Modeling microRNA-driven post-transcriptional regulation using exon-intron split analysis in pigs

Area of Science:

• Animal science
• Molecular biology
• Genomics

Background:

• MicroRNA (miRNA) regulation of mRNA is crucial but often conflated with transcriptional changes.
• Distinguishing transcriptional from post-transcriptional mRNA regulation is key to understanding gene expression control.

Purpose of the Study:

• To differentiate transcriptional and post-transcriptional mRNA changes in porcine muscle and adipose tissue.
• To identify miRNA targets and their roles in physiological states like feeding and obesity.
• To assess the contribution of miRNAs to mRNA repression in different tissues.

Main Methods:

• RNA-sequencing (RNA-seq) data analysis using exon-intron split.
• Identification of downregulated mRNAs with high post-transcriptional signals.
• Prediction of miRNA binding sites for upregulated miRNAs.

Main Results:

• In fed gilts' muscle, 26 downregulated mRNAs showed high post-transcriptional signals, with 21 predicted miRNA targets.
• In obese minipigs' adipose tissue, 44 downregulated mRNAs had high post-transcriptional signals, with 25 predicted miRNA targets.
• miRNA-mediated repression appeared more prominent in skeletal muscle than adipose tissue.

Conclusions:

• Exon-intron split analysis effectively distinguishes transcriptional and post-transcriptional gene regulation.
• miRNAs play a significant role in post-transcriptional mRNA repression, especially in porcine skeletal muscle.
• Identified key genes (DKK2, PDK4, SESN3, ESRRG) involved in energy homeostasis in pig muscle and adipose tissue.