Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2008 Jul 15;68(14):5753-9.
doi: 10.1158/0008-5472.CAN-08-0700.

Defining a chromatin pattern that characterizes DNA-hypermethylated genes in colon cancer cells

Kelly M McGarvey  1 , Leander Van Neste, Leslie Cope, Joyce E Ohm, James G Herman, Wim Van Criekinge, Kornel E Schuebel, Stephen B Baylin
Affiliations

Defining a chromatin pattern that characterizes DNA-hypermethylated genes in colon cancer cells

Kelly M McGarvey et al. Cancer Res. .

Abstract

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 chromatin immunoprecipitation-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 demethylated and reexpressed, they adopt a bivalent chromatin pattern, which is associated with the poised gene expression state of a large group of embryonic stem 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 reexpression of DNA-hypermethylated genes for the treatment of cancer.

PubMed Disclaimer

Figures

Figure 1
Figure 1
Chromatin signature of active and DNA hypermethylated genes in colorectal cancer cells. (a) Box plot showing ranges of expression for key gene groups in HCT116 and DKO cells. Y-axis shows log of normalized single channel signal from the Agilent 44K expression microarray. Average expression range is shown for: all genes in HCT116 cells, 4500 actively expressed genes with CpG islands in HCT 116 cells, 42 verified DNA hypermethylated genes in HCT 116 cells, all top tier and next tier candidate DNA hypermethylated genes (fig. 2a), the 42 verified DNA methylated genes in DKO cells, and the top and next tier genes in DKO cells. Orange lines represent limits separating active, intermediate and silent expression zones. TT is top tier and NT is next tier. (b) Plot showing normalized enrichment (bound/input) of histone marks (y-axis), as a function of distance (x-axis with 0 = annotated transcription start site) at the active CDKN2B gene promoter in HCT116 cells. (c) Composite graph showing average normalized enrichment of histone marks at over 4,500 active genes with CpG island containing promoters in HCT116 cells. (d) Plot showing normalized enrichment of histone marks at the hypermethylated and silent GATA4 gene promoter in HCT116 cells. (e) Composite graph showing average normalized enrichment of histone marks at 42 verified DNA hypermethylated and silent genes in HCT116 cells. (f) Box plot showing range of enrichment for H3K27me3 at active, DNA hypermethylated and silent, and genes with highest H3K27 enrichment.
Figure 2
Figure 2
Chromatin and expression patterns can improve the identification of DNA hypermethylated genes. (a) Schematic showing expression behavior after treatment with either DAC or TSA. The increase for response of genes to TSA treatment alone is mapped on the X-axis, and the increase for DAC induced expression changes (similar to that for fold increases in DKO cells) is on the Y-axis. The lack of TSA response is mapped from -0.5 to +0.5 on the X-axis and key zones 1-4 used in the text to characterize genes are shown. Zones 1 and 2 are the key zones which we have previously defined to contain the best candidate genes with promoter CpG island DNA methylation (6). (b) Composite graph showing average enrichment of H3K4me2 at top and next tier genes separated by the levels of basal expression shown in Fig. 1a. (c) Composite graph showing average histone enrichment of 23 genes falsely identified as DNA hypermethylated and silent in HCT116 cells in our recently published study (6). (d) Composite graph showing average histone enrichment at 610 of the top and next tier gene candidates with the lowest basal expression (silent zone -Fig. 1a) in HCT116 cells.
Figure 3
Figure 3
Hypermethylated genes adopt a bivalent chromatin pattern upon re-expression after DNA demethylation. (a) Plot showing normalized enrichment of H3K4me2 at the SFRP1 gene promoter when hypermethylated and silent in HCT116 cells and when re-expressed in DKO cells. (b) Plot showing normalized enrichment of H3K27me3 at the SFRP1 gene promoter when hypermethylated and silent in HCT116 cells and when re-expressed in DKO cells. (c) Composite graph showing average histone methylation enrichment at 42 genes verified as DNA hypermethylated and silent in HCT116 cells and re-expressed in DKO cells. (d) Composite graph showing average histone methylation enrichment at the 610 low expressing, top and next tier candidate genes, for DNA methylation associated silencing in HCT116 cells and re-expression in DKO cells.
Figure 4
Figure 4
H3K4me2 enrichment distinguishes TSA responsive genes from those which respond only to DAC. (a) Box plot showing expression range for genes responsive to only DAC (zones 1 and 2 in Fig. 2a), only TSA (zone 3 in Fig. 2a), or to both DAC alone and TSA alone (zone 4 in Fig. 2a). Orange lines represent limits separating active, intermediate and silent expression zones. (b) Plot showing normalized enrichment of histone marks at 84 genes with low basal expression in HCT116 cells that respond only to TSA alone (zone 3 in Fig. 2a). (c) Plot showing normalized enrichment of histone marks at 141 genes with low basal expression in HCT116 cells that respond to either DAC alone or TSA alone (zone 4 in Fig. 2a).
See this image and copyright information in PMC

Similar articles

See all similar articles

Cited by

See all "Cited by" articles

References

    1. Jones PA, Baylin SB. The Epigenomics of Cancer. Cell. 2007;128:683–92. - PMC - PubMed
    1. Egger G, Liang G, Aparicio A, Jones PA. Epigenetics in human disease and prospects for epigenetic therapy. Nature. 2004;429:457–63. - PubMed
    1. Rhee I, Bachman KE, Park BH, et al. DNMT1 and DNMT3b cooperate to silence genes in human cancer cells. Nature. 2002;416:552–6. - PubMed
    1. McGarvey KM, Fahrner JA, Greene E, Martens J, Jenuwein T, Baylin SB. Silenced tumor suppressor genes reactivated by DNA demethylation do not return to a fully euchromatic chromatin state. Cancer Res. 2006;66:3541–9. - PubMed
    1. Bernstein BE, Mikkelsen TS, Xie X, et al. A bivalent chromatin structure marks key developmental genes in embryonic stem cells. Cell. 2006;125:315–26. - PubMed

Publication types