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Series GSE151899 Query DataSets for GSE151899
Status Public on Oct 11, 2021
Title A Polycomb domain found in committed cells impairs differentiation when introduced into PRC1 in pluripotent cells (ChIP-seq, CUT&RUN datasets)
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary The CBX family of proteins is central to proper mammalian development via key roles in Polycomb-mediated maintenance of repression. CBX proteins in differentiated lineages have chromatin compaction and phase separation activities that might contribute to maintaining repressed chromatin. The predominant CBX protein in pluripotent cells, CBX7, lacks the domain required for these activities. We inserted this functional domain into CBX7 in embryonic stem cells to test the hypothesis that it contributes a key epigenetic function. ESCs expressing this chimeric CBX7 were impaired in their ability to properly form embryoid bodies and neural progenitor cells and showed reduced activation of lineage-specific genes across differentiation. Neural progenitors exhibited a corresponding inappropriate maintenance of Polycomb binding at neural-specific loci over the course of differentiation. We propose that a switch in the ability to compact and phase separate is a central aspect of Polycomb group function during the transition from pluripotency to differentiated lineages.
Overall design Embryonic stem cells expressing different versions of CBX7 (WT, CaPS, KO) were differentiated into embryoid bodies and neural progenitor cells. Localization of PRC1 and H3K27me3 was determined in ESCs and differentiated cells by ChIP-Seq and by CUT&RUN. ChIP-Seq peaks were called over input values, and CUT&RUN peaks were called over IgG control values. Replicates were averaged where present. All comparisons were made between experiments that were performed at the same time.
Contributor(s) Jaensch ES, Kingston RE
Citation(s) 34637753
Submission date Jun 05, 2020
Last update date Jan 11, 2022
Contact name Robert Kingston
Organization name Massachusetts General Hospital
Department Molecular Biology
Lab Kingston Lab
Street address 185 Cambridge Street, 7th Floor
City Boston
State/province MA
ZIP/Postal code 02114
Country USA
Platforms (1)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
Samples (71)
GSM4593061 WT_ESC_input_TF_group1
GSM4593062 WT_ESC_CBX7_ChIP_group1
GSM4593063 WT_ESC_RING1B_ChIP_group1
This SubSeries is part of SuperSeries:
GSE151901 A Polycomb domain found in committed cells impairs differentiation when introduced into PRC1 in pluripotent cells
BioProject PRJNA637608
SRA SRP266146

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SOFT formatted family file(s) SOFTHelp
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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE151899_EB10_RING1B_CR_peaks_annotated.txt.gz 561.9 Kb (ftp)(http) TXT
GSE151899_ESC_CBX7_ChIP_peaks_annotated.txt.gz 643.4 Kb (ftp)(http) TXT
GSE151899_ESC_H3K27me3_CR_peaks_annotated.txt.gz 428.2 Kb (ftp)(http) TXT
GSE151899_ESC_H3K27me3_ChIP_annotated_peaks.txt.gz 805.1 Kb (ftp)(http) TXT
GSE151899_ESC_RING1B_CR_annotated_peaks.txt.gz 887.1 Kb (ftp)(http) TXT
GSE151899_ESC_RING1B_CR_peaks_annotated.txt.gz 863.0 Kb (ftp)(http) TXT
GSE151899_ESC_RING1B_ChIP_peaks_annotated.txt.gz 653.7 Kb (ftp)(http) TXT
GSE151899_NPC8_H3K27me3_ChIP_peaks_annotated.txt.gz 724.6 Kb (ftp)(http) TXT
GSE151899_NPC8_RING1B_ChIP_peaks_annotated.txt.gz 517.2 Kb (ftp)(http) TXT
GSE151899_NPC_timecourse_RING1B_ChIP_annotated_peaks.txt.gz 1.6 Mb (ftp)(http) TXT
GSE151899_RAW.tar 19.0 Gb (http)(custom) TAR (of BIGWIG)
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Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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