Figure 2

Progressive steps in the identification of epigenetically regulated miRNAs in prostate cells. Venn diagrams show the number of miRNA loci changed in LNCaP (L) with respect to PrEC (P) cells called significant by tiling arrays analysis using a t-statistic ≤-2 or ≥2 for regions +/-500 bp from the relevant miRNA. (A, B) Overlap of pri- and mature miRNA expression levels identified by tiling array and TLDA, respectively (TLDA miRNA expression data was normalized to RNU48, using a significance cutoff at p < 0.05 and ≥1.5 -fold change). Concomitant changes in active (H3K9Ac) or repressive (DNA methylation) epigenetic marks were then considered for miRNAs displaying significantly changed expression. (C, D) miRNA loci significantly changed in MeDIP-chip and H3K9Ac ChIP-chip tiling array analysis. (E, F) Four-way Venn diagrams showing the overlap of tiling array data with mature miRNA level upon 5-Aza-CdR treatment. MiR-615 lies at the four-way intersection indicating epigenetic up-regulation and miR-205, miR-196b and miR-21 are at the intersection of epigenetic down-regulation in LNCaP cells.