Decreased CTCF Expression Directs DNA Hypermethylation Events in Cancer

Methylation profiling of immortalized human prostate epithelial cells after CTCF knockdown by short hairpin RNA. Methylated DNA was immunoprecipitated with anti-methylcytosine antibodies from genomic DNA and detected by Affymetrix CytoScanHD chips. Methylated DNA was purified by 5-mC antibodies and Affymetrix CytoScanHD arrays were performed according to the manufacturer's protocols. Copy number analysis of Affymetrix CytoScanHD arrays were performed and immunoprecipitated methylated DNA and matched input samples. Input samples were used to normalize copy number variation specific effects. Raw intensity data was extracted from .CEL files using Affymetrix Power Tools and normalized using RMA style background adjustment. Log2 transformed values for input samples were subtracted from immunoprecipitated samples. Each probe represents the probe detected by the Affymetrix CytoScan HD Array.