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Series GSE200582 Query DataSets for GSE200582
Status Public on Apr 30, 2023
Title Chromatin opening by p53 is confined by Trim24 in a histone methylation-dependent manner [ATAC-seq]
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Chromatin modifications are thought to provide additional context dependence for sequence-based gene activation. Binding sites of the transcription factor (TF) and important tumor suppressor p53 are unusually diverse with regards to their chromatin accessibility and histone modifications, suggesting different modes of binding. Here, we show that the ability of p53 to open chromatin and activate its target genes upon DNA damage is locally restricted by its cofactor Trim24. The histone-binding domains of Trim24 limit the role of p53 at closed chromatin but not at accessible chromatin where Trim24 is blocked by histone 3 methylation at lysine 4. In turn p53 regulates gene expression as a function of the naïve chromatin state prior to activation. These findings establish a set of p53 response genes in closed chromatin that are Trim24-regulated and illustrate how histone modification sensing cofactors bridge local chromatin state and TF potency.
 
Overall design Examination of p53 and Trim24 function in cell lines including mouse embryonic stem cells. Includes ATACseq in WT mouse ESCs in untreated/p53activated conditions (duplicates), ATACseq in p53-degron tagged mouse ESC lines under p53degraded/untreated/p53activated conditions (duplicates), ATACseq in Trim24-degron tagged mouse ESC lines under Trim24degraded/untreated/p53activated/p53activated;Trim24degraded conditions (duplicates), ATACseq in Trim24-degron tagged mouse ESC line under p53activated/p53activated;Trim24degraded conditions at multiple timepoints after treatment including 0 hours/1 hours (duplicates)/2 hours (duplicates)/4 hours (duplicates)/8 hours (duplicates)/12 hours, ATACseq in Trim24-degron tagged mouse ESC line under p53activated/p53activated;Trim24degraded conditions with alternative p53 activation conditions by nutlin3a (20uM) or irradiation (60Gy)(duplicates). All conditions to activate p53 or degrade degron tagged alleles performed for 4 hours unless specified in a timecourse series.
 
Contributor(s) Isbel L, Iskar M, Schübeler D
Citation(s) 37386214
Submission date Apr 11, 2022
Last update date Jul 31, 2023
Contact name Luke Thomas Isbel
E-mail(s) luke.isbel@adelaide.edu.au
Organization name SAiGENCI
Lab Isbel
Street address 4 North Terrace, AHMS, Lvl 9
City Adelaide
State/province South Australia
ZIP/Postal code 5000
Country Australia
 
Platforms (2)
GPL19057 Illumina NextSeq 500 (Mus musculus)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
Samples (58)
GSM6038143 ATACseq_ESC_wt_Unt_r1
GSM6038144 ATACseq_ESC_wt_Unt_r2
GSM6038145 ATACseq_ESC_wt_Act_r1
This SubSeries is part of SuperSeries:
GSE200586 Chromatin opening by p53 is confined by Trim24 in a histone methylation-dependent manner
Relations
BioProject PRJNA825470

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE200582_RAW.tar 791.7 Mb (http)(custom) TAR (of BW, WIG)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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