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An improved method for genome wide DNA methylation profiling correlated to transcription and genomic instability in two breast cancer cell lines.

BMC genomics (2009-05-15)
Jian Li, Fei Gao, Ning Li, Shengting Li, Guangliang Yin, Geng Tian, Shangang Jia, Kai Wang, Xiuqing Zhang, Huanming Yang, Anders Lade Nielsen, Lars Bolund
ABSTRACT

DNA 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. We 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. The MMSDK method will be a valuable tool to increase the current knowledge of genome wide DNA methylation profiles.

MATERIALS
Product Number
Brand
Product Description

Sigma-Aldrich
TRI Reagent®, For processing tissues, cells cultured in monolayer or cell pellets
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TRI Reagent®, for DNA, RNA and protein isolation
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GenElute Plasmid Miniprep Kit, sufficient for 70 purifications
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GenElute Plasmid Miniprep Kit, sufficient for 350 purifications
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TRI Reagent®, LS, For processing fluid samples such as cell suspensions, CSF, and amniotic fluid.
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TRI Reagent®, BD, For processing whole blood, plasma, or serum.
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Resuspension Solution, Add RNase A before use. After addition of RNAse, store at 2-8ºC.

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