Abstract
BackgroundCancer cells undergo massive alterations to their DNA methylation patterns that result in aberrant gene expression and malignant phenotypes. However, the mechanisms that underlie methylome changes are not well understood nor is the genomic distribution of DNA methylation changes well characterized.ResultsHere, we performed methylated DNA immunoprecipitation combined with high-throughput sequencing (MeDIP-seq) to obtain whole-genome DNA methylation profiles for eight human breast cancer cell (BCC) lines and for normal human mammary epithelial cells (HMEC). The MeDIP-seq analysis generated non-biased DNA methylation maps by covering almost the entire genome with sufficient depth and resolution. The most prominent feature of the BCC lines compared to HMEC was a massively reduced methylation level particularly in CpG-poor regions. While hypomethylation did not appear to be associated with particular genomic features, hypermethylation preferentially occurred at CpG-rich gene-related regions independently of the distance from transcription start sites. We also investigated methylome alterations during epithelial-to-mesenchymal transition (EMT) in MCF7 cells. EMT induction was associated with specific alterations to the methylation patterns of gene-related CpG-rich regions, although overall methylation levels were not significantly altered. Moreover, approximately 40% of the epithelial cell-specific methylation patterns in gene-related regions were altered to those typical of mesenchymal cells, suggesting a cell-type specific regulation of DNA methylation.ConclusionsThis study provides the most comprehensive analysis to date of the methylome of human mammary cell lines and has produced novel insights into the mechanisms of methylome alteration during tumorigenesis and the interdependence between DNA methylome alterations and morphological changes.
Highlights
Cancer cells undergo massive alterations to their deoxyribonucleic acid (DNA) methylation patterns that result in aberrant gene expression and malignant phenotypes
To investigate the mechanisms of methylome alteration and determine the effects of such changes on the morphology of breast cancer cell (BCC) lines, we identified alterations to the methylation profile that occurred during the epithelialto-mesenchymal transition (EMT) in MCF7 cells treated with tumor growth factor beta 1 (TGFb) and tumor necrosis factor (TNFa)
The influence of genomic amplifications and deletions in the BCC lines was investigated by high-throughput sequencing of input DNA fragments from each samples, with the exception of MDAMB453 and MRKnu1 which yielded an insufficient number of reads
Summary
Cancer cells undergo massive alterations to their DNA methylation patterns that result in aberrant gene expression and malignant phenotypes. The mechanisms that underlie methylome changes are not well understood nor is the genomic distribution of DNA methylation changes well characterized. DNA methylation is an indispensable epigenetic modification of mammalian genomes. In mammals, it occurs predominantly at CpG dinucleotides which are sparsely distributed through the genome except at short genomic regions called CpG islands (CGIs) [1]. The entire genomic distribution of aberrant methylations and the molecular mechanisms underlying the methylome alterations in cancers remain unclear, mainly due to the limitations of existing techniques for analyzing DNA methylation at specific sequences [12]. The conventional strategies using methylation-sensitive restriction enzymes require high-molecular-weight DNA and are limited by the sequence context of the chosen enzyme
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