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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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RYBP and Cbx7 define specific biological functions of PRC1 complexes in mouse embryonic stem cells

ABSTRACT: We report the ChIP-seq data of several PRC1 and PRC2 members from mouse embryonic stem cells Examination of DNA binding profile of Polycomb subunits

ORGANISM(S): Mus musculus

SUBMITTER: Luciano Di Croce

PROVIDER: E-GEOD-42466 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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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

Zrf1 is required to establish and maintain neural progenitor identity (ChIP-Seq)

Project description:We report ChIP-seq data for Zrf1 and Ring1B occupancy in NPC Examination and comparison of DNA binding profile of Zrf1 and Ring1B in NPC

2013-12-21 | E-GEOD-53540 | biostudies-arrayexpress

RYBP and Cbx7 define specific biological functions of PRC1 complexes in mouse embryonic stem cells

Project description:We report the ChIP-seq data of several PRC1 and PRC2 members from mouse embryonic stem cells

2013-01-01 | GSE42466 | GEO

PCGF homologs, CBX proteins, and RYBP define functionally distinct PRC1 family complexes.

Project description: Not available

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RYBP stimulates PRC1 to shape chromatin-based communication between Polycomb repressive complexes.

Project description: Not available

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The Polycomb protein Pcgf2/Mel18 regulates mesoderm cell fate-specification of embryonic stem cells through multiple mechanisms

Project description:Polycomb complexes are essential regulators of stem cell identity, yet very little is known about their molecular mechanisms during cell differentiation. Pcgf proteins (Pcgf1/2/3/4/5/6) are core subunits of the Polycomb repressive complex 1 (PRC1). It has been recently proposed that specific Pcgf proteins are associated to particular PRC1 complexes, yet the molecular and biological functions of different Pcgf proteins remains largely elusive. Using specific differentiation protocols, we have elucidated a role for Pcgf2/Mel18 in specifically regulating mesoderm differentiation. Mechanistically, during early cardiac mesoderm differentiation, Pcgf2/Mel18 functions as a classical Polycomb protein by repressing pluripotency, lineage specification, late cardiac differentiation and negative regulators of the BMP pathway, yet Pcgf2/Mel18 also positively regulates the expression of key mesoderm transcription factors, revealing a novel function of Pcgf2/Mel18 in gene activation during cardiac differentiation. Mel18 depletion results in an unbalance of pathways that positively and negatively regulate cardiac differentiation. We propose that Mel18 is a novel epigenetic factor that controls mesoderm differentiation by opposing molecular mechanisms. List of ChIPseq samples: Mel18 in ESCs and MES, Ring1b, RYBP and Cbx2 in MES, IgG in MESs. List of RNAseq experiments: Mel18 KD, Ring1b KO and CTR in ESCs, Mel18 KD and CTR in MES, Mel18 KD and CTR in CMs.

2015-09-04 | E-GEOD-67868 | biostudies-arrayexpress

RYBP modulates embryonic neurogenesis involving the Notch signaling pathway in a PRC1-independent pattern.

Project description: Not available

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SCL/TAL1 cooperates with Polycomb RYBP-PRC1 to suppress alternative lineages in blood-fated cells.

Project description: Not available

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RYBP-PRC1 complexes mediate H2A ubiquitylation at polycomb target sites independently of PRC2 and H3K27me3.

Project description: Not available

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The PRC2-associated factor C17orf96 is a novel CpG island regulator in mouse ES cells

Project description:CpG islands (CGIs) are key DNA regulatory elements in the vertebrate genome and are often found at gene promoters. In mammalian embryonic stem (ES) cells, CGIs are decorated by either the active or repressive histone marks, H3K4me3 and H3K27me3, respectively, or by both modifications (‘bivalent domains’), but their precise regulation is incompletely understood. Remarkably, we find that the polycomb repressive complex 2 (PRC2)-associated protein C17orf96 (a.k.a. esPRC2p48 and E130012A19Rik) is present at most CGIs in mouse ES cells. At PRC2-rich CGIs, loss of C17orf96 results in an increased chromatin binding of Suz12 and elevated H3K27me3 levels concomitant with gene repression. In contrast, at PRC2-poor CGIs, located at actively transcribed genes, C17orf96 colocalizes with RNA polymerase II and its depletion leads to a focusing of H3K4me3 in the core of CGIs. Our findings thus identify C17orf96 as a novel context-dependent CGI regulator. ChIP-seq of C17orf96, H3K4me3 and H3K27me3 in mouse ES cells (E14).

2015-04-29 | E-GEOD-63491 | biostudies-arrayexpress

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