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

ABSTRACT: 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.

ORGANISM(S): Mus musculus

SUBMITTER: Leonid Bystrykh

PROVIDER: E-GEOD-36658 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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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.

2012-12-21 | GSE36658 | GEO

Genome wide co-localization of Polycomb orthologs and their effects on gene expression in human fibroblasts

Project description:We have identfied antibodies that support chromatin immunoprecipitation (ChIP) of 11 components of Polycomb repressive complex 1 (PRC1) and shown that multiple variants of PRC1 associate with the same DNA. By performing ChIP-seq with antibodies against CBX6, CBX7, CBX8, RING1 and RING2, in two strains of human fibroblasts, we find that all five proteins co-localize at multiple sites in the genome. The binding profiles have inherent architecture that is conserved between the two strains, but there are also a substantial number of differences between the strains, possibly reflecting their anatomical position. The presence of PcG proteins does not equate with gene silencing and their genomic position does not change at senescence. Chromatin immunoprecipitation and sequencing (ChIP-seq) in two strains of human fibroblasts using antibodies against three Pc orthologs (CBX6, CBX7 and CBX8) and both Psc orthologs (RING1 and 2). Validation by ChIP-PCR and re-ChIP. Strand specific RNA-seq and validation by qRT-PCR.

2013-12-19 | E-GEOD-40740 | biostudies-arrayexpress

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. Examination of cbx8 in ES E14 mouse cells in 2 condition before and after 72h stimulation with retinoic acid compared with IgG

2014-11-04 | E-GEOD-54052 | biostudies-arrayexpress

Transcriptome of CBX7 and CBX8 overexpressing CD34+ HSPCs

Project description:Transcriptome of CBX7 and CBX8 overexpressing CD34+ HSPCs

| PRJEB22831 | ENA

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 [ChIP-Seq]

2014-11-04 | GSE54052 | GEO

Genome-wide analysis of TIAR RNA ligands in mouse macrophages before and after LPS stimulation

Project description:TIA-1 related protein (TIAR) is a RNA-binding protein involved in several steps of gene expression such RNA splicing and translation. TIAR contains three RNA recognition motifs (RRMs) allowing its interaction with specific sequences localized in the untranslated regions (UTRs) of several mRNAs. In myeloid cells, TIAR has been shown to bind and regulate the translation and stability of various mRNAs encoding proteins important for the inflammatory response, such as TNFÎ±, Cox-2 or IL-8 . Here, we generated two macrophage-like RAW 264.7 cell lines expressing either a tagged full-length TIAR protein or a RRM2-truncated mutant unable to bind RNA with high affinity . By a combination of RNA-IP and microarray analysis (RIP-chip), we identified mRNAs specifically bound by the full-length protein both in basal conditions and in response to LPS. Microarray hybridization was performed on TIAR-FLAG-associated mRNAs or TIARÎRRM2-FLAG-associated mRNAs in unstimulated and LPS-stimulated RAW264.7 cells. Enrichment of TIAR-FLAG-associated mRNAs and TIARÎRRM2-FLAG-associated mRNAS were normalized to total transcriptome of TIAR-FLAG and TIARÎRRM2-FLAG expressing-RAW264.7 cells respectively. After amplification and labelling, sample pairs were hybridized onto Mouse Exonic Evidence Based Oligonucleotide (MEEBO) arrays containing on average 38784 mouse 70mer oligonucleotide probes (Stanford University, US). Hybridizations were replicated with dye swap.

2016-02-05 | E-GEOD-77577 | biostudies-arrayexpress

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

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. Four biological replicates were used for each condition (untreated and after 72h of retinoic acid stimulation) and samples were prepared and hybridized to SurePrint G3 Gene Expression Microarrays (Agilent technologies) following the supplier's instructions. Analyses were essentially performed as described (Uribesalgo et al. 2011) selecting differentially expressed probes with a FDR of 0.05 and fold change of > 1.5.

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

Proteogenomics analysis reveals specific genomic orientations at distal regulatory regions composed by non-canonical histone variants

Project description:Histone variants (H3.1, H3.3, H2A, and macroH2A) were studied about their proteomic and genomic distribution in Hela cells HeLa S3 cells stably expressing either FLAG-tagged H3.1, and H3.3 were grown in suspension in Joklik media containing 10% newborn calf serum (Hyclone), 1% GlutaMAX (Invitrogen), and 1% penicillin-streptomycin, and cells were harvested at log phase. Nuclei were isolated, mononucleosomes were subsequently obtained from these cell lines. Cells were lysed in hypotonic TMSD buffer to isolate nuclei, which were then digested with micrococcal nuclease. The resulting mononucleosomes were immunoprecipitated with anti-FLAG M2-agarose beads (Sigma) and eluted with FLAG peptide (Sigma)

2015-12-22 | E-GEOD-64652 | biostudies-arrayexpress

Identification of Merlin binding proteins

Project description:To identify proteins interacting with Merlin in response to calcium signaling, Flag-tagged Merlin was stably transduced into LN229 cells. These cells and empty vector-transduced LN229 cells were treated with DMSO or thapsigargin for 15 minutes and subjected to immunoprecipitation followed by Mass Spectrometry.

2020-12-07 | PXD021058 | Pride

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