Defining a Chromatin Pattern That Characterizes DNA Hypermethylated Genes in Colon Cancer Cells

Epigenetic gene regulation is a key determinant of heritable gene expression patterns and is critical for normal cellular function. Dysregulation of epigenetic transcriptional control is a fundamental feature of cancer, particularly manifesting as increased promoter DNA methylation with associated aberrant gene silencing which plays a significant role in tumor progression. We now globally map key chromatin parameters for genes with promoter CpG island DNA hypermethylation in colon cancer cells by combining microarray gene expression analyses with ChIP on chip technology. We first show that the silent state of such genes universally correlates with a broad distribution of a low, but distinct, level of the PcG mediated histone modification, methylation of lysine 27 of histone 3 (H3K27me) and a very low level of the active mark, H3K4me2. This chromatin pattern, and particularly H3K4me2 levels, crisply separates DNA hypermethylated genes from those where histone deacetylation is responsible for transcriptional silencing. Moreover, the chromatin pattern can markedly enhance identification of truly silent and DNA hypermethylated genes. We additionally find that when DNA hypermethylated genes are de-methylated and re-expressed, they adopt a “bivalent” chromatin pattern which is associated with the poised gene expression state of a large group of ES cell genes, and is characterized by an increase in levels of both the H3K27me3 and H3K4me2 marks. Our data have great relevance for the increasing interest in re-expression of DNA hypermethylated genes for the treatment of cancer. Keywords: DNA methylation, chromatin, histone modifications, cancer, epigenetic, ChIP-chip, expression microarray, hypermethylome, DNA-hypermethylation, DAC, TSA, colorectal cancer Cell Culture. HCT116 and DKO cells were maintained in McCoy’s 5A modified medium supplemented with 10% fetal bovine serum (Gemini Bio-Products) and 1% penicillin/streptomycin (Invitrogen) and grown at 37°C in 5% CO2 atmosphere. ChIP-chip. Chromatin immunoprecipitation was combined with DNA microarray analysis results (Schuebel KE et al., PLoS Genetics, 2007) on HCT116 colorectal cancer cells and DKO cells in duplicate using antibodies specific for H3K27me3 (Perez-Burgos L et al., Methods Enzymol, 2004), H3K4me2 (Upstate) or an IgG control (Upstate). Using 5 x 10^7 cells per experiment, chromatin immunoprecipitation, DNA amplification, labeling, and array hybridization were performed as previously described (Boyer LA et al., Cell, 2005). Independent batches of HCT116 and DKO cells were used to perform independent ChIP experiments and ChIPs for each antibody were hybridized to independent Agilent array sets. Whole genome expanded promoter 244K arrays from Agilent Technologies that span roughly 5 Kb upstream to 2 Kb downstream from gene transcription start sites were used. Analyses. The data preprocessing for the tiling arrays was performed according to the manufacturers recommendations using the Agilent® ChIP Analytics 1.3 software, i.e. a median blanks subtraction followed by an inter-array median normalization and a dye-bias median normalization. The data was imported into R for downstream analysis. The expression arrays were preprocessed as previously described (Schuebel KE et al., PLoS Genetics, 2007).