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| Status |
Public on Apr 21, 2011 |
| Title |
Genome-wide Regulation of 5hmC, 5mC and Gene Expression by Tet1 Hydroxylase in Mouse Embryonic Stem Cells (bisulfite sequencing data) |
| Organism |
Mus musculus |
| Experiment type |
Methylation profiling by high throughput sequencing
|
| Summary |
DNA methylation of C5-cytosine (5mC) in the mammalian genome is a key epigenetic event that is critical for various cellular processes. However, how the genome-wide 5mC pattern is dynamically regulated remains a fundamental question in epigenetic biology. The TET family of 5mC hydroxylases, which convert 5mC to 5-hydroxymethylcytosine (5hmC), have provided a new potential mechanism for the dynamic regulation of DNA methylation. The extent to which individual Tet family members contribute to the genome-wide 5mC and 5hmC patterns and associated gene network remains largely unknown. Here we report genome-wide mapping of Tet1 and 5hmC in mESCs and reveal a mechanism of action by which Tet1 controls 5hmC and 5mC levels in mESCs. In combination with microarray and mRNA-seq expression profiling, we identify a comprehensive yet intricate gene network influenced by Tet1. We propose a model whereby Tet1 controls DNA methylation both by binding to CpG-rich regions to prevent unwanted DNA methyltransferase activity, and by converting the existing 5mC to 5hmC through its enzymatic activity. This Tet1-mediated antagonism of CpG methylation imparts differential maintenance of DNA methylation status at Tet1 target loci, thereby providing a new regulatory mechanism for establishing the epigenetic landscape of mESCs, which ultimately contributes to mESC differentiation and the onset of embryonic development.
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| Overall design |
To determine the genome-wide DNA methylation changes caused by Tet1 depletion in mouse ES cells. Tet1 protein was depleted by specific siRNA treatment. The DNA methylation levels in control and Tet1 siRNA-transfected ES cells were determined by targeted bisulfite sequencing.
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| Contributor(s) |
Xu Y, Shi Y |
| Citation(s) |
21514197 |
| Submission date |
Apr 11, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Feizhen Wu |
| E-mail(s) |
wufz@fudan.edu.cn
|
| Phone |
86-21-54237821
|
| Organization name |
Fudan Univ, Shanghai, China
|
| Department |
Institutes of Biomedical Sciences
|
| Lab |
Epigenetics lab
|
| Street address |
Dongan Road 131, Rm 511 Mingdao Building
|
| City |
Shanghai |
| State/province |
Shanghai |
| ZIP/Postal code |
200032 |
| Country |
China |
| |
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| Platforms (1) |
| GPL11002 |
Illumina Genome Analyzer IIx (Mus musculus) |
|
| Samples (4)
|
| GSM706683 |
Control_CH_Methylation_bisulfite_sequencing |
| GSM706684 |
TET1_CH_Methylation_bisulfite_sequencing |
| GSM706685 |
Control_CpG_Methylation_bisulfite_sequencing |
| GSM706686 |
TET1_CpG_Methylation_bisulfite_sequencing |
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| This SubSeries is part of SuperSeries: |
| GSE28500 |
Genome-wide Regulation of 5hmC, 5mC and Gene Expression by Tet1 Hydroxylase in Mouse Embryonic Stem Cells |
|
| Relations |
| SRA |
SRP006419 |
| BioProject |
PRJNA143029 |
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