|
| Status |
Public on Jul 31, 2023 |
| Title |
Thymine DNA glycosylase regulates cell-cycle-driven p53 |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Other
|
| Summary |
Cell cycle progression is linked to transcriptome dynamics and variations in the response of pluripotent cells to differentiation cues, mostly through unknown determinants. Here, we characterized the cell-cycleassociated transcriptome and proteome of mouse embryonic stem cells (mESCs) in naive ground state. We found that the thymine DNA glycosylase (TDG) is a cell-cycle-regulated co-factor of the tumor suppressor p53. Furthermore, TDG and p53 co-bind ESC-specific cis-regulatory elements and thereby control transcription of p53-dependent genes during self-renewal. We determined that the dynamic expression of TDG is required to promote the cell-cycle-associated transcriptional heterogeneity. Moreover, we demonstrated that transient depletion of TDG influences cell fate decisions during the early differentiation of mESCs. Our findings reveal an unanticipated role of TDG in promoting molecular heterogeneity during the cell cycle and highlight the central role of protein dynamics for the temporal control of cell fate during development.
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| |
|
| Overall design |
ChIP-seq (10 samples), DIP-seq (12 samples), RNA-seq (36 samples), ATAC-seq (1 sample). Nomenclature: siC means Control (Wild-type) and siTdg/shTdg mean knocking-down the Tdg gene; SG2M means cells in S/G2/M phases, G1 means cells in G1 phase of the cell cycle.
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| |
|
| Contributor(s) |
Aranda S, Blanco E |
| Citation(s) |
37506700 |
| |
| Submission date |
Nov 11, 2021 |
| Last update date |
Aug 01, 2023 |
| Contact name |
Enrique Blanco |
| E-mail(s) |
enrique.blanco@crg.eu
|
| Phone |
+34 93 316 01 00
|
| Organization name |
Center for Genomic Regulation (CRG)
|
| Department |
Gene Regulation, Stem Cells and Cancer
|
| Lab |
Epigenetic Events in Cancer (L. Di Croce's lab)
|
| Street address |
Dr. Aiguader 88
|
| City |
Barcelona |
| ZIP/Postal code |
08003 |
| Country |
Spain |
| |
|
| Platforms (2) |
| GPL13112 |
Illumina HiSeq 2000 (Mus musculus) |
| GPL17021 |
Illumina HiSeq 2500 (Mus musculus) |
|
| Samples (47)
|
|
| Relations |
| BioProject |
PRJNA779731 |
| SRA |
SRP345653 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE188636_0h_paired_RPKMs.txt.gz |
684.3 Kb |
(ftp)(http) |
TXT |
| GSE188636_0h_paired_results.txt.gz |
960.3 Kb |
(ftp)(http) |
TXT |
| GSE188636_48h_paired_RPKMs.txt.gz |
672.6 Kb |
(ftp)(http) |
TXT |
| GSE188636_48h_paired_results.txt.gz |
900.2 Kb |
(ftp)(http) |
TXT |
| GSE188636_96h_paired_RPKMs.txt.gz |
673.7 Kb |
(ftp)(http) |
TXT |
| GSE188636_96h_paired_results.txt.gz |
660.7 Kb |
(ftp)(http) |
TXT |
| GSE188636_G1_siC-G2_siC_paired_RPKMs.txt.gz |
701.5 Kb |
(ftp)(http) |
TXT |
| GSE188636_G1_siC-G2_siC_paired_results.txt.gz |
974.2 Kb |
(ftp)(http) |
TXT |
| GSE188636_G1_siTdg-G2_siTdg_paired_RPKMs.txt.gz |
703.9 Kb |
(ftp)(http) |
TXT |
| GSE188636_G1_siTdg-G2_siTdg_paired_results.txt.gz |
969.2 Kb |
(ftp)(http) |
TXT |
| GSE188636_RAW.tar |
2.0 Gb |
(http)(custom) |
TAR (of BEDGRAPH) |
| GSE188636_TDG_peaks.bed.gz |
6.1 Kb |
(ftp)(http) |
BED |
| GSE188636_day11_paired_RPKMs.txt.gz |
705.2 Kb |
(ftp)(http) |
TXT |
| GSE188636_day11_paired_results.txt.gz |
909.5 Kb |
(ftp)(http) |
TXT |
| GSE188636_p53_peaks.bed.gz |
42.5 Kb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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