation network analysis(WGCNA)was used to speculate the co-expressed genes related to the embryonic skeletal muscle development of pigs,and then the difference analysis of these genes was carried out to speculate the candidate genes that cause differences in the skeletal muscle development of different breeds of pigs;And further combined with the results of GWAS to speculate on candidate genes that affect muscle fiber diameter and muscle fiber density.In total,21638,35447 and 60181 ACRs(Accessible chromatin regions)were found across the embryos at gestation period of 45,70 and 100 in Large White,respectively.13%-29% ACRs were located in proximal promoter.722,989,and 5688 stage-specific ACRs annotation genes were detected at 45,70,and 100 dpc(day post-coitus),respectively,and these genes can be significantly enriched in muscle development-related pathways.MYOG was significantly enriched at 45 dpc;MEF2A,MEF2 C and MEF2 D were significantly enriched at 100 dpc;and a potential transcription repressor was detected at 70 dpc,namely E2F6.In LW70 vs LW45,LW100 vs LW70,and LW100 vs LW45 comparisions,3,20,and 113 genes were found to be down-regulated in ATAC-seq but up-regulated in RNA-seq,and 0,5,and 12 genes were found in ATAC-seq.Genes that are up-regulated in seq but tend to be down-regulated in RNA-seq.35088,61676 and 58264 ACRs(Accessible chromatin regions)were found across the embryos at gestation period of 45,70 and 100 in Min pigs,respectively.5587,13355,and 18795 significantly different ACRs and 831,1497 and 2671 genes with significant difference were obtained in M70 vs M45,M100 vs M70,and M100 vs M45 comparisions,respectively.The combined analysis of differential ACRs and differential genes found that 340,1498,and 2815 differential ACRs were obtained in M70 vs M45,M100 vs M70,and M100 vs M45,corresponding to 183,613,and 1167 differential genes,respectively.These genes can be significantly enriched in biological processes related to muscle development.The genes such as ALPK2,NMRK2,PDLIM3,CD9,CSRP3,FGF9 and FOS in these pathways may play an important role in the development of skeletal muscle in pigs.794,1959 and 2779 differential ACRs were obtained in LW45 vs M45,LW70 vs M70 and LW100 vs M100,respectively.Using WGCNA analysis,a total of 6 candidate modules related to embryonic age were detected.Further GO enrichment analysis of these 6 modules found that 45 dpc-related module genes were significantly enriched in biological processes related to cell proliferation,cell cycle and skeletal muscle development.Many biological processes related to the development of skeletal muscle tissue were significantly enriched in 70 dpc-related module genes.Many biological processes related to protein modification were significantly enriched in 100 dpc-related module genes.Differential analysis of 45 dpc-and 70 dpc-related module genes found that 1576 and 205 differential genes were obtained in diffetent breeds,respectively.Among them,the differential expression of genes such as S100A11,DLK2,MYH7,TNFAIP1,LCP1,SVEP1,VCAM1,FGFRL1,PARQ7 and TUFT1 may be candidate genes that affect the differences in skeletal muscle development between large white pigs and Min pigs.This study demonstrated the dynamic changes in chromatin accessibility that occurs during embryonic muscle development,which largely enriches the profile of chromatin accessibility in swine,and increases our understanding of chromatin accessibility in swine.This study can therefore be used as a reference for future research on muscle development in mammals.