Secondary structures and miRNA-complementary regions of the PD- modified U1 and RP11-462G22.1 lncRNAs.

<p>The spliceosomal PD altered lncRNA U1 and the altered RP11-462G22.1 were predicted as targeting numerous microRNAs (miRNAs) by a method based on support vector machine that predicts both conserved and non-conserved miRNA targets through MirTarget2. The secondary structures of U1 (A) and of RP11-462G22.1 (lnc-FRG1-3) (B) were computed using RNAfold (minimum free energy: −412.07 and −271.93 Kcal/Mole, accordingly). Complementary seed-matching sites for one predicted miRNA were marked for each of the two lncRNAs: hsa-miR-125b-5p (A) and hsa-miR-25-5p (B), enlarged. Red nucleotide color marks the matched miRNA-seed lncRNA sequence region. In both cases, the predicted biding site was found in a single strand region predicted as having a loop structure. U1 was predicted as having a series of stem-loop structures, while RP11-462G22.1 exhibited a more complex structure compared to U1.