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| Status |
Public on Jan 06, 2012 |
| Title |
Acute depletion of Tet1-dependent 5-hydroxymethylcytosine levels impairs LIF/Stat3 signaling and results in loss of embryonic stem cell identity [MRE-seq] |
| Organism |
Mus musculus |
| Experiment type |
Methylation profiling by high throughput sequencing
|
| Summary |
The TET family of FE(II) and 2-oxoglutarate-dependent enzymes (Tet1/2/3) promote DNA demethylation by converting 5-methylcytosine to 5-hydroxymethylcytosine (5hmC), which they further oxidize into 5-formylcytosine and 5-carboxylcytosine. Tet1 is robustly expressed in mouse embryonic stem cells (mESCs) and has been implicated in mESC maintenance. Here we demonstrate that, unlike genetic deletion, RNAi-mediated depletion of Tet1 in mESCs led to a significant reduction in 5hmC and loss of mESC identity. The differentiation phenotype due to Tet1 depletion positively correlated with the extent of 5hmC loss. Meta-analyses of genomic datasets suggested interaction between Tet1 and leukemia inhibitory factor (LIF) signaling. LIF signaling is known to promote self-renewal and pluripo-tency in mESCs partly by opposing MAPK/ERK mediated differentiation. Withdrawal of LIF leads to differentiation of mESCs. We discovered that Tet1 depletion impaired LIF-dependent Stat3-mediated gene activation by affecting Stat3's ability to bind to its target sites on chromatin. Nanog overexpression or inhibition of MAPK/ERK signaling, both known to maintain mESCs in the absence of LIF, rescued Tet1 depletion, further supporting the dependence of LIF/Stat3 signaling on Tet1. These data support the conclusion that analysis of mESCs in the hours/days immediately following efficient Tet1 depletion reveals Tet1’s normal physiological role in maintaining the pluripotent state that may be subject to homeostatic compensation in genetic models.
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| Overall design |
Genome-wide mapping of 5hmC and microarray gene expression profiling in E14Tg2a mESCs after transfection with indicated siRNAs: Tet1 siRNA #1 (Invitrogen, MSS284895), Tet1 siRNA #2 (Invitrogen, MSS284897), and Control siRNA duplex targeting firefly luciferase.
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| Contributor(s) |
Jothi R, Hu G, Freudenberg J |
| Citation(s) |
22210859 |
| Submission date |
Jan 05, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Raja Jothi |
| E-mail(s) |
jothi@mail.nih.gov
|
| Organization name |
National Institutes of Health
|
| Department |
National Institute of Environmental Health Sciences
|
| Lab |
Systems Biology
|
| Street address |
111 TW Alexander Drive; A314
|
| City |
RTP |
| State/province |
NC |
| ZIP/Postal code |
27709 |
| Country |
USA |
| |
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| Platforms (1) |
| GPL9250 |
Illumina Genome Analyzer II (Mus musculus) |
|
| Samples (4)
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| GSM857135 |
Control ES cells 96hr, untreated DNA-Seq |
| GSM857136 |
Control ES cells 96hr, 5hmC glucosyltransferase treated DNA-Seq |
| GSM857137 |
Tet1-KD ES cells 96hr, untreated DNA-Seq |
| GSM857138 |
Tet1-KD ES cells 96hr, 5hmC glucosyltransferase treated DNA-Seq |
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| This SubSeries is part of SuperSeries: |
| GSE34267 |
Acute depletion of Tet1-dependent 5-hydroxymethylcytosine levels impairs LIF/Stat3 signaling and results in loss of embryonic stem cell identity |
|
| Relations |
| SRA |
SRP010149 |
| BioProject |
PRJNA156267 |
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