Expression And Functional Prediction Analysis Of CircRNA And MRNA In Xiang Pigs With Wrinkled Skin

Circular RNA(circ RNA)is a kind of endogenous noncoding RNA(nc RNA)which produced by reverse splicing process and without 5' terminal cap structure and 3' terminal ploy A tail.It is different from general linear RNA molecules,becase it has no free terminal,so it is more stabler than general linear RNA.Circ RNA not only acts as a sponge for micro RNA(mi RNA),but also cis-regulates the expression of host genes.At present,some studies have found that some skin diseases may be related to the regulation of circ RNA,but there is no studies have been found on the expression and regulation of circ RNA in the skin tissues of Xiang pig with wrinkled skin.In this study we selected four head of the Xiang pigs with wrinkled skin and the normal Xiang pigs were around two years old as the research material,through the RNA-Seq sequencing and bioinformatics methods for circ RNA and m RNA sequencing data analysis of normal Xiang pigs skin tissue and Xiang pigs with wrinkled skin,firstly we selected the circ RNA sequencing data and analysis its characteristics and expression,and screen differentially expressed circ RNA and differential expression of m RNA.To differentially expressed circ RNA for parent and differentially expressed genes m RNA enrichment of function analysis,in addition to forecast 64 circ RNAs differences in the expression in the adsorption of mi RNAs,then predicted target genes for these mi RNAs,and the enrichment of target gene function analysis,to find may be associated with wrinkled skin characteristic of the signal path,finally united gene expression,analysis on the related pathways of the expression of target genes,explore circ RNA-mi RNA-m RNA network interaction mechanism,The corresponding circ RNA-mi RNA-m RNA network interaction diagram was constructed to further illustrate the function of circ RNAs in the skin tissues of wrinkled and normal pigs.The main results of this study are as follows:(1)In this study,there were a total of 8 RNA-seq libraries.After sequencing,about 1191708930 reads were obtained,and over 86.33% could be compared to the reference genome(Sus scrofa 11.1).After differential expression analysis,there were 602 differentially expressed genes(|log2(fold change)|>1.5,(padj)<0.05),among which 363 genes were up-regulated and 239 genes were down-regulated.Analyzing function of enrichment of differentially expressed genes found that enrichment significantly(P < 0.05)access mainly includes: the regulation of adipose decompose,AMPK pathway,metabolic pathway,PPAR signaling pathways,valine,leucine and isoleucine,protein digestion and absorption,the biodegradation of ECM receptor interactions,PI3K-Akt signaling pathways and biological pathways.(2)There was a total of 4176 circ RNAs were identified,among which 2761 circ RNAs were expressed in both Xiang pig with wrinkled skin and normal Xiang pigs,among which 990 were expressed in Xiang pig with wrinkled skin and 425 in normal Xiang pigs.The percentage of circ RNAs in the skin tissues of Xiang pig with wrinkled skin and normal Xiang pigs was mainly derived from exons,which were 94.3% and 94%,respectively.The percentage of introns and interstitial spacer was similar,in which the introns accounted for 2.4% and 2.6%,respectively,and the interstitial spacer accounted for 3.3% and 3.4%.Wrinkled skin fragrant pig pig skin tissues from normal circ RNAs in chromosome 1~18,X,Y chromosomes are distributed,and the corresponding chromosome circ RNAs percentage,both on chromosome 1 most,least Y chromosome distribution,and only expressed in normal pig,in addition,part of this comes from the mitochondria,and the percentage is consistent.(3)We analysed the circ RNA expression values(RPM values)in the skin tissues of Xiang pigs with wrinkled skin and normal Xiang pigs,it was found that there were 2,309 and 2,100 circ RNAs with RPM values of >100,among which 145 and 180 circ RNAs with RPM values of >1000(high expression values),respectively.Among the first 20 circ RNAs expressed in the skin tissues of Xiang pigs with wrinkled skin and normal Xiang pigs,7 circ RNAs were found to be the same.Analysis showed that these highly expressed circ RNAs may be related to substance metabolism,adhesion link,cell cycle,cell differentiation,some cancers and infection pathways,etc.(4)We obtained a total of 400 differentially expressed circ RNAs(|log2(fold change)|>1.5,(padj)<0.05)by analysis of circ RNA differentially expressed in the skin tissues of Xiang pigs with wrinkled skin and normal Xiang pigs.270 circ RNAs were up-regulated in the Xiang pigs with wrinkled skin and 130 were down-regulated in the Xiang pigs with wrinkled skin.Functional enrichment analysis of the differentially expressed circ RNAs parent genes showed significant enrichment(P<0.05)in the following signal pathways: ubiquitin-mediated proteolysis,viral carcinogenesis,RNA degradation,cell cycle,mitochondrial autophagy,adhesion links,and some cancers.(5)We choosed 64 differentially expressed circ RNAs for predicting target mi RNA,and a total of 179 binding sites and 139 mi RNAs were obtained.Target genes of these 139 mi RNAs were respectively predicted.The results showed that there were 1210 target genes of mi RNAs corresponding to up-regulated circ RNAs and 712 target genes corresponding to down-regulated circ RNAs.After functional enrichment analysis of target genes,it is found that target genes are involved in many biological processes of life activities.In order to further elucidate the function of circ RNA in the skin tissues of ruff and normal pig;32 signaling pathways that may be related to the skin characteristics of wrinkled skin fragrant pigs were selected,such as PI3K-Akt signaling pathway,cell adhesion molecule(CAMs),cell apoptosis,adhesion link,chemokine signaling pathway and cell senescence.Finally,the expression of the combined genes and the expression of the upper target genes in the related pathways were analyzed,and the interaction mechanism of the 13 circ RNA-mi RNA-m RNA networks was finally obtained,which may be related to the characteristics of Xiang pigs with wrinkled skin,folding and redness.The 13 circ RNA-mi RNA-m RNA regulation networks including 20 circ RNAs,22 mi RNAs and 16 m RNAs,which further demonstrated the function of circ RNAs in the skin tissues of the pigs.