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Series GSE29069 Query DataSets for GSE29069
Status Public on Sep 16, 2011
Title Global DNA Hypomethylation Coupled to Repressive Chromatin Domain Formation and Gene Silencing in Breast Cancer
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Expression profiling by high throughput sequencing
Methylation profiling by high throughput sequencing
Summary While genetic mutation is a hallmark of cancer, many cancers also acquire epigenetic alterations during tumorigenesis including aberrant DNA hypermethylation of tumor suppressors as well as changes in chromatin modifications as caused by genetic mutations of the chromatin-modifying machinery. However, the extent of epigenetic alterations in cancer cells has not been fully characterized. Here, we describe the first complete methylome maps at single nucleotide resolution of a low-passage breast cancer cell line and primary human mammary epithelial cells. We find widespread DNA hypomethylation in the cancer cell, primarily at partially methylated domains (PMDs) in normal breast cells. Unexpectedly, genes within these regions are largely silenced in cancer cells. The loss of DNA methylation in these regions is accompanied by formation of repressive chromatin, with a significant fraction displaying allelic DNA methylation where one allele is DNA methylated while the other allele is occupied by histone modifications H3K9me3 or H3K27me3. Our results show a mutually exclusive and complementary relationship between DNA methylation and H3K9me3 or H3K27me3. These results suggest that global DNA hypomethylation in breast cancer is tightly linked to the formation of repressive chromatin domains and gene silencing, thus identifying a potential epigenetic pathway for gene regulation in cancer cells and suggesting a possible new approach toward the development of cancer therapeutics.

This SuperSeries is composed of the SubSeries listed below.
Overall design Examination of histone modifications, DNA methylation, and gene expression in HCC1954 breast cancer cells and HMEC primary human mammary epithelial cells
Contributor(s) Hon GC, Ren B
Citation(s) 22156296
Submission date May 04, 2011
Last update date May 15, 2019
Contact name Gary Chung Hon
Organization name UT Southwestern
Department OB/GYN
Street address 5323 Harry Hines Blvd.
City Dallas
State/province TX
ZIP/Postal code 75390
Country USA
Platforms (2)
GPL10999 Illumina Genome Analyzer IIx (Homo sapiens)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
Samples (14)
GSM721133 HCC1954: chromatin IP against H3K4me1
GSM721134 HCC1954: chromatin IP against H3K4me3
GSM721135 HCC1954: chromatin IP against H3K9me3
This SuperSeries is composed of the following SubSeries:
GSE29118 Genome-wide location analysis in breast cancer cells (HCC1954)
GSE29119 Gene expression analysis of breast cancer (HCC1954) and normal breast cells (HMEC)
GSE29120 Bisulfite sequencing of ChIP DNA on breast cancer cells (HCC1954)
BioProject PRJNA140397

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE29069_RAW.tar 121.4 Gb (http)(custom) TAR (of BAM)
SRA Run SelectorHelp
Raw data provided as supplementary file
Processed data provided as supplementary file

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