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Series GSE39738 Query DataSets for GSE39738
Status Public on Dec 24, 2013
Title Transcription factor occupancy is linked to DNA methylation turnover at active regulatory regions [MeDIP-Seq]
Organism Mus musculus
Experiment type Methylation profiling by high throughput sequencing
Summary Genome wide analysis revealed that distal regulatory elements form Low Methylated Regions (LMRs). Even though transcription factor binding is required for LMR formation, we show for the test case CTCF that actual occupancy does not distinguish DNA methylation states. However, in line with a dynamic model of binding and DNA methylation turnover, we find that the product of active demethylation, 5-hydroxymethylcytosine (5hmC), is enriched at LMRs. 5hmC is present at active regulatory regions in stem and somatic cells and as a result a substantial fraction of changes in 5hmC occurs at LMRs. This suggests that transcription factor binding mediates active turnover of DNA methylation as an integral part of reprogramming of regulatory regions.
Overall design hMeDIP sequencing in mouse embryonic stem cells (ES) and derived neuronal progenitors (NP).
Contributor(s) Ivanek R, Feldmann A, Murr R, Gaidatzis D, Burger L, Schübeler D
Citation(s) 24367273
Submission date Jul 30, 2012
Last update date May 15, 2019
Contact name Dirk Schuebeler
Organization name Friedrich Miescher Institute for Biomedical Research
Street address Maulbeerstrasse 66
City Basel
ZIP/Postal code 4058
Country Switzerland
Platforms (2)
GPL11002 Illumina Genome Analyzer IIx (Mus musculus)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
Samples (7)
GSM978374 ES_hMeDIPseq_rep1
GSM978375 ES_hMeDIPseq_rep2
GSM978376 NP_hMeDIPseq_rep1
This SubSeries is part of SuperSeries:
GSE39739 Transcription factor occupancy is linked to DNA methylation turnover at active regulatory regions
BioProject PRJNA171569
SRA SRP014627

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Supplementary file Size Download File type/resource
GSE39738_RAW.tar 454.9 Mb (http)(custom) TAR (of WIG)
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Raw data are available in SRA
Processed data provided as supplementary file

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