Methylted DNMT3B Target Genes in RKO cells identified by ChIP on Chip.

Association of DNMT3B to the target genes and their methylation status was determined by ChIP-CHOP assay. Formaldehyde-cross-linked chromatin from RKO cells was immunoprecipitated with anti-DNMT3B or pre-immune IgG. DNA pulled down was divided into three aliquots, which were either undigested or digested with Hpa II, Msp I and subjected to PCR with primers specific for CGIs of different genes that harbor Hpa II/Msp I sites. PCR products were resolved by agarose gel electrophoresis. Generation of PCR product in Hpa II digested DNA indicates methylation.