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| Status |
Public on Apr 22, 2013 |
| Title |
Inactive or moderately active human promoters are enriched for inter-individual epialleles [Methylation BeadChip] |
| Organism |
Homo sapiens |
| Experiment type |
Methylation profiling by array
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| 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.
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| Overall design |
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
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| 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 18, 2013 |
| Last update date |
Mar 22, 2019 |
| Contact name |
Thomas A Down |
| E-mail(s) |
thomas.down@gurdon.cam.ac.uk
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| Organization name |
University of Cambridge
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| Department |
WT/CRUK Gurdon Institute
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| Street address |
Tennis Court Road
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| City |
Cambridge |
| ZIP/Postal code |
CB2 1QN |
| Country |
United Kingdom |
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| Platforms (1) |
| GPL13534 |
Illumina HumanMethylation450 BeadChip (HumanMethylation450_15017482) |
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| Samples (14)
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| GSM1125308 |
genomic DNA from CD14 B-cells, 1st pair 1st individual_T11 (BeadChip) |
| GSM1125309 |
genomic DNA from CD14 B-cells, 2nd pair, 1st individual_T21 (BeadChip) |
| GSM1125310 |
genomic DNA from CD14 B-cells, 2nd pair, 2nd individual_T22 (BeadChip) |
| GSM1125311 |
genomic DNA from CD14 B-cells, 3rd pair, 1st individual_T31 (BeadChip) |
| GSM1125312 |
genomic DNA from CD14 B-cells, 3rd pair, 2nd individual_T32 (BeadChip) |
| GSM1125313 |
genomic DNA from CD14 B-cells_C111 (BeadChip) |
| GSM1125314 |
genomic DNA from CD14 B-cells_C112 (BeadChip) |
| GSM1125315 |
genomic DNA from CD14 B-cells_C121 (BeadChip) |
| GSM1125316 |
genomic DNA from CD14 B-cells_C122 (BeadChip) |
| GSM1125317 |
genomic DNA from CD14 B-cells_C211 (BeadChip) |
| GSM1125318 |
genomic DNA from CD14 B-cells_C212 (BeadChip) |
| GSM1125319 |
genomic DNA from CD14 B-cells_C213 (BeadChip) |
| GSM1125320 |
genomic DNA from CD14 B-cells_C221 (BeadChip) |
| GSM1125321 |
genomic DNA from CD14 B-cells_C222 (BeadChip) |
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| This SubSeries is part of SuperSeries: |
| GSE46220 |
Inactive or moderately active human promoters are enriched for inter-individual epialleles |
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| Relations |
| BioProject |
PRJNA198093 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE46168_RAW.tar |
183.1 Mb |
(http)(custom) |
TAR |
| GSE46168_TE_intensities.txt.gz |
30.9 Mb |
(ftp)(http) |
TXT |
| Processed data included within Sample table |
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