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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Apr 06, 2016 |
| Title |
Protracted NP95 binding to hemimethylated DNA disrupts SETDB1-mediated proviral silencing [RNA-seq] |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Genetic ablation of the maintenance methyltransferase Dnmt1 induces widespread demethylation and transcriptional activation of CpG-rich IAP (intracisternal A particle) proviruses. Here, we report that this phenomenon is not simply a consequence of loss of DNA methylation. By exploiting conditional deletions of Dnmt1 and Np95, each of which is essential for maintenance methylation, we find that while IAPs are indeed de-repressed in Dnmt1-ablated embryos and embryonic stem cells (ESCs), these proviruses remain silenced in Np95-ablated cells, despite similar kinetics of passive demethylation. Paradoxically, transient IAP activation in Dnmt1-ablated ESCs requires the presence of NP95. We subsequently show that in the absence of NP95, the H3K9 methyltransferase SETDB1 maintains IAP silencing; while in the absence of DNMT1, prolonged binding of NP95 to hemimethylated DNA perturbs SETDB1-dependent H3K9me3 deposition. Taken together, these observations reveal that following acute loss of Dnmt1, H3K9 methylation-dependent IAP silencing is disrupted by aberrant NP95 binding to hemimethylated DNA.
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| Overall design |
RNA-seq for Np95, Dnmt1 and Setdb1 wt, single conditional KO (cKO) and double cKO ES cells; RRBS-seq for Dnmt1 and Np95 single and double cKO ESCs; Myc-tagged NP95, DNMT1 ChIP-seq; and wt and Np95wt and cKO H3K9me3 ChIP-seq.
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| Contributor(s) |
Koseki H, Lorincz MC, Sharif J |
| Citation(s) |
27151458 |
| Submission date |
Feb 10, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Takaho A. Endo |
| E-mail(s) |
takaho.endo@riken.jp
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| Organization name |
RIKEN
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| Department |
IMS
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| Lab |
Laboratory for Integrative Genomics
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| Street address |
1-7-22 Suehiro, Tsurumi
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| City |
Yokohama |
| State/province |
Kanagawa |
| ZIP/Postal code |
230-0045 |
| Country |
Japan |
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| Platforms (1) |
| GPL18480 |
Illumina HiSeq 1500 (Mus musculus) |
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| Samples (26)
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| GSM2059157 |
DN+Myc-Np95 wt ESC [RNA-seq] |
| GSM2059158 |
DNcDKO ESC, replicate 1 [RNA-seq] |
| GSM2059159 |
DNcdKO ESC, replicate 2 [RNA-seq] |
| GSM2059160 |
Dnmt1 wt ESC, replicate 1 [RNA-seq] |
| GSM2059161 |
Dnmt1 wt ESC, replicate 2 [RNA-seq] |
| GSM2059162 |
Dnmt1cKO ESC, replicate 1 [RNA-seq] |
| GSM2059163 |
Dnmt1cKO ESC, replicate 2 [RNA-seq] |
| GSM2059164 |
Dnmt1cKO ESC, replicate 3 [RNA-seq] |
| GSM2059165 |
Dnmt1cKO ESC, replicate 4 [RNA-seq] |
| GSM2059166 |
Np95 wt ESC, replicate 1 [RNA-seq] |
| GSM2059167 |
Np95 wt ESC, replicate 2 [RNA-seq] |
| GSM2059168 |
Np95cKO ESC, replicate 1 [RNA-seq] |
| GSM2059169 |
Np95cKO ESC, replicate 2 [RNA-seq] |
| GSM2059170 |
SD wt ESC, replicate 1 [RNA-seq] |
| GSM2059171 |
SD wt ESC, replicate 2 [RNA-seq] |
| GSM2059172 |
SDcDKO ESC, replicate 1 [RNA-seq] |
| GSM2059173 |
SDcDKO ESC, replicate 2 [RNA-seq] |
| GSM2059174 |
SN wt ESC, replicate 1 [RNA-seq] |
| GSM2059175 |
SN wt ESC, replicate 2 [RNA-seq] |
| GSM2059176 |
SN wt ESC, replicate 3 [RNA-seq] |
| GSM2059177 |
SNcDKO ESC, replicate 1 [RNA-seq] |
| GSM2059178 |
SNcDKO ESC, replicate 2 [RNA-seq] |
| GSM2059179 |
SNcDKO ESC, replicate 3 [RNA-seq] |
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| This SubSeries is part of SuperSeries: |
| GSE77781 |
Protracted NP95 binding to hemimethylated DNA disrupts SETDB1-mediated proviral silencing |
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| Relations |
| BioProject |
PRJNA311545 |
| SRA |
SRP069861 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE77778_table_v2.fpkm.txt.gz |
1.4 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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