Gene expression analysis of miR-214 over-expressing melanoma cells (MA-2)

Growing evidence shows a strong interplay between post-transcriptional regulation, mediated by miRs and epigenetic regulation. Nevertheless, the number of experimentally validated miRs (called epimiRs) involved in these regulatory circuitries is still very small. Material & methods:We propose a pipeline to prioritize candidate epi-miRs and to identify potential epigenetic interactors of any given miR starting from miR transfection experiment datasets. Results & conclusion: We identified 34 candidate epi-miRs: 19 of them are known epi-miRs, while 15 are new. Moreover, using an in-house generated gene expression dataset, we experimentally proved that a component of the polycomb-repressive complex 2, the histone methyltransferase enhancer of zeste homolog 2 (EZH2), interacts with miR-214, a well-known prometastatic miR in melanoma and breast cancer, highlighting a miR-214-EZH2 regulatory axis potentially relevant in tumor progression. Gene expression profiling was carried out on controls and miR-214 overexpressing cells by using the Whole Human Genome Microarray platform (G4112F, Agilent Technologies). Total RNA was obtained from approximately 106 cells for each biological replicate. Three biological replicates were analyzed for controls and miR-214 overexpressing cells respectively for a total of 12 microarray experiments.