Tissue-Specific Expression and Regulatory Networks of Pig MicroRNAome

Abstract

BackgroundDespite 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.ResultsWe 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.ConclusionsOur 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.

Lipid utilization in skeletal muscle cells is modulated in vitro and in vivo by specific miRNAs

“…Quantitative RT-PCR measures of 55 miRNAs confirmed the NGS results with a correlation of 0.78 (Figure S4B and Dataset S8). Certain miRNA-3p/miRNA-5p couples were differentially expressed across different myofibers, as already evidenced in other tissue types (Martini et al, 2014).…”

A Comprehensive Profile of Mature MicroRNA in the Pig

“…Knowledge of human development, physiology, and pathology can be obtained from suitable animal models, especially the mouse and rat, but many of their physiological parameters (e.g., size, respiratory rate) are significantly different from those in humans [2].…”

“…Although relatively expensive to breed and with a relatively long gestation period (about 114 days) [2], the pig is still an ideal animal model for biomedical research because of its close phylogenetic proximity and similarities with humans, such as organ size, anatomical features, physiology, and organ development, compared with the mouse [3].…”

“…One might think that the pig should also have a similar number of microRNAs (miRNAs). However, the number of porcine miRNAs available in public databases is still limited, with only 411 mature miRNAs in the miRBase (v21) compared to human (2,588) and mouse (1,982) [8], partly because only part of the porcine genome is available for study [9]. The common research strategy on miRNA may include three aims: (i) characterization of miRNAs (including identification of novel miRNAs), (ii) determination of target genes, and (iii) illumination of function of miRNAs and target genes.…”

Expression and Regulation Profile of Mature MicroRNA in the Pig: Relevance to Xenotransplantation

“…One might think that the pig should also have a similar number of microRNAs (miRNAs). However, the number of porcine miRNAs available in public databases is still limited, with only 411 mature miRNAs in the miRBase (v21) compared to human (2,588) and mouse (1,982) 8 , partly because only part of the porcine genome is available for study 9 . The common research strategy on miRNA may include three aims: (i) characterization of miRNAs (including identification of novel miRNAs), (ii) determination of target genes, and (iii) illumination of function of miRNAs and target genes.…”