Modeling microRNA-driven post-transcriptional regulation using exon–intron split analysis in pigs
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Modeling microRNA-driven post-transcriptional regulation using exon–intron split analysis in pigs. / Mármol-Sánchez, Emilio; Cirera, Susanna; Zingaretti, Laura M.; Jacobsen, Mette Juul; Ramayo-Caldas, Yuliaxis; Jørgensen, Claus B.; Fredholm, Merete; Cardoso, Tainã Figueiredo; Quintanilla, Raquel; Amills, Marcel.
In: Animal Genetics, Vol. 53, No. 5, 2022, p. 613-626.Research output: Contribution to journal › Journal article › Research › peer-review
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TY - JOUR
T1 - Modeling microRNA-driven post-transcriptional regulation using exon–intron split analysis in pigs
AU - Mármol-Sánchez, Emilio
AU - Cirera, Susanna
AU - Zingaretti, Laura M.
AU - Jacobsen, Mette Juul
AU - Ramayo-Caldas, Yuliaxis
AU - Jørgensen, Claus B.
AU - Fredholm, Merete
AU - Cardoso, Tainã Figueiredo
AU - Quintanilla, Raquel
AU - Amills, Marcel
N1 - Publisher Copyright: © 2022 Stichting International Foundation for Animal Genetics.
PY - 2022
Y1 - 2022
N2 - The contribution of microRNAs (miRNAs) to mRNA post-transcriptional regulation has often been explored by the post hoc selection of downregulated genes and determining whether they harbor binding sites for miRNAs of interest. This approach, however, does not discriminate whether these mRNAs are also downregulated at the transcriptional level. Here, we have characterized the transcriptional and post-transcriptional changes in mRNA expression in two porcine tissues: gluteus medius muscle of fasted and fed Duroc gilts and adipose tissue of lean and obese Duroc–Göttingen minipigs. Exon–intron split analysis of RNA-seq data allowed us to identify downregulated mRNAs with high post-transcriptional signals in fed or obese states, and we assessed whether they harbor binding sites for upregulated miRNAs in any of these two physiological states. We found 26 downregulated mRNAs with high post-transcriptional signals in the muscle of fed gilts and 21 of these were predicted targets of miRNAs upregulated in fed pigs. For adipose tissue, 44 downregulated mRNAs in obese minipigs displayed high post-transcriptional signals, and 25 of these were predicted targets of miRNAs upregulated in the obese state. These results suggest that the contribution of miRNAs to mRNA repression is more prominent in the skeletal muscle system. Finally, we identified several genes that may play relevant roles in the energy homeostasis of the pig skeletal muscle (DKK2 and PDK4) and adipose (SESN3 and ESRRG) tissues. By differentiating transcriptional from post-transcriptional changes in mRNA expression, exon–intron split analysis provides a valuable view of the regulation of gene expression, complementary to canonical differential expression analyses.
AB - The contribution of microRNAs (miRNAs) to mRNA post-transcriptional regulation has often been explored by the post hoc selection of downregulated genes and determining whether they harbor binding sites for miRNAs of interest. This approach, however, does not discriminate whether these mRNAs are also downregulated at the transcriptional level. Here, we have characterized the transcriptional and post-transcriptional changes in mRNA expression in two porcine tissues: gluteus medius muscle of fasted and fed Duroc gilts and adipose tissue of lean and obese Duroc–Göttingen minipigs. Exon–intron split analysis of RNA-seq data allowed us to identify downregulated mRNAs with high post-transcriptional signals in fed or obese states, and we assessed whether they harbor binding sites for upregulated miRNAs in any of these two physiological states. We found 26 downregulated mRNAs with high post-transcriptional signals in the muscle of fed gilts and 21 of these were predicted targets of miRNAs upregulated in fed pigs. For adipose tissue, 44 downregulated mRNAs in obese minipigs displayed high post-transcriptional signals, and 25 of these were predicted targets of miRNAs upregulated in the obese state. These results suggest that the contribution of miRNAs to mRNA repression is more prominent in the skeletal muscle system. Finally, we identified several genes that may play relevant roles in the energy homeostasis of the pig skeletal muscle (DKK2 and PDK4) and adipose (SESN3 and ESRRG) tissues. By differentiating transcriptional from post-transcriptional changes in mRNA expression, exon–intron split analysis provides a valuable view of the regulation of gene expression, complementary to canonical differential expression analyses.
KW - energy homeostasis
KW - exon–intron split analysis
KW - microRNA
KW - pigs
U2 - 10.1111/age.13238
DO - 10.1111/age.13238
M3 - Journal article
C2 - 35811409
AN - SCOPUS:85133713700
VL - 53
SP - 613
EP - 626
JO - Animal Genetics
JF - Animal Genetics
SN - 0268-9146
IS - 5
ER -
ID: 317106545