ARE and URM motifs affect miRNA mediated repression. (A) Expression changes for the 11 HeLA miRNA transfection experiments were standardized and pooled. ARE genes are defined as genes with UAUUUAU overrepresentation at the P < 0.05 level. miRNA target genes are genes with a target site of the transfected miRNA in the given experiments. The plot shows that miRNA target genes with ARE stability motifs were significantly up-regulated compared with miRNA targets without ARE motifs (P < 1.3 × 10−8, Kolmogorov-Smirnov one-tailed test, pooled data). (B) The same analysis was carried out for endogenous miRNA target genes. Endogenous miRNA target genes are defined as genes with predicted conserved target sites for an endogenous miRNA and no target sites for the transfected miRNA mimic in the individual experiment. Endogenous miRNA target genes with ARE stability motifs were significantly up-regulated compared with endogenous miRNA targets without ARE motifs (P < 9.1 × 10−13, Kolmogorov-Smirnov one-tailed test). (C) Similar to A, but using genes with URM1 motif overrepresentation. miRNA target genes with URM1 overrepresentation were significantly down-regulated compared with genes with miRNA target sites alone (P < 2.5 × 10−9, Kolmogorov-Smirnov one-tailed test).
