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Genome-wide methylation and expression analysis of two breast cancer cell lines [Methyl-MAPS]

ABSTRACT: To improve our understanding of the relationships between methylation and expression we profiled mRNA expression and single-base resolution methylation levels for two breast cancer cell lines, MCF7 and T47D. Expression was profiled using RNA-seq. Methylation was assayed using Methyl-MAPS, which uses methylation-sensitive and -dependent restriction enzyme digests followed by high-throughput sequencing to identify methylation levels at individual CpGs (Edwards et al. 2010, Genome Research). DNA Methylation was assayed for two breast cancer cell lines using Methyl-MAPS.

ORGANISM(S): Homo sapiens

SUBMITTER: Nathan VanderKraats

PROVIDER: E-GEOD-45336 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Discovering high-resolution patterns of differential DNA methylation that correlate with gene expression changes.

Vanderkraats Nathan D ND Hiken Jeffrey F JF Decker Keith F KF Edwards John R JR

Nucleic acids research 20130607 14

Methylation of the CpG-rich region (CpG island) overlapping a gene's promoter is a generally accepted mechanism for silencing expression. While recent technological advances have enabled measurement of DNA methylation and expression changes genome-wide, only modest correlations between differential methylation at gene promoters and expression have been found. We hypothesize that stronger associations are not observed because existing analysis methods oversimplify their representation of the data ...[more]

PMID: 23748561

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