Gene Set: KONDO_COLON_CANCER_HCP_WITH_H3K27ME3

Standard name KONDO_COLON_CANCER_HCP_WITH_H3K27ME3
Systematic name M697
Brief description Genes with high histone H3 tri-methylation mark at K27 (H3K27me3) in SW48 cells (colon cancer), by ChIP-chip assay on a 12K CpG array (high-CpG-density promoters, HCP).
Full description or abstract Epigenetic silencing in cancer cells is mediated by at least two distinct histone modifications, polycomb-based histone H3 lysine 27 trimethylation (H3K27triM) and H3K9 dimethylation. The relationship between DNA hypermethylation and these histone modifications is not completely understood. Using chromatin immunoprecipitation microarrays (ChIP-chip) in prostate cancer cells compared to normal prostate, we found that up to 5% of promoters (16% CpG islands and 84% non-CpG islands) were enriched with H3K27triM. These genes were silenced specifically in prostate cancer, and those CpG islands affected showed low levels of DNA methylation. Downregulation of the EZH2 histone methyltransferase restored expression of the H3K27triM target genes alone or in synergy with histone deacetylase inhibition, without affecting promoter DNA methylation, and with no effect on the expression of genes silenced by DNA hypermethylation. These data establish EZH2-mediated H3K27triM as a mechanism of tumor-suppressor gene silencing in cancer that is potentially independent of promoter DNA methylation.
Collection C2: curated gene sets
      CGP: chemical and genetic perturbations
Source publication Pubmed 18488029   Authors: Kondo Y,Shen L,Cheng AS,Ahmed S,Boumber Y,Charo C,Yamochi T,Urano T,Furukawa K,Kwabi-Addo B,Gold DL,Sekido Y,Huang TH,Issa JP
Exact source Table 3S: H3K27me3 in SW48
Related gene sets (show 4 additional gene sets from the source publication)

(show 8 gene sets from the same authors)
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Organism Homo sapiens
Contributed by Jessica Robertson (Broad Institute)
Source platform SEQ_ACCESSION
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Compendia expression profiles Human tissue compendium (Novartis)
NCI-60 cell lines (National Cancer Institute)
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