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Series GSE52025 Query DataSets for GSE52025
Status Public on Dec 10, 2013
Title The relationship between DNA methylation, genetic and expression inter-individual variation in untransformed human fibroblasts [methylation profiling]
Organism Homo sapiens
Experiment type Methylation profiling by genome tiling array
Summary Background DNA methylation has long been known to play an essential role in the epigenetic regulation of gene expression and other cellular functions, and has been in some cases linked to genetic variation. While its presence near the transcription start site of a gene has been associated with reduced expression, the variation in methylation levels across individuals, its environmental or genetic causes, and its association with gene expression remain poorly understood.
Results We report the joint analysis of sequence variants, gene expression and DNA methylation in primary fibroblast samples derived from a set of 62 unrelated individuals. Approximately 2% of the most variable CpG sites are mappable in cis to sequence variation, usually within 5kb. However, only 5% of those mappable CpG sites also have methylation levels that correlate in cis with a gene's expression level. Methylation and gene expression are often correlated but not always in the expected direction (negative for promoter CpGs, positive for gene body CpGs). Population-level correlation between methylation and expression is strongest in a subset of developmentally significant genes, including all four HOX clusters. The presence and sign of this correlation are best predicted using specific histone marks or DNase hypersensitivity rather than position of the CpG site with respect to the gene, showing that other epigenetic markers are necessary to interpret downstream effects of individual methylation variants.
Conclusion Our results indicate strong relationships between gene expression and DNA methylation in untransformed adult human fibroblasts, with considerable involvement of chromatin features and relatively modest involvement of sequence variation.
Overall design 62 human skin fibroblast samples obtained from Coriell and McGill Cellbank, bisulfite converted DNA was hybridized to the Illumina Infinium 450K chip.
Contributor(s) Wagner JR, Busche S, Ge B, Kwan T, Pastinen T, Blanchette M
Citation(s) 24555846
Submission date Nov 02, 2013
Last update date Mar 22, 2019
Contact name Stephan Busche
Organization name McGill University
Department Human Genetics
Street address 740 Dr. Penfield Avenue
City Montreal
State/province Quebec
ZIP/Postal code H3A 0G1
Country Canada
Platforms (1)
GPL13534 Illumina HumanMethylation450 BeadChip (HumanMethylation450_15017482)
Samples (62)
GSM1257669 GM02704
GSM1257670 GM02706
GSM1257671 GM01650
This SubSeries is part of SuperSeries:
GSE53261 The relationship between DNA methylation, genetic and expression inter-individual variation in untransformed human fibroblasts
BioProject PRJNA226264

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
GSE52025_RAW.tar 692.8 Mb (http)(custom) TAR (of IDAT)
GSE52025_signals.txt.gz 144.4 Mb (ftp)(http) TXT
Processed data included within Sample table

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