Gene silencing in cancer by histone H3 lysine 27 trimethylation independent of promoter DNA methylation

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.

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Figure 1: Two distinct histone codes at loci silenced in cancer.
Figure 2: Global assessment of H3K27 modifications in cancer.
Figure 3: H3K27triM and its related gene silencing as a cancer-specific event in prostate cancers.
Figure 4: Global assessment of DNA methylation and H3K27triM in normal and cancer cell lines.
Figure 5: Reactivation of silenced gene expression by inhibition of DNA methylation, histone deacetylation or EZH2 expression.
Figure 6: H3K27triM and its related gene silencing are cancer-relevant events in prostate and breast cancers.
Figure 7: Effects of EZH2 knockdown (EZH2 KD) in cancer cell lines.

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Acknowledgements

This work was supported in part by US National Institutes of Health by grants P50CA100632, R33CA89837 and RO1CA098006 to J.-P.J.I. and grant P50CA058204 to B.K.-A. J.-P.J.I. is an American Cancer Society Clinical Research Professor supported by a generous gift from the F.M. Kirby Foundation. Y.K. was supported by an Odyssey Fellowship at the M.D. Anderson Cancer Center and the Cell Science Research Foundation. We especially thank Y. Guo and X. Chen for their technical assistance.

Author information

Y.K. and J.-P.J.I. designed the research; Y.K., L.S., A.S.C., S.A., Y.B. and C.C. performed the research; T.Y., T.U., K.F., Y.S. and T.H.-M.H. designed the assays; D.L.G. analyzed microarray data; B.K.-A. collected and analyzed clinical samples; and Y.K. and J.-P.J.I. wrote the paper.

Correspondence to Jean-Pierre J Issa.

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Kondo, Y., Shen, L., Cheng, A. et al. Gene silencing in cancer by histone H3 lysine 27 trimethylation independent of promoter DNA methylation. Nat Genet 40, 741–750 (2008). https://doi.org/10.1038/ng.159

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