BACKGROUND: Gene expression is epigenetically regulated by a combination of histone modifications and methylation of CpG dinucleotides in promoters. In normal cells, CpG-rich promoters are typically unmethylated, marked with histone modifications such as H3K4me3, and are highly active. During neoplastic transformation, CpG dinucleotides of CG-rich promoters become aberrantly methylated, corresponding with the removal of active histone modifications and transcriptional silencing. Outside of promoter regions, distal enhancers play a major role in the cell type-specific regulation of gene expression. Enhancers, which function by bringing activating complexes to promoters through chromosomal looping, are also modulated by a combination of DNA methylation and histone modifications.
RESULTS: Here we use HCT116 colorectal cancer cells with and without mutations in DNA methyltransferases, the latter of which results in a 95% reduction in global DNA methylation levels. These cells are used to study the relationship between DNA methylation, histone modifications, and gene expression. We find that the loss of DNA methylation is not sufficient to reactivate most of the silenced promoters. In contrast, the removal of DNA methylation results in the activation of a large number of enhancer regions as determined by the acquisition of active histone marks.
CONCLUSIONS: Although the transcriptome is largely unaffected by the loss of DNA methylation, we identify two distinct mechanisms resulting in the upregulation of distinct sets of genes. One is a direct result of DNA methylation loss at a set of promoter regions and the other is due to the presence of new intragenic enhancers.
Bibliographical noteFunding Information:
The H3K4me3 HCT116 ChIP-seq was produced by the laboratory of John Stamatoyannopoulos at the University of Washington and the H3K27ac and H3K4me1 HCT116 ChIP-seq data was produced by the Farnham laboratory, each as part of the ENCODE Consortium  and is available at (http:// genome.ucsc.edu); all data used in this study is past the 9 month moratorium. One replicate of H3K4me3 and one replicate of H3K27ac ChIP-seq in DKO, in addition to one replicate of RNA-seq in each cell type was produced by Fides Lay in the laboratory of Peter Jones at the University of Southern California. We thank them for this data and for their commentary on the project. This work was supported in part by 1U01ES017154, U54HG006996, and P30CA014089 from the National Cancer Institute; AB was supported in part by a pre-doctoral training fellowship from the National Human Genome Research Institute of the National Institutes of Health under grant number F3100HG6114. BB, YL, and LY were supported in part by National Institutes of Health under grant number U01ES017054. We thank Selene Tyndale and Helen Truong for services rendered at the USC Molecular Genomics Sequencing core. We thank Meng Li and Yibu Chen at the USC Norris Medical Library Bioinformatics Services Program for their assistance in running Partek Flow. We thank Matt Grimmer and the members of Farnham laboratory for helpful discussions.