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

Emilio Mármol-Sánchez1, Susanna Cirera2, Laura M Zingaretti3

  • 1Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de Barcelona, Bellaterra, Spain.

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Summary

MicroRNAs (miRNAs) significantly regulate gene expression post-transcriptionally, particularly in pig skeletal muscle. This study differentiates transcriptional and post-transcriptional changes, revealing miRNA roles in energy homeostasis.

Keywords:
energy homeostasisexon-intron split analysismicroRNApigs

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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.