E-GEOD-46217 - Inactive or moderately active human promoters are enriched for inter-individual epialleles [Seq]

Status
Released on 22 April 2013, last updated on 2 May 2014
Organism
Homo sapiens
Samples (10)
Protocols (3)
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. H2A.z ChIP-seq, RNA-seq, and DNA methylation data (submitted separately) were collected for five normal individuals. T21/T22 and T31/T32 are monozygotic twins.
Experiment types
ChIP-seq, RNA-seq of coding RNA 
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
MINSEQE
Exp. designProtocolsVariablesProcessedSeq. reads
Files
Investigation descriptionE-GEOD-46217.idf.txt
Sample and data relationshipE-GEOD-46217.sdrf.txt
Processed data (1)E-GEOD-46217.processed.1.zip
Links