Epigenetic reprogramming plays important roles in the development of cancer. Aberrant DNA methylation has been observed in various kinds of tumors, and different tumors have different DNA methylation pattern. Recent studies suggest that there may be instructive mechanisms underlying the DNA methylation. Polycomb repressive complex has been reported to be associated with DNA methylation in cancer.  In this study, we used both the promoter array and the CpG island array to study the histone modification pattern of H3K4 and H3K27, as well as the Suz12 binding region in follicular lymphoma cells (RL cell line). By comparing Suz12 RL targets with the reported embryonic Suz12 targeting sites, the results showed that the distribution of Suz12 in RL cells was different from that in the embryonic stem cells, and that the methylated genes, which are also commonly hypermethylated in cancers, depleted Suz12 binding in RL cells. To know which Suz12 targets in RL cells are still associated with DNA methylation, we developed a ChIP-chop-chip method based on ChIP-chip assay. We identified 104 genes with both DNA methylation and the Suz12 binding in the same CpG island region in RL cells.