Fig. 1

Methylation-oriented interrogation of regulatory gene-domains. a Library construction: Regulatory chromatin blocks were identified among glioblastoma (GBM) tumors in two megabases windows surrounding 125 driver and 52 reference cancer genes. The fractions of tumors carrying the general marker of regulatory chromatin H3K4Me1, or the marker of active chromatin H3K27ac, are schematically outlined in purple. Following random segmentation of tumor DNAs, the segments encompassing CpG methylation sites were captured using biotinylated RNA probes (blue dots). The obtained target-enriched libraries, representing the spectrum of methylation and sequence variations of the targeted regions, were used for following stages. b Experimental assessments of regulatory functions: a representative tumor library were cloned into gene-reporter vectors, downstream to minimal promoters, and assessed for enhancing or silencing of the vector’s basal transcription level, before or after DNA methylation. c Mapping of gene regulatory circuits: Methylation levels of the captured sites were assessed, and associated with expression levels of the studied genes, across the tumors. Schematic positive and negative circuits of a representative gene are shown. d Integration of the regulatory principles learned from the experimental assay, with actual gene-regulatory data, allows disclosing of cis-regulatory networks which govern inter-patient heterogeneity in the expression level of cancer driver genes