Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

13 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

A Cbx8-containing Polycomb complex facilitates gene activation during ES cell differentiation [ChIP-Seq]

ABSTRACT: Polycomb proteins play an essential role in maintaining the repression of developmental genes in self-renewing embryonic stem cells. The exact mechanism allowing the derepression of polycomb target genes during cell differentiation remains unclear. Here, we show that several differentiation genes transiently recruit a Cbx8-containing Polycomb repressive complex (PRC) 1 during their early activation. Depletion of Cbx8 partially impairs the transcriptional activation of these genes. This correlates with a reduction in low but detectable levels of histone H3 lysine 27 acetylation. Prolonged gene activation results in eviction of PRC1 despite persisting H3K27me3. The composition of PRC1 is highly modular and changes when ES cells commit to differentiation. We further demonstrate that the exchange of Cbx7 for Cbx8 is required for the effective activation of differentiation genes. Taken together our results establish a function for a Cbx8-containing complex in facilitating the transition from a Polycomb-repressed chromatin state to an active state. As this affects several key regulatory differentiation genes this mechanism is likely to contribute to the robust execution of differentiation programs. Examination of cbx8 in ES E14 mouse cells in 2 condition before and after 72h stimulation with retinoic acid compared with IgG

ORGANISM(S): Mus musculus

SUBMITTER: Roberto Malinverni

PROVIDER: E-GEOD-54052 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

A Cbx8-containing Polycomb complex facilitates gene activation during ES cell differentiation [ChIP-Seq]

Project description:Polycomb proteins play an essential role in maintaining the repression of developmental genes in self-renewing embryonic stem cells. The exact mechanism allowing the derepression of polycomb target genes during cell differentiation remains unclear. Here, we show that several differentiation genes transiently recruit a Cbx8-containing Polycomb repressive complex (PRC) 1 during their early activation. Depletion of Cbx8 partially impairs the transcriptional activation of these genes. This correlates with a reduction in low but detectable levels of histone H3 lysine 27 acetylation. Prolonged gene activation results in eviction of PRC1 despite persisting H3K27me3. The composition of PRC1 is highly modular and changes when ES cells commit to differentiation. We further demonstrate that the exchange of Cbx7 for Cbx8 is required for the effective activation of differentiation genes. Taken together our results establish a function for a Cbx8-containing complex in facilitating the transition from a Polycomb-repressed chromatin state to an active state. As this affects several key regulatory differentiation genes this mechanism is likely to contribute to the robust execution of differentiation programs.

2014-11-04 | GSE54052 | GEO

A Cbx8-containing Polycomb complex facilitates gene activation during ES cell differentiation [Agilent Array]

2014-11-04 | GSE54051 | GEO

A Cbx8-containing Polycomb complex facilitates gene activation during ES cell differentiation [Agilent Array]

2014-11-04 | E-GEOD-54051 | biostudies-arrayexpress

Identification of neuron lineage-specific PRC1 targets in olfactory neuron precursors

2020-12-25 | GSE124440 | GEO

Whole-transcriptome profiling of regenerating olfactory epithelium following loss of CBX paralogs

Project description:The polycomb group protein, CBX8, is a neuron-specific component of Polycomb repressive complex 1 (PRC1) in the adult olfactory epithelium. We performed loss of function assays in an in vitro model of the regeneratng olfactory epithelium to determine the role of CBX8 in adult olfactory neurogenesis. Whole-transcriptome analysis highlighted the importance of CBX8-PRC1 in the regulation of adult neurogenesis in the olfactory epithelium.

2020-12-25 | GSE124441 | GEO

Helin M.musculus Identification of genes repressed by CBX8 and BMI1

Project description:The polycomb group proteins form large repressive complexes. It has recently become evident, via ChIP on chip analysis, that the polycomb complexes, PRC1 and PRC2, target a large number of genes (Boyer et al., 2006; Bracken et al., 2006; Tolhuis et al., 2006), which are involved in cell fate decisions. In order to identify genes which are truly regulated by the polycomb group proteins, CBX8 and BMI1, we expressed these two proteins in mouse embryonic fibroblasts (MEFs) by retroviral infection.

2007-03-05 | E-MEXP-793 | biostudies-arrayexpress

Murine Embryonic Stems Cells: H3K27me3 in Undifferentiated (UD) and Day 3 (D3) differentiated ES cells

Project description:ChIP on chip for H3K27me3 in murine ES cells comparing Undifferentiated and Day 3 differentiated. Paper Abstract: How polycomb group proteins repress gene expression in vivo is not known. Whilst histone modifying activities of the polycomb repressive complexes have been studied extensively, in vitro data has suggested a direct activity of the PRC1 complex in compacting chromatin. Here, we investigate higher-order chromatin compaction of polycomb targets in vivo. We show that polycomb repressive complexes are required to maintain a compact chromatin state at Hox loci in embryonic stem (ES) cells. There is specific decompaction in the absence of PRC2 or PRC1. This is due to PRC1, since decompaction occurs in Ring1B null cells that still have PRC2-mediated H3K27 methylation. Moreover, we show that the ability of Ring1B to restore a compact chromatin state, and to repress Hox gene expression in ES cells, is not dependent on its histone ubiquitination activity. We suggest that Ring1B-mediated chromatin compaction acts to directly limit transcription in vivo. Biological replicates: 3 independently grown, harvested, micrococcal nuclease digested and ChIP for H3K27me3. 6 Technical replicates.

2010-05-14 | E-GEOD-20201 | biostudies-arrayexpress

Fbxl10 regulates PRC1 recruitment to CpG islands and H2A ubiquitination

Project description:Polycomb repressive complex 1 (PRC1) catalyzes H2A monoubiquitination (uH2A) and regulates pluripotency in embryonic stem cells (ESCs). However the mechanisms controlling PRC1 recruitment and activity are largely unknown. Here we show that Fbxl10 interacts with Ring1B and Nspc1, forming a non-canonical PRC1. We demonstrate that Fbxl10-PRC1 is essential for H2A ubiquitination in mouse ESCs. Genome-wide analyses reveal that Fbxl10 preferentially binds to CpG islands and co-localizes with Ring1B on Polycomb target genes. Notably, Fbxl10 depletion causes modest dissociation of Ring1B but a major loss of uH2A on target genes. Furthermore rescue experiments for Fbxl10 reveal that its DNA binding capability and integration into PRC1 are required for proper H2A ubiquitination. ES cells lacking Fbxl10, like previously characterized Polycomb mutants, show a severely compromised capacity for successful differentiation. Our results shed light on a novel mechanism how CpG islands regulate chromatin function by affecting polycomb recruitment and activity. All ChIP-seq reactions were performed in either untransfected cells, cells expressing scrambled shRNA or Fbxl10 shRNA, Ring1b-/- or Suz12-/- mouse ES cells

2012-12-31 | E-GEOD-37930 | biostudies-arrayexpress

Phf19 links methylated lysine 36 of histone H3 to regulation of Polycomb activity [ChIP-Seq]

Project description:Polycomb group proteins are transcriptional repressors that play essential roles in regulating genes required for differentiation and embryonic development. The Polycomb repressive complex 2 (PRC2) contains the methyltransferase activity for lysine 27 on histone 3 (H3K27me3), which is a docking site for the PRC1 complex and leads to gene repression. However, the role of other histone modifications in regulating PRC2 activity is just beginning to be understood. Here we show that direct recognition of histone H3 methylated at lysine 36 (H3K36me), an mark associated with activation, by the PRC2 subunit Phf19 is required for the full enzymatic activity of the PRC2 complex. We provide structural evidence for this interaction by nuclear magnetic resonance spectroscopy (NMR). Using genome-wide chromatin binding analyses and expression analyses, we show that Phf19 binds to a subset of PRC2 targets in embryonic stem (ES) cells, and that this is required for their repression and for H3K27me3 deposition. These findings reveal that the H3K36me2/3-Phf19 interaction is essential for PRC2 complex activity and for proper regulation of gene repression in ES cells. We determined the genome binding/occupancy profile of Phf19, H3K36me3, H3K36me2, H3K27me3 and Suz12 by high throughput sequencing in mouse embryonic stem cells. For Phf19 two independent biological replicas were performed and Phf19 binding sites were defined as those sites (ChIP-seq peaks) present in both replicas. H3K27me3 was evaluated in control ES cells and cells depleted of Phf19 (shRd and shPhf19 respectively).

2012-10-16 | E-GEOD-41589 | biostudies-arrayexpress

A Cbx8-containing Polycomb complex facilitates gene activation during ES cell differentiation

Project description:A Cbx8-containing Polycomb complex facilitates gene activation during ES cell differentiation

| PRJNA234481 | ENA