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Tissue-specific expression and regulatory networks of pig microRNAome.

Martini P, Sales G, Brugiolo M, Gandaglia A, Naso F, De Pittà C, Spina M, Gerosa G, Chemello F, Romualdi C, Cagnin S, Lanfranchi G - PLoS ONE (2014)

Bottom Line: We experimentally identified candidate miRNAs sequences grouped in high-confidence (424) and medium-confidence (353) miRNAs according to RNA-seq results.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.

View Article: PubMed Central - PubMed

Affiliation: Department of Biology, University of Padova, Padova, Italy; CRIBI Biotechnology Centre, University of Padova, Padova, Italy.

ABSTRACT

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.

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Related in: MedlinePlus

Structural features of pig pre-miRNAs and alternative expression profiles of derived miRNA-miRNA* pairs.The left column reports the pre-miRNA hairpin structures as defined by the RNAfold algorithm. For each pre-miRNA, uppercase letters indicate miRNA mature sequences and black arrows their alternative 5′- and 3′-ends. The right column shows the expression signatures of miRNA-miRNA* pairs derived from pre-miRNA hairpin depicted in the left column. Expression was monitored by microarray RAKE on 14 different pig tissues (for tissue symbols see description in the caption of figure 4). The color intensity scale reported on top of the heat maps is proportional to the concentration of miRNAs and varies from black (low concentration) to bright yellow (14 pM concentrated). Gray squares indicate concentration under detection limit. MicroRNA identifications are composed of features (letters and numbers) divided by underscores as explained below. The first feature is the miRNA name and could be P (standing for predicted and referring to the de-novo identification), the Ensembl, or the Ver. 14 miRBase identifications (homology identification). The second feature indicates the chromosome number where the pre-miRNA is located. The third and fourth features indicate the start and stop nucleotide positions of pre-miRNAs in the pig genome. The fifth feature (+ or −) shows the template DNA strand. The sixth feature (3p or 5p) distinguishes the two arms of pre-miRNA hairpins. MicroRNA and miRNA* show an opposite expression profile across the different tissues that support a different functional role for miRNA and miRNA* in specific tissues. For example, mir-183_18_17172201_17172332_-_3p is highly expressed in L.V and L.A., but not in the Liver, L.N., Spleen and Lung where its 5p counterpart is instead more expressed.
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pone-0089755-g005: Structural features of pig pre-miRNAs and alternative expression profiles of derived miRNA-miRNA* pairs.The left column reports the pre-miRNA hairpin structures as defined by the RNAfold algorithm. For each pre-miRNA, uppercase letters indicate miRNA mature sequences and black arrows their alternative 5′- and 3′-ends. The right column shows the expression signatures of miRNA-miRNA* pairs derived from pre-miRNA hairpin depicted in the left column. Expression was monitored by microarray RAKE on 14 different pig tissues (for tissue symbols see description in the caption of figure 4). The color intensity scale reported on top of the heat maps is proportional to the concentration of miRNAs and varies from black (low concentration) to bright yellow (14 pM concentrated). Gray squares indicate concentration under detection limit. MicroRNA identifications are composed of features (letters and numbers) divided by underscores as explained below. The first feature is the miRNA name and could be P (standing for predicted and referring to the de-novo identification), the Ensembl, or the Ver. 14 miRBase identifications (homology identification). The second feature indicates the chromosome number where the pre-miRNA is located. The third and fourth features indicate the start and stop nucleotide positions of pre-miRNAs in the pig genome. The fifth feature (+ or −) shows the template DNA strand. The sixth feature (3p or 5p) distinguishes the two arms of pre-miRNA hairpins. MicroRNA and miRNA* show an opposite expression profile across the different tissues that support a different functional role for miRNA and miRNA* in specific tissues. For example, mir-183_18_17172201_17172332_-_3p is highly expressed in L.V and L.A., but not in the Liver, L.N., Spleen and Lung where its 5p counterpart is instead more expressed.

Mentions: Interestingly, miRNA/miRNA* couples show a peculiar and different expression pattern across different tissues (Figure 5), indicating that the two members of the couples may have different functions and could be retained in the RISC complex according to the specific function exerted in different cellular environments.


Tissue-specific expression and regulatory networks of pig microRNAome.

Martini P, Sales G, Brugiolo M, Gandaglia A, Naso F, De Pittà C, Spina M, Gerosa G, Chemello F, Romualdi C, Cagnin S, Lanfranchi G - PLoS ONE (2014)

Structural features of pig pre-miRNAs and alternative expression profiles of derived miRNA-miRNA* pairs.The left column reports the pre-miRNA hairpin structures as defined by the RNAfold algorithm. For each pre-miRNA, uppercase letters indicate miRNA mature sequences and black arrows their alternative 5′- and 3′-ends. The right column shows the expression signatures of miRNA-miRNA* pairs derived from pre-miRNA hairpin depicted in the left column. Expression was monitored by microarray RAKE on 14 different pig tissues (for tissue symbols see description in the caption of figure 4). The color intensity scale reported on top of the heat maps is proportional to the concentration of miRNAs and varies from black (low concentration) to bright yellow (14 pM concentrated). Gray squares indicate concentration under detection limit. MicroRNA identifications are composed of features (letters and numbers) divided by underscores as explained below. The first feature is the miRNA name and could be P (standing for predicted and referring to the de-novo identification), the Ensembl, or the Ver. 14 miRBase identifications (homology identification). The second feature indicates the chromosome number where the pre-miRNA is located. The third and fourth features indicate the start and stop nucleotide positions of pre-miRNAs in the pig genome. The fifth feature (+ or −) shows the template DNA strand. The sixth feature (3p or 5p) distinguishes the two arms of pre-miRNA hairpins. MicroRNA and miRNA* show an opposite expression profile across the different tissues that support a different functional role for miRNA and miRNA* in specific tissues. For example, mir-183_18_17172201_17172332_-_3p is highly expressed in L.V and L.A., but not in the Liver, L.N., Spleen and Lung where its 5p counterpart is instead more expressed.
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pone-0089755-g005: Structural features of pig pre-miRNAs and alternative expression profiles of derived miRNA-miRNA* pairs.The left column reports the pre-miRNA hairpin structures as defined by the RNAfold algorithm. For each pre-miRNA, uppercase letters indicate miRNA mature sequences and black arrows their alternative 5′- and 3′-ends. The right column shows the expression signatures of miRNA-miRNA* pairs derived from pre-miRNA hairpin depicted in the left column. Expression was monitored by microarray RAKE on 14 different pig tissues (for tissue symbols see description in the caption of figure 4). The color intensity scale reported on top of the heat maps is proportional to the concentration of miRNAs and varies from black (low concentration) to bright yellow (14 pM concentrated). Gray squares indicate concentration under detection limit. MicroRNA identifications are composed of features (letters and numbers) divided by underscores as explained below. The first feature is the miRNA name and could be P (standing for predicted and referring to the de-novo identification), the Ensembl, or the Ver. 14 miRBase identifications (homology identification). The second feature indicates the chromosome number where the pre-miRNA is located. The third and fourth features indicate the start and stop nucleotide positions of pre-miRNAs in the pig genome. The fifth feature (+ or −) shows the template DNA strand. The sixth feature (3p or 5p) distinguishes the two arms of pre-miRNA hairpins. MicroRNA and miRNA* show an opposite expression profile across the different tissues that support a different functional role for miRNA and miRNA* in specific tissues. For example, mir-183_18_17172201_17172332_-_3p is highly expressed in L.V and L.A., but not in the Liver, L.N., Spleen and Lung where its 5p counterpart is instead more expressed.
Mentions: Interestingly, miRNA/miRNA* couples show a peculiar and different expression pattern across different tissues (Figure 5), indicating that the two members of the couples may have different functions and could be retained in the RISC complex according to the specific function exerted in different cellular environments.

Bottom Line: We experimentally identified candidate miRNAs sequences grouped in high-confidence (424) and medium-confidence (353) miRNAs according to RNA-seq results.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.

View Article: PubMed Central - PubMed

Affiliation: Department of Biology, University of Padova, Padova, Italy; CRIBI Biotechnology Centre, University of Padova, Padova, Italy.

ABSTRACT

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.

Show MeSH
Related in: MedlinePlus