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Protein interactions within PLEIOHOMEOTIC-repressive complex are critical for its recruitment to Polycomb target genes

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Homo sapiens Drosophila melanogaster

PROVIDER: GSE41854 | GEO | 2014/06/07

SECONDARY ACCESSION(S): PRJNA178657

REPOSITORIES: GEO

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Protein interactions within PLEIOHOMEOTIC-repressive complex are critical for its recruitment to Polycomb target genes

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2014-06-07 | E-GEOD-41854 | biostudies-arrayexpress

Protein interactions within PLEIOHOMEOTIC-repressive complex are critical for its recruitment to Polycomb target genes (Human)

Project description:PcG proteins are critical epigenetic regulators of development. Here we have determined genomic distributions of H3K27me3, BMI1, MEL18, EZH2 and YY1 proteins on chromosomes 8, 11,12 of cultured human NTERA-2 cl.D1 cells by hybridization of ChIP products with tiling microarrays. genomic distributions of H3K27me3, BMI1, MEL18, EZH2 and YY1 proteins on chromosomes 8, 11,12 of cultured human NTERA-2 cl.D1 cells by hybridization of ChIP products with tiling microarrays.

2014-06-07 | E-GEOD-41853 | biostudies-arrayexpress

Protein interactions within PLEIOHOMEOTIC-repressive complex are critical for its recruitment to Polycomb target genes (Fruit Fly)

Project description:PcG proteins are critical epigenetic regulators of development. Here we have determined genomic distributions of PHO, PHOL and SFMBT proteins in cultured Drosophila cells by hybridization of ChIP products with tiling microarrays. genomic distributions of PHO, PHOL and SFMBT proteins in cultured Drosophila cells by hybridization of ChIP products with tiling microarrays.

2014-06-07 | E-GEOD-41852 | biostudies-arrayexpress

Protein interactions within PLEIOHOMEOTIC-repressive complex are critical for its recruitment to Polycomb target genes (Human)

2014-06-07 | GSE41853 | GEO

Protein interactions within PLEIOHOMEOTIC-repressive complex are critical for its recruitment to Polycomb target genes (Fruit Fly)

2014-06-07 | GSE41852 | GEO

Short RNAs are transcribed from repressed polycomb target genes and interact with polycomb repressive complex-2.

Project description:Polycomb proteins maintain cell identity by repressing the expression of developmental regulators specific for other cell types. Polycomb repressive complex-2 (PRC2) catalyzes trimethylation of histone H3 lysine-27 (H3K27me3). Although repressed, PRC2 targets are generally associated with the transcriptional initiation marker H3K4me3, but the significance of this remains unclear. Here, we identify a class of short RNAs, approximately 50-200 nucleotides in length, transcribed from the 5' end of polycomb target genes in primary T cells and embryonic stem cells. Short RNA transcription is associated with RNA polymerase II and H3K4me3, occurs in the absence of mRNA transcription, and is independent of polycomb activity. Short RNAs form stem-loop structures resembling PRC2 binding sites in Xist, interact with PRC2 through SUZ12, cause gene repression in cis, and are depleted from polycomb target genes activated during cell differentiation. We propose that short RNAs play a role in the association of PRC2 with its target genes.

| S-EPMC2886029 | biostudies-literature

Polycomb repressive complex 1 shapes the nucleosome landscape but not accessibility at target genes.

Project description:Polycomb group (PcG) proteins are transcriptional repressors that play important roles in regulating gene expression during animal development. In vitro experiments have shown that PcG protein complexes can compact chromatin to limit the activity of chromatin remodeling enzymes and access of the transcriptional machinery to DNA. In fitting with these ideas, gene promoters associated with PcG proteins have been reported to be less accessible than other gene promoters. However, it remains largely untested in vivo whether PcG proteins define chromatin accessibility or other chromatin features. To address this important question, we examine the chromatin accessibility and nucleosome landscape at PcG protein-bound promoters in mouse embryonic stem cells using the assay for transposase accessible chromatin (ATAC)-seq. Combined with genetic ablation strategies, we unexpectedly discover that although PcG protein-occupied gene promoters exhibit reduced accessibility, this does not rely on PcG proteins. Instead, the Polycomb repressive complex 1 (PRC1) appears to play a unique role in driving elevated nucleosome occupancy and decreased nucleosomal spacing in Polycomb chromatin domains. Our new genome-scale observations argue, in contrast to the prevailing view, that PcG proteins do not significantly affect chromatin accessibility and highlight an underappreciated complexity in the relationship between chromatin accessibility, the nucleosome landscape, and PcG-mediated transcriptional repression.

| S-EPMC6169895 | biostudies-literature

Regulatory interactions between RNA and polycomb repressive complex 2.

Project description:Polycomb repressive complex 2 (PRC2) is a histone methyltransferase that is localized to thousands of mammalian genes. Though important to human disease and as a drug target, how PRC2 is recruited remains unclear. One model invokes cis-regulatory RNA. Herein, we biochemically and functionally probe PRC2's recognition of RNA using the X-inactivation model. We observe surprisingly high discriminatory capabilities. While SUZ12 and JARID2 subunits can bind RNA, EZH2 has highest affinity and is somewhat promiscuous. EED regulates the affinity of EZH2 for RNA, lending greater specificity to PRC2-RNA interactions. Intriguingly, while RNA is crucial for targeting, RNA inhibits EZH2's catalytic activity. JARID2 weakens PRC2's binding to RNA and relieves catalytic inhibition. We propose that RNA guides PRC2 to its target but inhibits its enzymatic activity until PRC2 associates with JARID2 on chromatin. Our study provides a molecular view of regulatory interactions between RNA and PRC2 at the chromatin interface.

| S-EPMC4107928 | biostudies-literature

Combinatorial interactions are required for the efficient recruitment of pho repressive complex (PhoRC) to polycomb response elements.

Project description:Polycomb Group (PcG) proteins are epigenetic repressors that control metazoan development and cell differentiation. In Drosophila, PcG proteins form five distinct complexes targeted to genes by Polycomb Response Elements (PREs). Of all PcG complexes PhoRC is the only one that contains a sequence-specific DNA binding subunit (PHO or PHOL), which led to a model that places PhoRC at the base of the recruitment hierarchy. Here we demonstrate that in vivo PHO is preferred to PHOL as a subunit of PhoRC and that PHO and PHOL associate with PREs and a subset of transcriptionally active promoters. Although the binding to the promoter sites depends on the quality of recognition sequences, the binding to PREs does not. Instead, the efficient recruitment of PhoRC to PREs requires the SFMBT subunit and crosstalk with Polycomb Repressive Complex 1. We find that human YY1 protein, the ortholog of PHO, binds sites at active promoters in the human genome but does not bind most PcG target genes, presumably because the interactions involved in the targeting to Drosophila PREs are lost in the mammalian lineage. We conclude that the recruitment of PhoRC to PREs is based on combinatorial interactions and propose that such a recruitment strategy is important to attenuate the binding of PcG proteins when the target genes are transcriptionally active. Our findings allow the appropriate placement of PhoRC in the PcG recruitment hierarchy and provide a rationale to explain why YY1 is unlikely to serve as a general recruiter of mammalian Polycomb complexes despite its reported ability to participate in PcG repression in flies.

| S-EPMC4091789 | biostudies-literature

Dynamic Protein Interactions of the Polycomb Repressive Complex 2 during Differentiation of Pluripotent Cells.

Project description:Polycomb proteins assemble to form complexes with important roles in epigenetic regulation. The Polycomb Repressive Complex 2 (PRC2) modulates the di- and tri-methylation of lysine 27 on histone H3, each of which are associated with gene repression. Although three subunits, EZH1/2, SUZ12, and EED, form the catalytic core of PRC2, a wider group of proteins associate with low stoichiometry. This raises the question of whether dynamic variation of the PRC2 interactome results in alternative forms of the complex during differentiation. Here we compared the physical interactions of PRC2 in undifferentiated and differentiated states of NTERA2 pluripotent embryonic carcinoma cells. Label-free quantitative proteomics was used to assess endogenous immunoprecipitation of the EZH2 and SUZ12 subunits of PRC2. A high stringency data set reflecting the endogenous state of PRC2 was produced that included all previously reported core and associated PRC2 components, and several novel interacting proteins. Comparison of the interactomes obtained in undifferentiated and differentiated cells revealed candidate proteins that were enriched in complexes isolated from one of the two states. For example, SALL4 and ZNF281 associate with PRC2 in pluripotent cells, whereas PCL1 and SMAD3 preferentially associate with PRC2 in differentiating cells. Analysis of the mRNA and protein levels of these factors revealed that their association with PRC2 correlated with their cell state-specific expression. Taken together, we propose that dynamic changes to the PRC2 interactome during differentiation may contribute to directing its activity during cell fate transitions.

| S-EPMC5098042 | biostudies-literature

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