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Non-Overlapping Functions of the Polycomb group Cbx Family of Proteins in Embryonic Stem Cells

ABSTRACT: Gene expression profile in control and Cbx7 depleted (shRNA#33) mouse embryonic stem cells and embryoid bodies at day 9

ORGANISM(S): Mus musculus

PROVIDER: GSE34191 | GEO | 2012/01/06

SECONDARY ACCESSION(S): PRJNA149825

REPOSITORIES: GEO

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Non-Overlapping Functions of the Polycomb group Cbx Family of Proteins in Embryonic Stem Cells

Project description:Gene expression profile in control and Cbx7 depleted (shRNA#33) mouse embryonic stem cells and embryoid bodies at day 9 4 samples, each one contains four biological replicas, except for ES-shCtr which contains 3 replicas

2012-01-06 | E-GEOD-34191 | biostudies-arrayexpress

Polycomb Cbx orthologs mediate the balance between Hematopoietic Stem Cell self-renewal and differentiation

2012-12-21 | GSE36658 | GEO

Polycomb Cbx orthologs mediate the balance between Hematopoietic Stem Cell self-renewal and differentiation

Project description:By genome-wide ChIP-seq analyses we show that Cbx7 and Cbx8 share ~95% of their targets in bone marrow cells. Cbx7 and Cbx8 have only ~200 targets that are not overlapping between the two proteins. These distinct Cbx7 and Cbx8 targets show reciprocal expression patterns along hematopoietic differentiation. Overexpression of empty vector (negative control), flag-Cbx7 and flag-Cbx8 in 5-FU treated bone marrow cells (progenitor and stem cells), followed by 1 week culture and subsequent ChIP using flag-M2 agarose beads.

2012-12-21 | E-GEOD-36658 | biostudies-arrayexpress

Different polycomb group CBX family proteins associate with distinct regions of chromatin using nonhomologous protein sequences.

Project description:Polycomb group proteins are transcriptional repressors recruited to many developmental control genes. The specificity of polycomb group protein targeting is incompletely understood. Subunits of polycomb repressive complexes (PRC) are encoded by multigene families in vertebrates. Five chromodomain-containing CBX family proteins are thought to mediate chromatin association by PRC1 complexes. We visualized the recruitment of CBX proteins to chromatin using bimolecular fluorescence complementation (BiFC) analysis, wherein fragments of fluorescent proteins fused to CBX family members and histone H3 form a fluorescent complex when the CBX proteins bind to nucleosomes. Different CBX family proteins associated with nucleosomes in different subnuclear regions in both ES cells and fibroblasts. The total populations of most CBX proteins had distributions distinct from those of the chromatin-associated complexes, indicating that most of these CBX proteins were not bound to nucleosomes. The conserved chromodomain and chromobox regions of CBX proteins were dispensable for chromatin association. The absence of H3 K27 trimethylation in EED null ES cells had minimal effects on chromatin association by CBX proteins. The BiFC complexes did not colocalize with anti-trimethyl-K27 immunofluorescence, with the exception of inactive X. Metaphase spreads derived from stable cell lines with inducible CBX fusion expression revealed reciprocal patterns of chromosome association by CBX2 and CBX6 BiFC complexes. H3.2 purified from CBX2-H3.2 BiFC complexes was enriched in trimethyl-K27, dimethyl-K4, and acetyl-K9 modifications. We conclude that different CBX proteins are recruited to distinct chromatin regions through nonconserved interactions, expanding the regulatory diversity of polycomb group proteins.

| S-EPMC2568982 | biostudies-literature

A Polycomb domain found in committed cells impairs differentiation when introduced into PRC1 in pluripotent cells (EBs/NPCs RNA-seq datasets)

Project description: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.

2021-10-11 | GSE151900 | GEO

A Polycomb domain found in committed cells impairs differentiation when introduced into PRC1 in pluripotent cells (ChIP-seq, CUT&RUN datasets)

2021-10-11 | GSE151899 | GEO

Polycomb-dependent H3K27me1 and H3K27me2 regulate active transcription and enhancer fidelity

Project description:These data include the genome wide location of different histone modifications by ChIP sequencing in mouse ES cells, and RNA Seq data generated from wild type and EED KO mouse ES cells and knocked down for unrelated protein and Setd2 protein. ChIP-Seq: Immuno-precipitation of formaldehyde cross-linked chromatin prepared from wild type mouse E14 ES cells, wild type E36 ES cells, EED KO E36 ES cells, wild type Embryoid bodies (Ebs), EED KO Embryoid bodies (Ebs EED KO) using specific antibody against different histone modifications. RNA-Seq: Total RNA extracted from wild type E36 ES cells, EED KO E36 ES cells, wild type E36 Embryoid bodies (Ebs), EED KO Embryoid bodies (Ebs EED KO), E14 Ctrl KD, E14 Setd2 KD.

2013-12-05 | E-GEOD-51006 | biostudies-arrayexpress

Polycomb CBX7 represses expression of tumor suppressor genes

Project description:Polycomb CBX7 was stably expressed in embryonal carcinoma cells in order to identify target genes. The study was specifically geared toward unveiling gene targets that are susceptible to DNA hypermethylation in adult cancer. A number of CBX7 target tumor suppressor genes were thereby identified and used in further studies to characterize the mechanism surrounding CBX7 mediated gene suppression. Keywords: CBX7 target gene identification A cDNA encoding the ORF of polycomb CBX7 under the control of EF1alpha promoter was transfected into the Tera-2 embryonal carcinoma cell line. Empty vector was used to transfect control cells. The cells were subject to stable selection using puromycin and a pooled population of CBX7 overexpressing cells was established. Gene expression analysis was performed by comparing the gene expression profile of CBX7 cells to empty vector control cells.

2009-09-23 | E-GEOD-10541 | biostudies-arrayexpress

Polycomb CBX7 represses expression of tumor suppressor genes

2009-09-23 | GSE10541 | GEO

The Polycomb group protein CBX6 is an essential regulator of embryonic stem cell identity

Project description:Polycomb group proteins are transcriptional repressors that control cell identity and development. In mammals, at least five different CBX proteins are believed to associate with the core Polycomb repressive complex 1 (PRC1). CBX6 and CBX7 are the most highly expressed CBX proteins in embryonic stem cells (ESCs), yet little is known about the function of CBX6 in these cells. Here we show that CBX6 is an essential regulator of ESC identity, since ablation of CBX6 function destabilizes the pluripotency network and triggers differentiation. At the molecular level, CBX6 is linked to the canonical PRC1 (cPRC1) complex; however, contrary to expectations, our results indicate that CBX6 also has a non-canonical PRC1 function. Taken together, our findings reveal that CBX6 is an essential component for ESC biology and contributes to the structural and functional complexity of the PRC1 complex.

2017-09-25 | PXD007577 | Pride

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