|
| Status |
Public on Nov 26, 2019 |
| Title |
Dynamic regulation of chromatin accessibility by pluripotency transcription factors across the cell cycle [OCT4-AID ATAC-seq] |
| Organism |
Mus musculus |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
The pioneer activity of transcription factors allows for opening of inaccessible regulatory elements and has been extensively studied in the context of cellular differentiation and reprogramming. In contrast, the function of pioneer activity in self-renewing cell divisions and across the cell cycle is poorly understood. Here we assessed the interplay between OCT4 and SOX2 in controlling chromatin accessibility of mouse embryonic stem cells. We found that OCT4 and SOX2 operate in a largely independent manner even at co-occupied sites, and that their cooperative binding is mostly mediated indirectly through regulation of chromatin accessibility. Controlled protein degradation strategies revealed that the uninterrupted presence of OCT4 is required for post-mitotic re-establishment and interphase maintenance of chromatin accessibility, and that highly OCT4-bound enhancers are particularly vulnerable to transient loss of OCT4 expression. Our study sheds light on the constant pioneer activity required to maintain the dynamic pluripotency regulatory landscape in an accessible state.
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| |
|
| Overall design |
ZHBTc4 cells expressing Ypet-MD and mCherry-OCT4-AID were treated with doxycycline for 24 hours before treatment with different IAA regimes, stained with Hoechst, sorted for different cell cycle phases, and subjected to ATAC-seq
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| |
|
| Contributor(s) |
Suter DM, Friman ET |
| Citation(s) |
31794382 |
| |
| Submission date |
Jul 22, 2019 |
| Last update date |
Dec 04, 2019 |
| Contact name |
David Michael Suter |
| Organization name |
École polytechnique fédérale de Lausanne
|
| Department |
Institute of Bioengineering
|
| Lab |
UPSUTER
|
| Street address |
EPFL SV-IN Station 19
|
| City |
Lausanne |
| ZIP/Postal code |
1015 |
| Country |
Switzerland |
| |
|
| Platforms (1) |
| GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
|
| Samples (54)
|
|
| This SubSeries is part of SuperSeries: |
| GSE134680 |
Dynamic regulation of chromatin accessibility by pluripotency transcription factors across the cell cycle |
|
| Relations |
| BioProject |
PRJNA556315 |
| SRA |
SRP216285 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE134675_OCT4-AID_DE.xlsx |
32.2 Mb |
(ftp)(http) |
XLSX |
| GSE134675_OCT4-AID_EG1_IAA.bw |
190.7 Mb |
(ftp)(http) |
BW |
| GSE134675_OCT4-AID_EG1_ctrl.bw |
182.4 Mb |
(ftp)(http) |
BW |
| GSE134675_OCT4-AID_IAA_timepoints_0h.bw |
163.4 Mb |
(ftp)(http) |
BW |
| GSE134675_OCT4-AID_IAA_timepoints_10h.bw |
174.3 Mb |
(ftp)(http) |
BW |
| GSE134675_OCT4-AID_IAA_timepoints_1h.bw |
163.9 Mb |
(ftp)(http) |
BW |
| GSE134675_OCT4-AID_IAA_timepoints_2h.bw |
165.9 Mb |
(ftp)(http) |
BW |
| GSE134675_OCT4-AID_IAA_timepoints_30m.bw |
165.3 Mb |
(ftp)(http) |
BW |
| GSE134675_OCT4-AID_IAA_timepoints_3h.bw |
164.2 Mb |
(ftp)(http) |
BW |
| GSE134675_OCT4-AID_IAA_timepoints_4h.bw |
163.7 Mb |
(ftp)(http) |
BW |
| GSE134675_OCT4-AID_IAA_timepoints_6h.bw |
158.5 Mb |
(ftp)(http) |
BW |
| GSE134675_OCT4-AID_IAAwash_EG1.bw |
185.0 Mb |
(ftp)(http) |
BW |
| GSE134675_OCT4-AID_IAAwash_LG1.bw |
184.4 Mb |
(ftp)(http) |
BW |
| GSE134675_OCT4-AID_IAAwash_S.bw |
190.9 Mb |
(ftp)(http) |
BW |
| GSE134675_OCT4-AID_IAAwash_SG2.bw |
187.8 Mb |
(ftp)(http) |
BW |
| GSE134675_OCT4-AID_LG1_IAA.bw |
193.7 Mb |
(ftp)(http) |
BW |
| GSE134675_OCT4-AID_LG1_ctrl.bw |
190.8 Mb |
(ftp)(http) |
BW |
| GSE134675_OCT4-AID_SG2_IAA.bw |
169.6 Mb |
(ftp)(http) |
BW |
| GSE134675_OCT4-AID_SG2_ctrl.bw |
176.7 Mb |
(ftp)(http) |
BW |
| GSE134675_OCT4-AID_S_IAA.bw |
195.8 Mb |
(ftp)(http) |
BW |
| GSE134675_OCT4-AID_S_ctrl.bw |
182.0 Mb |
(ftp)(http) |
BW |
| GSE134675_OCT4-AID_controlwash_EG1.bw |
188.5 Mb |
(ftp)(http) |
BW |
| GSE134675_OCT4-AID_controlwash_LG1.bw |
194.7 Mb |
(ftp)(http) |
BW |
| GSE134675_OCT4-AID_controlwash_S.bw |
186.5 Mb |
(ftp)(http) |
BW |
| GSE134675_OCT4-AID_controlwash_SG2.bw |
187.3 Mb |
(ftp)(http) |
BW |
| GSE134675_OCT4-AID_mergepeaks.bed.gz |
884.1 Kb |
(ftp)(http) |
BED |
| GSE134675_OCT4-AID_timepoints_DE.xlsx |
26.5 Mb |
(ftp)(http) |
XLSX |
| GSE134675_OCT4-AID_timepoints_normalizedreads.xlsx |
4.0 Mb |
(ftp)(http) |
XLSX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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