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| Status |
Public on Dec 24, 2013 |
| Title |
Transcription factor occupancy is linked to DNA methylation turnover at active regulatory regions [Bisulfite-Seq] |
| Organism |
Mus musculus |
| Experiment type |
Methylation profiling by high throughput sequencing
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| 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.
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| Overall design |
CTCF ChIP bisulfite sequencing in mouse embryonic stem cells and whole genome shotgun bisulfite sequencing of RESTko mouse embryonic stem (ES) cells
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| 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
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| Street address |
Maulbeerstrasse 66
|
| City |
Basel |
| ZIP/Postal code |
4058 |
| Country |
Switzerland |
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| Platforms (2) |
| GPL11002 |
Illumina Genome Analyzer IIx (Mus musculus) |
| GPL13112 |
Illumina HiSeq 2000 (Mus musculus) |
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| Samples (3) |
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| This SubSeries is part of SuperSeries: |
| GSE39739 |
Transcription factor occupancy is linked to DNA methylation turnover at active regulatory regions |
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| Relations |
| BioProject |
PRJNA171568 |
| SRA |
SRP014623 |
