| The adipose tissue of pig is an important place for the body to store energy.In the breeding programs of pig,backfat thickness(BFT)is an important economic trait for pigs and is mainly determined by subcutaneous fat deposition.Fat deposition not only affects the growth performance of pig,but also it is closely related to the occurrence of many diseases.More and more studies have shown that long intergenic non-coding RNAs(linc RNAs)and polyadenylation sites(PASs)play important roles in many biological processes,but the identification of linc RNAs and PASs related to subcutaneous fat are currently very rare,and their functions and molecular mechanisms in subcutaneous fat deposition are unclear.Therefore,this study used published RNA-seq data of subcutaneous fat in pigs to identify the sequence characteristics and expression rules of linc RNAs and PASs in subcutaneous fat and conduct preliminary analysis of the function.The results obtained are as follows:(1)A total of 1,308 linc RNAs were identified through the analytical procedure established in our laboratory,of which 277 were novel linc RNAs.Compared with m RNA,the identified linc RNA has shorter transcript length,lower expression level,fewer exon number,and longer exon length.(2)Cis and trans regulation methods were used to predict the potential target genes of differentially expressed linc RNAs(DELs).It was found that they included PNPLA4,PRKCB,GPIHBP1 and other genes involved in the processes of adipogenesis and lipid catabolism.Moreover,quantitative trait locus(QTL)mapping analysis was performed on DELs.Nine DELs obtained 602 QTLs,and 153 QTLs were fatness trait type.The majority of fatness trait type was subcutaneous fat related QTLs,and each DEL was located in QTLs of fatness trait type.(3)A total of 21 gene modules were obtained through weighted gene co-expression network analysis(WGCNA)of linc RNAs and protein-coding genes.Two key modules were obtained based on the relationship between modules and traits,namely the purple module and the green module.Three and two hub linc RNAs were screened respectively.After enrichment analysis of the protein-coding genes in these two key modules found that they are involved in biological processes and pathways related to fat deposition,including the regulation of lipolysis in adipocytes and insulin signaling pathway.(4)A total of 12,370 PASs were identified by using RNA-seq data,corresponding to 10,450 highly reliable PAS clusters.There were 4,641(about 44.41%)PASs annotated to 3,176 genes,of which 942 genes(about 29.66%)contained at least two or more PASs,namely alternative polyadenylation(APA).By analyzing the distance between adjacent PASs in the APA gene,it was found that the distances between most adjacent PASs were less than 1 kb.(5)Through Pearson correlation analysis,it was found that the gene expression in lean,intermediate and obese groups showed weak positive correlations with the number of PAS and the covered reads of PAS in the corresponding genes.There were 49 differentially PASs between lean and obese groups,corresponding to 21 protein-coding genes.The results of enrichment analysis showed that these genes were involved in biological processes such as cholesterol binding.In summary,this study analyzed the pig subcutaneous fat RNA-seq data,and identified linc RNAs and PASs and completed the preliminary functional analysis,which helped to improve the current annotation of pig linc RNAs and PASs,it also provide the resources for the further exploration of the epigenetic mechanism and post-transcriptional modification mechanism of pig subcutaneous fat deposition. |
