Methylation-mediated retuning on the enhancer-to-silencer activity scale of networked regulatory elements guides driver-gene misregulation

Cancers arise when particular disease-driving genes adopt abnormal functions, but sequence analyses of coding and regulatory elements leave many of these abnormalities unexplained. We developed a strategy to explore the activities of silencers and enhancers in cancer tumors. Applying the method to human glioblastomas, we produced a driver-gene wide dataset of regulatory elements. Many genes were associated with multiple silencers and enhancers, which cooperatively controlled their expression. Surprisingly, DNA methylation induces enhancers and silencers to acquire new activity setpoints, ranging between strong transcriptional enhancing to strong silencing. Integration of these effects into mathematical models of gene expression resolved the molecular events underlying cancer-genes misregulation in hitherto unexplained tumors. Gene-malfunctioning events due to epigenetically-retuned enhancers or silencers outnumbered causative coding or regulatory sequence alterations, hence dominated driver-genes mutagenesis. The elucidation of this principal gene-transformation mechanism may open the way for methodological disclosing of the driving forces behind cancers and other diseases A new strategy for methylation-centered interrogations of functional gene-associated regulatory elements was applied to H3K4me1-marked chromatin within the regulatory domains of 125 pan-cancer and/or glioblastoma (GBM) driver genes, and 52 reference cancer genes. The effect of DNA methylation on gene transcription was analyzed for 38,050 targeted methylation sites in experimental massively paralleled reporter assay as well as in 24 GBM tumors. Technical and biological replicates provided as well.