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Series GSE46217 Query DataSets for GSE46217
Status Public on Apr 22, 2013
Title Inactive or moderately active human promoters are enriched for inter-individual epialleles [Seq]
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Expression profiling by high throughput sequencing
Summary 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.
Overall design 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.
Contributor(s) Gemma C, Ramagopalan SV, Down TA, Beyan H, Hawa MI, Holland ML, Hurd PJ, Giovannoni G, Leslie RD, Ebers GC, Rakyan VK
Citation(s) 23706135
Submission date Apr 19, 2013
Last update date May 15, 2019
Contact name Thomas A Down
Organization name University of Cambridge
Department WT/CRUK Gurdon Institute
Street address Tennis Court Road
City Cambridge
ZIP/Postal code CB2 1QN
Country United Kingdom
Platforms (1)
GPL10999 Illumina Genome Analyzer IIx (Homo sapiens)
Samples (10)
GSM1126511 T11_H2AZ_ChIP-Seq
GSM1126512 T21_H2AZ_ChIP-Seq
GSM1126513 T22_H2AZ_ChIP-Seq
This SubSeries is part of SuperSeries:
GSE46220 Inactive or moderately active human promoters are enriched for inter-individual epialleles
BioProject PRJNA198092
SRA SRP021191

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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE46217_RAW.tar 14.1 Mb (http)(custom) TAR (of TXT)
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Raw data are available in SRA
Processed data provided as supplementary file

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