Tissue-specific expression and regulatory networks of pig microRNAome.
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.
Department of Biology, University of Padova, Padova, Italy; CRIBI Biotechnology Centre, University of Padova, Padova, Italy.
Paolo
P
Martini
Department of Biology, University of Padova, Padova, Italy.
Gabriele
G
Sales
Department of Biology, University of Padova, Padova, Italy; CRIBI Biotechnology Centre, University of Padova, Padova, Italy.
Mattia
M
Brugiolo
Department of Cardiac, Thoracic and Vascular Sciences, University of Padova, Padova, Italy.
Alessandro
A
Gandaglia
Department of Cardiac, Thoracic and Vascular Sciences, University of Padova, Padova, Italy.
Filippo
F
Naso
Department of Biology, University of Padova, Padova, Italy.
Cristiano
C
De Pittà
Department of Biomedical Sciences, University of Padova, Padova, Italy.
Michele
M
Spina
Department of Cardiac, Thoracic and Vascular Sciences, University of Padova, Padova, Italy.
Gino
G
Gerosa
Department of Biology, University of Padova, Padova, Italy.
Francesco
F
Chemello
Department of Biology, University of Padova, Padova, Italy.
Chiara
C
Romualdi
Department of Biology, University of Padova, Padova, Italy; CRIBI Biotechnology Centre, University of Padova, Padova, Italy.
Stefano
S
Cagnin
Department of Biology, University of Padova, Padova, Italy; CRIBI Biotechnology Centre, University of Padova, Padova, Italy.
Gerolamo
G
Lanfranchi
D000818:Animals; D020029:Base Pairing; D001483:Base Sequence; D015415:Biomarkers / Q000032:analysis*; D019295:Computational Biology; D020869:Gene Expression Profiling; D053263:Gene Regulatory Networks; D059014:High-Throughput Nucleotide Sequencing; D051379:Mice; D035683:MicroRNAs / Q000235:genetics*; D008969:Molecular Sequence Data; D009928:Organ Specificity; D012333:RNA, Messenger / Q000235:genetics*; D051381:Rats; D060888:Real-Time Polymerase Chain Reaction; D020133:Reverse Transcriptase Polymerase Chain Reaction; D013552:Swine
D015415:Biomarkers; D035683:MicroRNAs; D012333:RNA, Messenger