Differences In MiRNA Expression Profile Between Liver And Muscle Tissues Of The F6 Individuals Of Heterogeneous Stock And Novel MiRNA Prediction

MicroRNA?miRNA?is a type of small RNA with a length of about 22bp.They can inhibit or directly degrade mRNAs by binding to the mRNA's 3'-UTR region.miRNAs are widely distributed in various species and have interspecies conservation characteristics.In recent years,with the rapid development of experimental techniques and the decrease in the cost of sequencing,more and more miRNAs have been discovered by researchers.So far,the miRbase database has contained more than 48,000 annotated miRNAs across more than 270 species.As a regulator for post-transcriptional level,many miRNAs play an important roles in the proliferation and differentiation of muscle cells.In this study,the miRNA-seq were conducted on 207 longissimus dorsi muscle samples and 10 liver samples from a heterogeneous stock?HS?F6 population by using high-throughput sequencing technology.The expression levels of miRNAs in these samples were quantified.Then,miRNA differential expression analysis between tissues,cluster analysis,the miRNA target-gene prediction,GO analysis and pathway analysis were performed.1)The lengths of the miRNA reads in porcine longissimus dorsi muscle were mainly distributed at 22bp,while most reads in liver tissue were distributed between 20bp and22bp.2)We found that only one MyomiRNA?ssc-miR-208b?was expressed at lower level in muscle of castrated boars than in that of sows?P=0.014?.But,no sex-differentiated miRNAs were detected in liver tissue.3)A total of 276 annotated miRNA were detected in muscle and liver tissues,of which 202 miRNAs expressed differentially between tissues,including 96 miRNAs down-regulated and 106 miRNAs upregulated in muscle.4)Through clustering analysis,5 highly and similarly expressed miRNAs were found in the liver and muscle tissues.Prediction of their target genes,GO analysis and pathway analysis of their common target gene set.The results were found to be enriched in the closely related pathways of biological function in their source tissues.The liver tissue analysis results are as follows:Pathway function is enriched in response to external stimuli(P=10^-6),oncogene-induced senescence(P=10^-5.7),and DNA transcription template initiation(P=10^-5.4).The GO function is enriched in the liver function related pathways such as cellular response to cyclic organic matter(p=10^-4.6),biogenic small molecule production(P=10^-3.5),and plasma membrane tissue function.The analysis of the longissimus dorsi muscles is as follows:Pathway enrichment in the regulation of homeostasis(P=10^-4.2),RNA localization(P=10^-4.2),termination of DNA transcription(P=10^-3.8),etc.;GO analysis enriched in muscle axon signal transduction(P=10^-4.6),nucleic acid metabolism(P=10^-3.4),biological small molecule transport(P=10^-3.4)and other muscle metabolism related functions.5)A total of 256 new miRNAs has been bioinformatic predicted in a large scale HS F6 samples with complex genetic background.These miRNAs shared seed sequences with human or mouse pre-miRNAs and possessed low folding free energy?P<0.05?.Thus,these predicted miRNAs are reliable.This study rigorously controlled and preliminary analyzed the miRNA sequencing data of>200 HS F6 individuals,we have annotated them complimented quality the control the annotation and quantification of miRNA profiles in them,which laid a solid foundation for the subsequent analyses of eQTL mapping QTT and mRNA-mRNA interaction network by combining with addition data of phenotype,genotype and mRNA level in those samples.The differentially expressed of miRNAs in liver and muscle tissues were determined.The functional clustering of similar common target genes was closely related to the function of the source tissues,demonstrating that the regulation of miRNAs is compensatory.The miRNA predictions provide the basis for subsequent experiments to demonstrate the existence and function of these novel miRNAs.