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


RESULTS
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.


CONCLUSIONS
The MMSDK method will be a valuable tool to increase the current knowledge of genome wide DNA methylation profiles.
Institute of Human Genetics, University of Aarhus, The Bartholin building, Aarhus C, Denmark. jianl@humgen.au.dk
Jian
J
Li
Fei
F
Gao
Ning
N
Li
Shengting
S
Li
Guangliang
G
Yin
Geng
G
Tian
Shangang
S
Jia
Kai
K
Wang
Xiuqing
X
Zhang
Huanming
H
Yang
Anders Lade
AL
Nielsen
Lars
L
Bolund
D045744:Cell Line, Tumor; D055028:Comparative Genomic Hybridization; D016172:DNA Fingerprinting / Q000379:methods*; D019175:DNA Methylation; D020869:Gene Expression Profiling; D042822:Genomic Instability; D023281:Genomics / Q000379:methods*; D006801:Humans; D007621:Karyotyping / Q000379:methods