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| Status |
Public on Nov 15, 2016 |
| Title |
DNA methylation is required for chromatin binding by Mbd2 and Mbd3 in ES cells (ChIP-Seq, meDIP-seq and hmDIP-seq) |
| Organism |
Mus musculus |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
Methylation profiling by high throughput sequencing
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| Summary |
Cytosine methylation on DNA is an important epigenetic and regulatory mark. Chromatin remodeling complexes containing methyl-CpG binding domain (MBD) proteins modulate chromatin structure and transcription at methylated loci. Two MBD proteins, Mbd2 and Mbd3, are mutually exclusive members of the NuRD chromatin remodeling complex, and have been shown to bind methylated or hydroxymethylated DNA, respectively. However, a recent study called both results into question, showing that chromatin binding by these proteins is partially (Mbd2) or completely (Mbd3) independent of DNA methylation/hydroxymethylation. Here we re-analyze these data and observe discrepancies with both conclusions. Furthermore, we describe multiple new datasets that demonstrate the dependence of endogenous Mbd2 and Mbd3 on DNA methylation. Interestingly, we find that Mbd2 and Mbd3 are also dependent on one another for binding, likely due to the fact that both are required for normal levels of DNA methylation/hydroxymethylation. These findings describe a regulatory loop controlling the DNA methylation machinery and its readers.
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| Overall design |
Examine Mbd2 and Mbd3 occupancy (ChIP-seq) and DNA methylation/hydroxymethylation (meDIP-seq/hmDIP-seq) in ES cells
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| |
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| Contributor(s) |
Hainer SJ, McCannell KN, Yu J, Ee L, Zhu LJ, Rando OJ, Fazzio TG |
| Citation(s) |
27849519 |
| NIH grant(s) |
| Grant ID |
Grant title |
Affiliation |
Name |
| R01 HD072122 |
Epigenetic control of the stem cell gene regulatory network |
UNIV OF MASSACHUSETTS MED SCHOOL |
THOMAS G. FAZZIO |
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| |
| Submission date |
Mar 31, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Sarah J Hainer |
| E-mail(s) |
sarah.hainer@pitt.edu
|
| Organization name |
University of Pittsburgh
|
| Department |
Department of Biological Sciecnes
|
| Lab |
Hainer Lab
|
| Street address |
4249 Fifth Ave
|
| City |
Pittsburgh |
| State/province |
PA |
| ZIP/Postal code |
15260 |
| Country |
USA |
| |
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| Platforms (1) |
| GPL13112 |
Illumina HiSeq 2000 (Mus musculus) |
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| Samples (58)
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| This SubSeries is part of SuperSeries: |
| GSE79771 |
DNA methylation is required for chromatin binding by Mbd2 and Mbd3 in ES cells |
|
| Relations |
| BioProject |
PRJNA316979 |
| SRA |
SRP072681 |
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