Transcriptome analysis of mRNA and microRNAs of the intramuscular fat tissues from castrated and intact male Chinese Qinchuan cattle. Bos taurus

We report the application of the second-generation sequencing technology for microRNA and mRNA gene expression profiling of intramuscular fat (IMF) in castrated male (CM) and intact male 24 months old Qinchuan cattle (IM) to explore the regulation of intramuscular fat deposition. By comparing the mRNA expression profiles of IMF between CM and IM, 580 upregulated and 1120 downregulated genes were identified as differentially expressed genes correlated with castration. The upregulated genes were mainly associated with lipid metabolism, lipogenesis and fatty acid transportation signaling pathway, and the downregulated genes were correlated with immune response, intracellular signal transduction. Concurrently, the DE miRNAs, which are the important player in adipose tissue accumulation induced by castration, were also examined in IMF tissues, and 52 DE miRNAs were identified. Additionally, the expression profiles of selected genes and miRNAs were confirmed by using quantitative real-time PCR (qRT-PCR) assays. Furthermore, by means of integrated analysis, a total of 951 differentially expressed miRNA-Mrna pairs including 103 DE miRNAs and 535 DE mRNAs were found to show a negative correlation and a pair bovine known microRNA-target network was constructed which were supported by targets validation using dual luciferase reporter system. Moreover, the Ingenuity Pathway Analysis (IPA) software was used to construct a molecular interaction network which might involve in regulating IMF after castration. This molecular network is closely associated with lipid metabolism and adipocyte differentiation, which is supported by the functional identification results of bta-let-7i on bovine preadipocytes. These results provided valuable insights into the molecular mechanisms resulting in the IMF phenotype difference between CM and IM cattle. Overall design: Intramuscular fat mRNA and microRNA profiles of castrated male (CM) and intact male (IM) 24 monthes old cattle were respectively generated by using Ion ProtonTM Sequencer and Illumina HiSeq 2500. Two cDNA libraries representing CM and IM groups (coming from a pooling of 6 CM and 6 IM IMF) were constructed for mRNA transcriptome analysis. A total of four small RNA libraries (CM1, CM2, IM1, and IM2, a pooling of 3 CM or IM IMF for each library) were constructed for microRNA transcriptome analysis.