E-GEOD-46168 - Inactive or moderately active human promoters are enriched for inter-individual epialleles [Methylation BeadChip]

Status
Released on 22 April 2013, last updated on 29 April 2013
Organism
Homo sapiens
Samples (14)
Array (1)
Protocols (5)
Description
We first demonstrate that non-genetically determined inter-individual differentially methylated regions (iiDMRs) can be temporally stable for at least two years. Then, we show that iiDMRS are associated with concomitant changes in chromatin state as measured by inter-individual differences in the levels of the histone variant H2A.Z. However, the correlation of promoter iiDMRs with gene expression is negligible and this correlation is not improved even by integrating H2A.Z information. We find that most promoter epialleles, whether genetically or non-genetically determined, are associated with low levels of transcriptional activity, depleted for house keeping genes, and either depleted for H3K4me3/enriched for H3K27me3, or lacking both these marks in human embryonic stem cells. These findings validate in an independent cohort. Interestingly, the key features of iiDMRs are reminiscent of those previously observed for promoters that undergo hyper-methylation in various cancers, in vitro cell culture, and human chronological ageing. DNA Methylation, H2A.z ChIP-seq, RNA-seq (submitted) separately were collected for five normal individuals (samples with "T" prefixes). T21/T22 and T31/T32 are monozygotic twins. Further DNA methylation data was collected from and additional two pairs of MZ twins with technical replication (samples with "C" prefixes - the three digits are pair number, individual number, and replicate number). Bisulphite converted DNA was hybridised to the Illumina Infinium 450k Human Methylation Beadchip
Experiment type
methylation profiling by array 
Contacts
Thomas A Down <thomas.down@gurdon.cam.ac.uk>, C Gemma, G C Ebers, G Giovannoni, H Beyan, M I Hawa, M L Holland, P J Hurd, R D Leslie, S V Ramagopalan, T A Down, V K Rakyan
MIAME
PlatformsProtocolsFactorsProcessedRaw
Files
Investigation descriptionE-GEOD-46168.idf.txt
Sample and data relationshipE-GEOD-46168.sdrf.txt
Processed data (1)E-GEOD-46168.processed.1.zip
Array designA-GEOD-13534.adf.txt
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