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Series GSE69894

Query DataSets for GSE69894

Status

Public on Apr 06, 2016

Title

Mapping of variable DNA methylation across multiple cell types defines a dynamic regulatory landscape of the human genome

Organism

Homo sapiens

Experiment type

Methylation profiling by high throughput sequencing
Third-party reanalysis

Summary

DNA methylation is an important epigenetic modification involved in many biological processes and diseases. Many studies have mapped DNA methylation changes associated with embryogenesis, cell differentiation and cancer at a genome-wide scale. Our understanding of genome-wide DNA methylation changes in a developmental or disease-related context has been steadily growing. However, the investigation of which CpGs are variably methylated in different normal cell or tissue types is still limited. Here we present an in-depth analysis of 54 single-CpG-resolution DNA methylomes of normal human cell types by integrating high-throughput sequencing-based methylation data. We find that the percentage of unmethylated CpGs is relatively fixed regardless of cell type. However, which CpGs are unmethylated is cell-type specific. We categorize the 26 million human autosomal CpGs based on their methylation levels across multiple cell types to identify variably methylated CpGs. Among all the autosomal CpGs, 22.6% exhibit variable DNA methylation across cell types included in our study. These variably methylated CpGs form 66 thousand variably methylated regions (VMRs), encompassing 11% of the genome. By integrating a multitude of genomic data, we found that VMRs enrich for histone modifications indicative of enhancers, suggesting their role as regulatory elements marking cell type specificity. VMRs enrich for transcription factor binding sites in a tissue-dependent manner. Importantly, they enrich for GWAS variants, suggesting VMRs could potentially be implicated in disease and complex traits. Taken together, our results highlight the link among CpG methylation variation, genetic variation and disease risk in a tissue-specific manner for many human cell types.

Overall design

Processed data includes new Samples and 75 Samples from GSE16368 and 2 Samples from GSE51565.

Contributor(s)

Gu J, Stevens M, Wang T, Xing X, Li D, Jarvis J, Payton J, Cicero T

Citation(s)

26888867

Submission date

Jun 15, 2015

Last update date

May 15, 2019

Contact name

Daofeng Li

E-mail(s)

lidaof@gmail.com

Phone

(314) 286-0866

Organization name

Washington University in St. Louis

Department

Genetics

Lab

Ting Wang Lab

Street address

4515 McKinley Avenue

City

SAINT LOUIS

State/province

ZIP/Postal code

63110

Country

USA

Platforms (2)

GPL9115	Illumina Genome Analyzer II (Homo sapiens)
GPL11154	Illumina HiSeq 2000 (Homo sapiens)

Samples (31)

More...

GSM1712059	CD14_Monocyte_1_MeDIP
GSM1712060	CD14_Monocyte_1_MRE
GSM1712061	CD14_Monocyte_2_MeDIP

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BioProject

SRA

Download family	Format
SOFT formatted family file(s)	SOFT
MINiML formatted family file(s)	MINiML
Series Matrix File(s)	TXT

Supplementary file	Size	Download	File type/resource
GSE69894_methylCRF54.txt.gz	834.9 Mb	(ftp)(http)	TXT
GSE69894_methylCRF54_header.txt.gz	307 b	(ftp)(http)	TXT
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Raw data are available in SRA
Processed data are available on Series record