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The dynamic interactome and genomic targets of Polycomb complexes during stem cell differentiation

ABSTRACT: While the core members of the Polycomb family of proteins (PRC2, PRC1, PR-DUB) are well-characterized, little is known about the specific composition of and protein-protein interactions within these complexes in different cell types. We performed quantitative interaction proteomics and cross-linking mass spectrometry on core Polycomb complex members to identify novel interactors, the relative abundance (stoichiometry) of subunits, and the architecture of these complexes in mouse embryonic stem cells (mESCs) and neural progenitor cells (NPCs). Differentiation to NPCs resulted in dramatic binding changes for several substoichiometric interactors of PRC2 and PRC1. ChIP-seq of core PRC2 and PRC1 subunits in mESCs and NPCs also identified dynamic changes in the genomic localization of these complexes. We observed a loss of PRC2 from most H3K27me3 sites during differentiation, whereas PRC1 is retained at these sites. Additionally, we found PRC1 at enhancers and promoters of active genes independent of PRC2 binding. Overexpression studies using NPC-specific PRC1 interactors demonstrated that the subunit switching observed during differentiation can change PRC1 target site binding. Altogether, these findings extend our understanding of Polycomb family composition, architecture, and genome-wide localization. ChIP-seq samples for Suz12, Ezh2, Ring1b, Pcgf2, and inputs from mouse embryonic stems cells (mES) and neural progenitor cells (NPC) as well as NPC histone H3K4me1 ChIP-seq.

ORGANISM(S): Mus musculus

SUBMITTER: Susan Kloet

PROVIDER: E-GEOD-74330 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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The dynamic interactome and genomic targets of Polycomb complexes during stem cell differentiation

Project description:While the core members of the Polycomb family of proteins (PRC2, PRC1, PR-DUB) are well-characterized, little is known about the specific composition of and protein-protein interactions within these complexes in different cell types. We performed quantitative interaction proteomics and cross-linking mass spectrometry on core Polycomb complex members to identify novel interactors, the relative abundance (stoichiometry) of subunits, and the architecture of these complexes in mouse embryonic stem cells (mESCs) and neural progenitor cells (NPCs). Differentiation to NPCs resulted in dramatic binding changes for several substoichiometric interactors of PRC2 and PRC1. ChIP-seq of core PRC2 and PRC1 subunits in mESCs and NPCs also identified dynamic changes in the genomic localization of these complexes. We observed a loss of PRC2 from most H3K27me3 sites during differentiation, whereas PRC1 is retained at these sites. Additionally, we found PRC1 at enhancers and promoters of active genes independent of PRC2 binding. Overexpression studies using NPC-specific PRC1 interactors demonstrated that the subunit switching observed during differentiation can change PRC1 target site binding. Altogether, these findings extend our understanding of Polycomb family composition, architecture, and genome-wide localization.

2016-05-17 | GSE74330 | GEO

The dynamic interactome of Polycomb family complexes during stem cell differentiation

Project description:While the core subunits of Polycomb group (PcG) complexes are well characterized, little is known about the dynamics of these protein complexes during cellular differentiation. We used quantitative interaction proteomics to study PcG proteins in mouse embryonic stem cells (mESCs) and neural progenitor cells (NPCs). We found the stoichiometry of PRC1 and PRC2 to be highly dynamic during neural differentiation.

2016-05-19 | PXD003758 | Pride

Two distinct functional axes of positive feedback-enforced PRC2 recruitment in mouse embryonic stem cells

Project description:Polycomb Repressive Complex 2 (PRC2) plays an essential role in development by catalysing trimethylation of histone H3 lysine 27 (H3K27me3), resulting in gene repression. PRC2 consists of two sub-complexes, PRC2.1 and PRC2.2, in which the PRC2 core associates with distinct ancillary subunits such as MTF2 and JARID2, respectively. Both MTF2, present in PRC2.1, and JARID2, present in PRC2.2, play a role in core PRC2 recruitment to target genes in mouse embryonic stem cells (mESCs). However, it remains unclear how these distinct sub-complexes cooperate to establish H3K27me3 domains. Here, we combine a range of Polycomb mutant mESCs with chemical inhibition of PRC2 catalytic activity, to systematically dissect their relative contributions to PRC2 binding to target loci. We find that PRC2.1 and PRC2.2 mediate two distinct paths for recruitment, with mutually reinforced binding. Part of the cross-talk between PRC2.1 and PRC2.2 occurs via their catalytic product H3K27me3, which is bound by the PRC2 core-subunit EED, thereby mediating a positive feedback. Strikingly, removal of either JARID2 or H3K27me3 only has a minor effect on PRC2 recruitment, whereas their combined ablation largely attenuates PRC2 recruitment. This strongly suggests an unexpected redundancy between JARID2 and EED-H3K27me3-mediated recruitment of PRC2. Furthermore, we demonstrate that all core PRC2 recruitment occurs through the combined action of MTF2-mediated recruitment of PRC2.1 to DNA and PRC1-mediated recruitment of JARID2-containing PRC2.2. Both axes of binding are supported by EED-H3K27me3 positive feedback, but to a different degree. Finally, we provide evidence that PRC1 and PRC2 mutually reinforce reciprocal binding. Together, these data disentangle the interdependent and cooperative interactions between Polycomb complexes that are important to establish Polycomb repression at target sites.

2020-08-07 | PXD014290 | Pride

Two distinct functional axes of positive feedback-enforced PRC2 recruitment in mouse embryonic stem cells

2021-09-22 | PXD020684 | Pride

Deletion of RING1A/B and loss of H2AK119ub1 affects PRC2 occupancy and H3K27me3 genome-wide

Project description:The chromatin modifying activities inherent to polycomb repressive complexes PRC1 and PRC2 play an essential role in gene regulation, cellular differentiation, and development. However, the mechanisms by which these complexes recognize their target sites and function together to form repressive chromatin domains remain poorly understood. Recruitment of PRC1 to target sites has been proposed to occur through a hierarchical process, dependent on the prior nucleation of PRC2 and placement of H3K27me3. Here, using a de novo targeting assay in mouse embryonic stem cells we unexpectedly discover that PRC1-dependent H2AK119ub1 leads to the recruitment of PRC2 and H3K27me3 to effectively initiate a polycomb domain. Genetic ablation of catalytic subunit of the PRC1 complex (RINGA/B) and ChIP-seq analysis of PRC1 and PRC2 components confirmed genome-wide decreases in PRC2 occupancy and H3K27me3 levels at PRC target sites. This activity is restricted to variant PRC1 complexes and genetic ablation experiments reveal that targeting of the variant PCGF1/PRC1 complex by KDM2B to CpG islands is required for polycomb domain formation and normal development. Together these observations provide a surprising new PRC1-dependent logic for PRC2 occupancy and polycomb domain formation. RING1A-/-;RING1Bfl/fl ES cells were treated with 800M-BM-5M tamoxifen for 48hours and compared to untreated control cells by ChIP-seq for RING1B, SUZ12, EZH2 and H3K27me3.

2014-05-27 | E-GEOD-55697 | biostudies-arrayexpress

H3K27me3 is not required for recruitment of Polycomb repressor complex 1 to target loci in mouse embryonic stem cells

Project description:The established hierarchical model explaining co-occupancy of Polycomb repressor complexes 1 and 2 (PRC 1 and 2) at target loci proposes that the chromodomain of the polycomb protein, a core PRC1 subunit, recognises the H3K27me3 histone modification catalysed by PRC2. We used chromatin immunoprecipitation to analyse PRC1 occupancy at target loci in Eed-/- mouse embryonic stem cells (ESCs) that lack H3K27me3. Occupancy of the core PRC1 proteins Ring1B and Mel18 was strongly reduced, consistent with the hierarchical model. However, levels of H2A ubiquitylation (H2AK119u1), the histone modification catalysed by PRC1, were similar to wild-type cells, suggesting PRC1 recruitment is independent of H3K27me3. ChIP-sequencing analysis of Ring1B occupancy genome wide substantiated this conclusion, demonstrating significant Ring1B levels at polycomb target loci in Eed-/- ESCs. Thus PRC1 and PRC2 are recruited independently to sites that they co-occupy. We conclude that the primary function of H3K27me3 is to increase the residency of PRC1 at target loci and thereby to contribute to the stability of PRC1 mediated silencing. Examination of Ring1B binding in WT, Eed ko and Input of ESCs Examination of CBX7 in WT and Eed ko of ESCs

2011-11-30 | E-GEOD-23716 | biostudies-arrayexpress

Transcription profiling of mouse embryonic stem cells FROM Eed knockout vs control

Project description:The Polycomb group (PcG) gene products mediate heritable silencing of developmental regulators in metazoans, participating in one of two distinct multimeric protein complexes, the Polycomb repressive complexes-1 (PRC1) and -2 (PRC2). PRC2 catalyses trimethylation of histone H3 at lysine 27 (H3K27) which in turn is thought to provide a recruitment site for PRC1. Recent studies demonstrate that mono-ubiquitylation of histone H2A at lysine 119 is important in PcG mediated silencing with the core PRC1 component Ring1A/B functioning as the E3 ligase8. PRC2 has been shown to share target genes with the core transcription network to maintain embryonic stem (ES) cells including Oct4 and Nanog. Here we identify an essential role for PRC1 in repressing developmental regulators in ES cells, and thereby in maintaining ES cell pluripotency. A significant proportion of the PRC1 target genes are also repressed by Oct4. We demonstrate that engagement of PRC1 and PRC2 at target genes is Oct4-dependent and moreover that Ring1B interacts with Oct4. Collectively these results show that PcG complexes are instrumental in Oct4-dependent repression required to maintain pluripotency of ES cells. This study provides a first functional link between a core ES cell regulator and global epigenetic regulation of the genome. Experiment Overall Design: Eed is a protein included in PRC2 (Polycomb repressor complex). Experiment Overall Design: We generated constitutive Eed KO mouse ES cells and observed gene expression using Affymetrix MOE430.2 microarray. Experiment Overall Design: These results were compared with other KO cells of PRC1 proteins (Ring1A, Ring1B) and other proteins in our study.

2008-04-07 | E-GEOD-10574 | biostudies-arrayexpress

Direct Recruitment of Polycomb Repressive Complex 1 (PRC1) to Chromatin by Core Binding Transcription Factors (ChIP-Seq)

Project description:Polycomb repressive complexes (PRCs) play key roles in developmental epigenetic regulation. Yet the mechanisms that target PRCs to specific loci in mammalian cells remain incompletely understood. In this study, we show that Bmi1, a core component of Polycomb Repressive Complex 1 (PRC1), binds directly to the Runx1/CBFbeta transcription factor complex. Genome-wide studies in megakaryocytic cells demonstrate considerable chromatin occupancy overlap between the PRC1 core component Ring1b and Runx1/CBFbeta and functional regulation of a significant fraction of commonly bound genes. Bmi1/Ring1b and Runx1/CBFbeta deficiency generate partial phenocopies of one another in vivo. We also show that Ring1b occupies key Runx1 binding sites in primary murine thymocytes and that this occurs via Polycomb Repressive Complex 2 (PRC2) independent mechanisms. Genetic depletion of Runx1 results in reduced Ring1b binding at these sites in vivo. These findings provide evidence for site-specific PRC1 chromatin recruitment by core binding transcription factors in mammalian cells. ChIP-seq against Runx1, CBFb and Ring1b in L8057 cells (induced & uninduced with biological replicates) and thymocytes from control and Runx1 KO mice

2012-02-10 | E-GEOD-33653 | biostudies-arrayexpress

Transcription profiling of mouse_Pou5f1 knockouts

Project description:The Polycomb group (PcG) gene products mediate heritable silencing of developmental regulators in metazoans, participating in one of two distinct multimeric protein complexes, the Polycomb repressive complexes-1 (PRC1) and -2 (PRC2)1-5. PRC2 catalyses trimethylation of histone H3 at lysine 27 (H3K27) which in turn is thought to provide a recruitment site for PRC13-7. Recent studies demonstrate that mono-ubiquitylation of histone H2A at lysine 119 is important in PcG mediated silencing with the core PRC1 component Ring1A/B functioning as the E3 ligase8. PRC2 has been shown to share target genes with the core transcription network to maintain embryonic stem (ES) cells including Oct4 and Nanog9. Here we identify an essential role for PRC1 in repressing developmental regulators in ES cells, and thereby in maintaining ES cell pluripotency. A significant proportion of the PRC1 target genes are also repressed by Oct4. We demonstrate that engagement of PRC1 and PRC2 at target genes is Oct4-dependent and moreover that Ring1B interacts with Oct4. Collectively these results show that PcG complexes are instrumental in Oct4-dependent repression required to maintain pluripotency of ES cells. This study provides a first functional link between a core ES cell regulator and global epigenetic regulation of the genome. Experiment Overall Design: These experiments were designed to investigate how gene expression would be affected in the absence of Oct3/4 in mouse ES cells. Because constitutive Oct3/4 KO cells are not maintained, we generated conditional KO cells.

2008-04-07 | E-GEOD-10477 | biostudies-arrayexpress

Transcription profiling of mouse Dnmt1 knockouts

Project description:The Polycomb group (PcG) gene products mediate heritable silencing of developmental regulators in metazoans, participating in one of two distinct multimeric protein complexes, the Polycomb repressive complexes-1 (PRC1) and -2 (PRC2)1-5. PRC2 catalyses trimethylation of histone H3 at lysine 27 (H3K27) which in turn is thought to provide a recruitment site for PRC13-7. Recent studies demonstrate that mono-ubiquitylation of histone H2A at lysine 119 is important in PcG mediated silencing with the core PRC1 component Ring1A/B functioning as the E3 ligase8. PRC2 has been shown to share target genes with the core transcription network to maintain embryonic stem (ES) cells including Oct4 and Nanog9. Here we identify an essential role for PRC1 in repressing developmental regulators in ES cells, and thereby in maintaining ES cell pluripotency. A significant proportion of the PRC1 target genes are also repressed by Oct4. We demonstrate that engagement of PRC1 and PRC2 at target genes is Oct4-dependent and moreover that Ring1B interacts with Oct4. Collectively these results show that PcG complexes are instrumental in Oct4-dependent repression required to maintain pluripotency of ES cells. This study provides a first functional link between a core ES cell regulator and global epigenetic regulation of the genome. Experiment Overall Design: Gene expression in Dnmt1-KO cells were observed using Affymetrix chip: MOE 430 2.0. Experiment Overall Design: These experiments were performed to obtain control of KO cells for other experiments that affect stem cell differentiation.

2008-04-07 | E-GEOD-10519 | biostudies-arrayexpress

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