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Series GSE38650 Query DataSets for GSE38650
Status Public on Jun 12, 2012
Title Histone H2A mono-ubiquitination is a crucial step to mediate PRC1 dependent repression of developmental genes to maintain ES cell identity.
Organism Mus musculus
Experiment type Expression profiling by array
Genome binding/occupancy profiling by array
Summary Two distinct Polycomb complexes, PRC1 and PRC2, collaborate to maintain epigenetic repression of key developmental loci in embryonic stem cells (ESCs). PRC1 and PRC2 have histone modifying activities, catalyzing mono-ubiquitination of histone H2A (H2AK119u1) and trimethylation of H3 lysine 27 (H3K27me3) respectively. Compared to H3K27me3, localization and role of H2AK119ub1 is not fully understood in ESCs. Here we present genome-wide H2AK119u1 maps in ESCs and identify a group of genes at which H2AK119u1 is deposited in a Ring1-dependent manner. These genes are a distinctive subset of genes with H3K27me3 enrichment and are the central targets of Polycomb silencing that are required to maintain ESC identity. We further show that the H2A ubiquitination activity of PRC1 is dispensable for its target binding and its activity to compact chromatin at Hox loci, but is indispensable for efficient repression of target genes and thereby ESC maintenance. These data demonstrate that multiple effector mechanisms including H2A ubiquitination and chromatin compaction combine to mediate PRC1-dependent repression of genes that are crucial for the maintenance of ESC identity. Utilization of these diverse effector mechanisms might provide a means to maintain a repressive state that is robust yet highly responsive to developmental cues during ES cell self-renewal and differentiation.

This SuperSeries is composed of the SubSeries listed below.
Overall design Total RNAs were extracted from the respective ES cells, and were subjected to microarray analysis using Affymetrix GeneChip Mouse Genome 430A 2.0 arrays.
ChIP on chip analysis was carried out using the Mouse Promoter ChIP-on-chip Microarray Set (G4490A, Agilent, Palo Alto, Calif., USA). MEFs were subjected to ChIP assay using various antibodies. Purified immunoprecipitated and input DNA was subjected to T7 RNA polymerase-based amplification. Labeling, hybridization and washing were carried out according to the Agilent mammalian ChIP-on-chip protocol (ver.9.0). Scanned images were quantified with Agilent Feature Extraction software under standard conditions.
Contributor(s) Endoh M, Endo TA, Koseki H
Citation(s) 22844243
Submission date Jun 11, 2012
Last update date Feb 11, 2019
Contact name Takaho A. Endo
Organization name RIKEN
Department IMS
Lab Laboratory for Integrative Genomics
Street address 1-7-22 Suehiro, Tsurumi
City Yokohama
State/province Kanagawa
ZIP/Postal code 230-0045
Country Japan
Platforms (3)
GPL1261 [Mouse430_2] Affymetrix Mouse Genome 430 2.0 Array
GPL14573 Agilent-014716 Mouse Promoter ChIP-on-Chip Set 244K, Microarray 1 of 2 (G4490A) (Probe Name version)
GPL14597 Agilent-014717 Mouse Promoter ChIP-on-Chip Set 244K, Microarray 2 of 2 (G4490A) (Probe Name version)
Samples (40)
GSM936970 Ring1A/B cKO mock (OHT-)
GSM936971 Ring1A/B cKO mock (OHT+)
GSM936972 Ring1A/B cKO expressing WT Ring1B #1 (OHT-)
This SuperSeries is composed of the following SubSeries:
GSE38224 Expression data from Ring1A(-/-);Ring1B(fl/fl);R26::CreERT2 ES cells expressing either of mock, WT or mutant Ring1B construct before or after OHT treatment
GSE38504 ChIP-on-chip analysis of Ring1B, Ring1A, H2AK119u1 and H3K27me3 in mouse ES cells
BioProject PRJNA168370

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
GSE38650_RAW.tar 1.8 Gb (http)(custom) TAR (of CEL, TXT)

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