Abstract
BackgroundDNA methylation is a widely studied epigenetic mechanism known to correlate with gene repression and genomic stability. Development of sensitive methods for global detection of DNA methylation events is of particular importance.ResultsWe here describe a technique, called modified methylation-specific digital karyotyping (MMSDK) based on methylation-specific digital karyotyping (MSDK) with a novel sequencing approach. Briefly, after a tandem digestion of genomic DNA with a methylation-sensitive mapping enzyme and a fragmenting enzyme, short sequence tags are obtained. These tags are amplified, followed by direct, massively parallel sequencing (Solexa 1G Genome Analyzer). This method allows high-throughput and low-cost genome-wide DNA methylation mapping. We applied this method to investigate global DNA methylation profiles for widely used breast cancer cell lines, MCF-7 and MDA-MB-231, which are representatives for luminal-like and mesenchymal-like cancer types, respectively. By comparison, a highly similar overall DNA methylation pattern was revealed for the two cell lines. However a cohort of individual genomic loci with significantly different DNA methylation status between two cell lines was identified. Furthermore, we revealed a genome-wide significant correlation between gene expression and the methylation status of gene promoters with CpG islands (CGIs) in the two cancer cell lines, and a correlation of gene expression and the methylation status of promoters without CGIs in MCF-7 cells.ConclusionThe MMSDK method will be a valuable tool to increase the current knowledge of genome wide DNA methylation profiles.
Highlights
DNA methylation is a widely studied epigenetic mechanism known to correlate with gene repression and genomic stability
Mal-like subtypes, respectively, and used these cell lines for comparative analysis by modified methylation-specific digital karyotyping (MMSDK), array comparative genomic hybridization and gene expression microarray analysis to explore the correlation between DNA methylation, genomic stability and gene expression
MMSDK To elucidate genome wide DNA methylation patterns we developed a modified version of methylation-specific digital karyotyping (MSDK), MMSDK
Summary
DNA methylation is a widely studied epigenetic mechanism known to correlate with gene repression and genomic stability. One key component of the cancer epigenome is an altered DNA methylation pattern by global hypomethylation and promoter localized hypermethylation [1]. These methylation changes can result in an alteration in structure and function of DNA, such as unwanted activation of repeat elements, abnormal transcriptional regulation of genes involved in cancer initiation and progression, and predisposition to genomic instability through disruption of chromosome replication control [2,3]. A comprehensive picture of DNA methylation patterns, DNA copy number alterations and gene expression levels genome wide for the two cell lines remains to be established
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