Figure 1

Schematic displaying experimental discovery pipeline used for identification of miRNAs epigenetically deregulated in cancer. To identify epigenetically regulated miRNAs, we employed an integrative approach assessing changes in epigenetic marks, primary miRNA transcript, and mature miRNA. (A, B) Custom tiling arrays probing all miRNA loci (miRBase12.0, 668 miRNA loci) were used to assay primary miRNA transcription and epigenetic marks (H3K9Ac and DNA methylation) from PrEC and LNCaP cells. Example tiling array intensity plots are shown of the 2000 bp region spanning the miR-205 gene for both expression (A), and DNA methylation (B), showing the chromosomal coordinate (x-axis) and the hybridization intensity (y-axis), with regions displaying significant differences highlighted. (C) Global mature miRNA expression levels in PrEC and LNCaP cells +/- 5-Aza-CdR treatment (3 μM LNCaP, 1 μM PrEC; 72 hours) as determined by TLDA qRT-PCR (368 miRNAs).