RT Journal Article SR Electronic T1 Modeling microRNA-driven post-transcriptional regulation by using exon-intron split analysis (EISA) in pigs JF bioRxiv FD Cold Spring Harbor Laboratory SP 2021.07.14.452370 DO 10.1101/2021.07.14.452370 A1 Emilio Mármol-Sánchez A1 Susanna Cirera A1 Laura M. Zingaretti A1 Mette Juul Jacobsen A1 Yuliaxis Ramayo-Caldas A1 Claus B. Jørgensen A1 Merete Fredholm A1 Tainã Figueiredo Cardoso A1 Raquel Quintanilla A1 Marcel Amills YR 2021 UL http://biorxiv.org/content/early/2021/10/15/2021.07.14.452370.abstract AB Background The contribution of microRNAs (miRNAs) to mRNA regulation has often been explored by selecting specific sets of 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 levels. 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.Results The EISA analysis revealed that in both cases the number of genes with significant transcriptional (Tc) signals (|FC| > 2; q-value < 0.05) was substantially higher than the number of genes showing significant post-transcriptional (PTc) signals, suggesting that most changes in gene expression are driven by effectors acting at the transcriptional level. We also observed important discrepancies between the lists of differentially expressed genes and those detected with EISA, thus demonstrating that the combination of both approaches yields a more comprehensive view about the molecular processes under study. We have also explored the potential contribution of miRNAs to the post-transcriptional regulation of mRNAs. 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 (N = 4) and skeletal muscle (N = 6) tissues, respectively. Enrichment analyses of the number of targeted genes by upregulated miRNAs revealed relevant results only for the skeletal muscle dataset, thus suggesting that in this experimental system the contribution of miRNAs to mRNA repression is more prominent than in the adipose tissue experimental system. Finally, the EISA analysis made possible to identify several genes related to carbohydrate and/or lipid metabolism, which 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.Conclusions Overall, the use of EISA reinforced the usefulness of this approach to discern transcriptional and post-transcriptional regulatory mechanisms, as well as to disentangle miRNA-mRNA interactions using exonic and intronic fractions of commonly available RNA-seq datasets.Competing Interest StatementThe authors have declared no competing interest.BMIbody mass indexCEScovariation enrichment scorecircRNAscircular RNAsDEdifferentially expressedEISAexon-intron split analysisFCfold-changeFDRfalse discovery rateGMgluteus mediusLDLlow density lipoproteinlncRNAslong non-coding RNAsmiRNAmicroRNAPCITpartial correlation with information theoryPTcpost-transcriptionalRBPsRNA binding proteinsTctranscriptionalTMMtrimmed mean of M-valuesρSpearman’s correlation coefficientΔExincrement of exonic countsΔIntincrement of intronic counts