Multi-omics Integrated Analysis Of Differences In Gene Transcription Regulation Of Stromal Vascular Fraction Between Porcine Subcutaneous And Visceral Adipose Tissue

Fat deposition is one of the most important economic traits in pig production.Excessive fat deposition will not only cause waste of feed resources,but also reduce the economic value of the carcass.According to the different distribution sites,two major anatomical depots of adipose tissues are recognized in pig: subcutaneous adipose tissues and visceral adipose tissues,and the amount of these two adipose tissues has different effects on carcass quality.The subcutaneous fat and visceral fat of pigs have obvious differences in growth rate and fat deposition capacity.However,the molecular mechanisms that contribute to these phenotypic differences are not well understood.Revealing the molecular mechanism of the difference in growth rate and fat deposition capacity between subcutaneous fat and visceral fat in pigs is of great significance for the improvement of fat deposition-related traits in pig breeding.In addition,it is generally accepted that the occurrence of obesity-related metabolic diseases are related more to distribution pattern of subcutaneous and visceral adipose tissues rather than total body fat.Pig is the most suitable biomedical model for studying human obesity.Using pig as a research animal to explore the molecular mechanism of physiological and pathological functional differences between subcutaneous and visceral adipose tissues during the occurrence of energy metabolism disorders.It is of great significance to understand the occurrence of obesity and obesity-related diseases in humans.Adipose tissue-derived stromal vascular fraction(SVF)cells are involved in the production of new adipocytes during adipose tissues growth and closely associated with inflammation and insulin resistance during obesity.In this study,Bama Xiang pig were used as the research object,we established the chromatin accessibility landscape of the SVF from porcine subcutaneous(S-SVF)and visceral(perirenal)adipose tissues(VSVF)using li DNase-seq,and to identify differential cis-regulatory elements and transcription factors between S-SVF and V-SVF.Subsequently,the H3K27 Ac modification and m RNA expression profiles of S-SVF and V-SVF were established using Ch IP-seq and RNA-seq,respectively.By integrating li DNase-seq with H3K27 ac Ch IP-seq and RNA-seq datasets,we investigated the molecular mechanisms and screened the functional genes that cause the different growth rate and fat deposition capacity between porcine subcutaneous and visceral(perirenal)adipose tissues,as well as the different physiopathological functions between theses two adipose tissue depots.The main findings were as follows:(1)3930 and 2801 DNase I hypersensitive sites(DHSs)were respectively identified in S-SVF and V-SVF by using li DNase-seq.1261 differential DHSs were identified between S-SVF and V-SVF.There are 790 genes were associated with differential DHSs.Differential DHS-associated genes were mainly enriched in GO functions and KEGG signaling pathway related to neuronal development,metabolism of lipids and carbohydrates,immune processes,and inflammation.(2)We performed motif enrichment analysis in these differential DHSs.The results found motifs for the Krüppel-like factor(KLF)family of TFs were significantly enriched.(3)29950 and 36031 H3K27 Ac peaks were respectively identified in S-SVF and V-SVF by using Ch IP-seq.By integrating li DNase-seq with H3K27 ac Ch IP-seq datasets,we found that there is a strong correlation between li DNaseq-seq DHSs and H3K27 ac peaks.In particular,there are 94.9% and 85.5% of DHSs located in the proximal promoter region of genes overlapped with H3K27 Ac peaks in S-SVF and VSVF,respectively.(4)We performed differential analysis and found 3162 differential H3K27 Ac peaks between S-SVF and V-SVF.There are 1359 genes were associated with differential H3K27 Ac peaks,104 of these genes overlapped with differential DHSassociated genes.These 104 genes were mainly enriched in GO functions and KEGG signaling pathway related to neuronal development,metabolism of lipids and carbohydrates,immune processes,and inflammation.(5)1784 differentially expressed genes were identified between S-SVF and V-SVF by using RNA-seq.By integrating li DNase-seq with RNA-seq datasets,we found that li DNase-seq signal intensity of differentially expressed genes were higher than nondifferentially expressed genes around gene loci(5 kb upstream and downstream)in both S-SVF and V-SVF,especially around the transcriptional start site.Specifically,the DHS signals of differentially expressed genes is 24.9% and 20.7% higher than that of nondifferentially expressed genes in S-SVF and V-SVF,respectively.(6)we intersected the 790 differential DHS-associated genes with 1359 differential H3K27 ac peaks-associated genes and 1784 differentially expressed genes to identify a set of 20 genes.Notably,the variation tendency of m RNA expression of these gene was consistent with the trend of DHS and H3K27 ac signal changes near the gene loci between S-SVF and V-SVF.These 20 genes were mainly enriched in GO functions related to metabolism of lipids and immune processes.In summary,using multi-omics integrated analysis of DNase-seq,H3K27 ac Ch IPseq and RNA-seq,we identified 20 key functional genes which are differentially expressed between S-SVF and V-SVF.These 20 genes are closely related to the different growth rate and fat deposition capacity of porcine subcutaneous and visceral(perirenal)adipose tissues,as well as the different physiopathological functions between theses two adipose tissue depots.However,it is necessary to further verify their specific functions and action mechanisms at the cellular level.The results of this study can not only provide a theoretical reference for the improvement of fat deposition-related traits in pig breeding,but also provide a theoretical reference for the studies of human obesity and obesity-related diseases.