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Series GSE48472 Query DataSets for GSE48472
Status Public on Aug 06, 2013
Title Identification and systematic annotation of tissue-specific differentially methylated regions using the Illumina 450k array
Organism Homo sapiens
Experiment type Methylation profiling by genome tiling array
Summary Background
DNA methylation has been recognized as a key mechanism in cell differentiation. Various studies have compared tissues to characterize epigenetically regulated genomic regions, but due to differences in study design and focus there still is no consensus as to the annotation of genomic regions predominantly involved in tissue-specific methylation. We used a new algorithm to identify and annotate tissue-specific Differentially Methylated Regions (tDMRs) in Illumina 450k chip data on four peripheral (blood, saliva, buccal swab and hair follicles) and six internal tissues (liver, muscle, pancreas, subcutaneous fat, omentum, spleen with matched blood samples).

The majority of tDMRs, in both relative and absolute terms, occurred in CpG-poor regions. Further analysis revealed that these regions were associated with alternative transcription events (alternative first exons, mutually exclusive exons and cassette exons). Only a minority of tDMRs mapped to gene-body CpG islands (13%) or CpG islands shores (25%) suggesting a less prominent role for these regions than indicated previously. Implementation of ENCODE annotations showed enrichment of tDMRs in DNase hypersensitive sites and transcription factor binding sites. Despite the predominance of tissue differences, inter-individual differences in DNA methylation in internal tissues were correlated with that in blood for a subset of CpG sites in a locus and tissue-specific manner.

We conclude that tDMRs preferentially occur in CpG-poor regions and are associated with alternative transcription. Furthermore, our data suggest the utility of creating an atlas cataloguing variably methylated regions in internal tissues that are marked by DNA methylation measured in easy accessible peripheral tissues.
Overall design Comparison of four peripheral (blood, saliva, buccal swab and hair follicles in n=5) and six internal tissues (liver, muscle, pancreas, subcutaneous fat, omentum, spleen with matched blood samples in n=6).
Contributor(s) Slieker RC, Bos SD, Goeman JJ, Bovée JV, Talens RP, van der Breggen R, Suchiman HE, Lameijer EM, Putter H, van den Akker EB, Zhang Y, Jukema JW, Slagboom PE, Meulenbelt I, Heijmans BT
Citation(s) 23919675
Submission date Jul 02, 2013
Last update date Mar 22, 2019
Contact name Roderick Slieker
Organization name Leiden University Medical Center
Department Molecular Cell Biology
Street address PO Box 9600
City Leiden
ZIP/Postal code 2333RC
Country Netherlands
Platforms (1)
GPL13534 Illumina HumanMethylation450 BeadChip (HumanMethylation450_15017482)
Samples (56)
GSM1179497 Blood_IT9
GSM1179498 Blood_IT13
GSM1179499 Blood_IT10
BioProject PRJNA210257

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
GSE48472_RAW.tar 642.8 Mb (http)(custom) TAR (of IDAT)
GSE48472_non-normalized.txt.gz 448.4 Mb (ftp)(http) TXT
Processed data included within Sample table

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