Sheep Intestinal Tissue Transcriptome Character Istic Analysis And Preliminary Crosstalk With Skeletal Muscle Transcriptional Regulation

Sheep are among the most important mutton domestic animals,different sheep breeds have great differences in their meat production ability,and this difference could ultimately resulted by digestion and absorbtion abilities.In order to elucidate the molecular mechanism between the sheep digestive and absorptive capacity and meat production traits,this study used meat-cultivated sheep species,Dorper sheep,and local sheep breeds,Small Tail Han sheep,as experimental materials.Their intestinal tissues(including the duodenum,cecum and colon)were applied for mRNA expression profile analysis,and mRNA-miRNA-lncRNA analysis,while those intestinal transcriptome results were then compared and crosstalked with the skeletal muscle transcriptome.The main results obtained in this study are as follows:1.In the differential expression analysis between the Dorper sheep and the Small Tail Han sheep on the three intestinal segments,2913,3000 and 3317 genes were differentially expressed in the duodenum,the caecum and the colon segment,respectively.The Dorper sheep up-regulated genes are mainly enriched in biological processes and pathways related to cell cycle regulation,lipids metabolism and carbohydrate metabolism.Small-tailed Han sheep up-regulated genes are mainly enriched in immune response,purine metabolism,pyrimidine metabolism,glycerophospholipids metabolism and other biological processes and pathways.Gene interaction network analysis revealed that five key regulatory modules and three key genes were involved in the sheep intestinal transcriptome regulation.Gene PIK3 CA was detected as key gene in all three intestinal segments,which indicates PIK3 CA might be a key regulator that caused differences between Dorper sheep and Small Tail Han sheep.2.In the differential expression analysis between three intestinal segments,2115 genes were differentially expressed between duodenum segment and the two large intestine segments.The duodenum up-regulated genes are mainly enriched in fatty acid digestion,absorption,lipid metabolism,carbohydrate metabolism related biological processes andpathways,while the caecum and colon up-regulated genes were mainly enriched in immune response,cell proliferation and apoptosis related biological processes and pathways.A total of 257 genes were found differentially expressed between the caecum and the colon.The caecum up-regulated genes did not receive and significantly enriched results,while the colon up-regulated genes were enriched to glycosphingolipid synthesis pathways.Gene interaction network analysis revealed that there are 3 key regulatory modules and 8 hub genes for differential analysis between intestinal segments,which might have important effects on the transcriptome difference between cecum and colon.3.In the intestinal transcriptome m RNA-mi RNA-lncRNA analysis,296 differentially expressed lncRNA genes were firstly identified.We then constructed an association regulatory network for 76 differential miRNAs,126 differential lncRNAs,and 822protein-coding genes;and also constructed ceRNA networks,while the 85 lncRNAs were judged as potential ceRNA.In the mRNA-miRNA-lncRNA analysis between two breeds,our results revealed that a total of 4 key miRNAs and 5 key lncRNAs were found to be involved in the regulation of DNA repair,cell proliferation,apoptosis regulation,stress,metabolism and other functions,indicating that non-coding RNA may play a key role in the post-transcriptional regulation of the intestinal transcriptome.In the combined analysis between intestinal segments,20 miRNAs and 47 lncRNAs were found to be involved in the post-transcriptional differential regulation between the duodenum and the large intestine.They may play major roles in carbohydrate metabolism and lipid metabolism.No ceRNA regulatory pattern was found between the cecum and colon,but it was found that two lncRNAs and miR-215 may play a key role in the post-transcriptional regulation differences between the two intestinal segments.5.The comparison preliminary crosstalk between the intestinal transcriptome results and the skeletal muscle transcriptome results showed that there were 182 protein coding genes and 4 lncRNAs differentially expressed between sheep breeds in the intestinal tissues and skeletal muscles,they may play regulatory roles in both intestinal and skeletal muscle tissues.Of these,40 protein-coding genes were found to be specifically highly expressed in the gut or skeletal muscles,and 18 were found to be differentially expressed during different developmental stages of the gut or skeletal muscle.These genes also satisfy the varietydifferences and tissue specificity,therefore are likely to be important genes affecting the digestibility and meat production traits of different sheep breeds.