TY - JOUR
T1 - Tissue-specific expression and regulatory networks of pig microRNAome
AU - Martini, Paolo
AU - Sales, Gabriele
AU - Brugiolo, Mattia
AU - Gandaglia, Alessandro
AU - Naso, Filippo
AU - De Pittà, Cristiano
AU - Spina, Michele
AU - Gerosa, Gino
AU - Chemello, Francesco
AU - Romualdi, Chiara
AU - Cagnin, Stefano
AU - Lanfranchi, Gerolamo
PY - 2014/4/3
Y1 - 2014/4/3
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=84899127253&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=84899127253&partnerID=8YFLogxK
U2 - 10.1371/journal.pone.0089755
DO - 10.1371/journal.pone.0089755
M3 - Article
C2 - 24699212
AN - SCOPUS:84899127253
SN - 1932-6203
VL - 9
JO - PloS one
JF - PloS one
IS - 4
M1 - e89755
ER -