Structural features of pig pre-miRNAs and alternative expression profiles of derived miRNA-miRNA* pairs.

<p>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 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0089755#pone-0089755-g004" target="_blank">figure 4</a>). 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 <i>de-novo</i> 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.