Figure 5

DNA methylation and histone modifications identified by COBRA and ChIP-PCR. A. The targets examined by COBRA and ChIP-PCR. Not I sites and regions for COBRA and ChIP-PCR are indicated. B. DNA methylation identified by COBRA. DNA from DBA2 mouse (U) and bisulfite treated DNA (M) were negative and positive controls, respectively. DNA from L1210 (L) was compared with controls. Arrows and stars indicate the methylated and unmethylated fragments, individually. C. Quantitative ChIP-PCR was conducted to examine the individual histone modifications of the same 12 selected genes including both methylated (right portion of graph) and unmethylated at CpG sites (left portion of graph). The histone modification level of each gene was compared with input genomic DNA from L1210 and indicated with bars: blank, acetyl-H3K9; black, dimethyl-H3K9. Each error bar represents the standard deviation calculated from triplicates.