Modeling microRNA-driven post-transcriptional regulation by using exon-intron split analysis (EISA) in pigs

Abstract

AbstractThe contribution of microRNAs (miRNAs) to mRNA regulation has often been explored by selecting specific downregulated genes and determining whether they harbor binding sites for miRNAs. One essential flaw of this approach is that it does not discriminate whether mRNA downregulation takes place at the transcriptional or post-transcriptional level. In the current work, we aimed to overcome this limitation by performing an exon-intron split analysis (EISA) on skeletal muscle and adipose tissue RNA-seq data from two independent pig populations. Our results revealed that transcriptional (Tc) signals were more prevalent than post-transcriptional (PTc) signals. We also observed important discrepancies between differentially expressed genes and those detected with EISA, demonstrating that the combination of both approaches yields a more comprehensive view about the molecular processes under study. Moreover, a total of 43 and 25 mRNA genes showed high PTc signals in adipose and skeletal muscle tissues, respectively. From these, 25 and 21 genes were predicted as mRNA targets of upregulated miRNAs in adipose and skeletal muscle tissues, respectively. Enrichment analyses of the number of targeted genes by upregulated miRNAs revealed relevant results only for the skeletal muscle dataset, suggesting that in this diet challenged experimental system the contribution of miRNAs to mRNA repression is more prominent. Finally, we identified several genes that may play relevant roles in the energy homeostasis of the pig skeletal muscle (e.g. DKK2 and PDK4) and adipose (e.g. SESN3 and ESRRG) tissues. In summary, EISA allowed us to disentangle miRNA-driven post-transcriptional regulatory signals in two distinct porcine tissues.