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Updated: May 1, 2026
MicroRNA Expression Profiles of Human iPS Cells, Retinal Pigment Epithelium Derived From iPS, and Fetal Retinal Pigment Epithelium
Published on: June 24, 2014
Tissue-specific expression and regulatory networks of pig microRNAome
Paolo Martini1, Gabriele Sales2, Mattia Brugiolo1
1Department of Biology, University of Padova, Padova, Italy; CRIBI Biotechnology Centre, University of Padova, Padova, Italy.
Background:
Despite the economic and medical importance of the pig, knowledge about its genome organization, gene expression regulation, and molecular mechanisms involved in physiological processes is far from that achieved for mouse and rat, the two most used model organisms in biomedical research. MicroRNAs (miRNAs) are a wide class of molecules that exert a recognized role in gene expression modulation, but only 280 miRNAs in pig have been characterized to date.
Results:
We applied a novel computational approach to predict species-specific and conserved miRNAs in the pig genome, which were then subjected to experimental validation. We experimentally identified candidate miRNAs sequences grouped in high-confidence (424) and medium-confidence (353) miRNAs according to RNA-seq results. A group of miRNAs was also validated by PCR experiments. We established the subtle variability in expression of isomiRs and miRNA-miRNA star couples supporting a biological function for these molecules. Finally, miRNA and mRNA expression profiles produced from the same sample of 20 different tissue of the animal were combined, using a correlation threshold to filter miRNA-target predictions, to identify tissue-specific regulatory networks.
Conclusions:
Our data represent a significant progress in the current understanding of miRNAome in pig. The identification of miRNAs, their target mRNAs, and the construction of regulatory circuits will provide new insights into the complex biological networks in several tissues of this important animal model.
Insights
Researchers identified numerous novel microRNAs (miRNAs) in pigs using computational and experimental methods. This significantly expands the known pig miRNAome, offering new insights into gene regulation in this important animal model.
Area of Science:
- Genomics
- Molecular Biology
- Bioinformatics
Background:
- Pigs are economically and medically important, yet their genome organization and gene regulation are less understood than in mice or rats.
- Only 280 microRNAs (miRNAs) were previously characterized in pigs, limiting our understanding of their gene expression modulation.
- A comprehensive understanding of pig molecular mechanisms is crucial for biomedical research.
Purpose of the Study:
- To predict and experimentally validate novel species-specific and conserved miRNAs in the pig genome.
- To characterize the expression profiles of identified miRNAs, including isomiRs and miRNA-miRNA star couples.
- To construct tissue-specific regulatory networks by integrating miRNA and messenger RNA (mRNA) expression data.
Main Methods:
- A novel computational approach was used to predict pig-specific and conserved miRNAs.
- Experimental validation included RNA sequencing (RNA-seq) and Polymerase Chain Reaction (PCR).
- Integrated miRNA and mRNA expression profiles from 20 different pig tissues were analyzed to identify regulatory networks.
Main Results:
- Experimentally identified 424 high-confidence and 353 medium-confidence candidate miRNA sequences.
- Validated the biological function of isomiRs and miRNA-miRNA star couples through expression variability analysis.
- Constructed tissue-specific regulatory networks by correlating miRNA and mRNA expression profiles.
Conclusions:
- This study significantly advances the understanding of the pig miRNAome.
- Identified miRNAs, their target mRNAs, and regulatory circuits provide new insights into pig biological networks.
- The findings offer valuable resources for future research utilizing pigs as a biomedical model.
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