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Multi-omics profiling of PcG proteins and related factors in Drosophila cell lines (ChIP-Seq)

ABSTRACT: To understand the combinatorial binding of different PcG proteins and their binding dynamics across cell types, we performed multi-omics profiling in three Drosophila cell lines, including S2, Kc167 and/or D17-c3 cells. The profiled data included: 1) RNA-seq; 2) ATAC-seq; 3) ChIP-seq of multiple PcG proteins and other related proteins, including E(z), GAGA, Pc, Pcl, Ph, Psc, Scm, Sfmbt, Pho, Spps; 4) Multiple active and repressive histone modifications, including H3K27ac, H3K27me3, H3Krme2, H3K4me3, H3K36me2, H3K36me3.

ORGANISM(S): Drosophila melanogaster

PROVIDER: GSE245077 | GEO | 2023/11/14

REPOSITORIES: GEO

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Multi-omics profiling of PcG proteins and related factors in Drosophila cell lines (RNA-Seq)

Project description:To understand the combinatorial binding of different PcG proteins and their binding dynamics across cell types, we performed multi-omics profiling in three Drosophila cell lines, including S2, Kc167 and/or D17-c3 cells. The profiled data included: 1) RNA-seq; 2) ATAC-seq; 3) ChIP-seq of multiple PcG proteins and other related proteins, including E(z), GAGA, Pc, Pcl, Ph, Psc, Scm, Sfmbt, Pho, Spps; 4) Multiple active and repressive histone modifications, including H3K27ac, H3K27me3, H3Krme2, H3K4me3, H3K36me2, H3K36me3.

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Multi-omics profiling of PcG proteins and related factors in Drosophila cell lines (ATAC-Seq)

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Global changes of H3K27me3 domains and PcG protein distribution in the absence of the PcG recruiters Spps or Pho

Project description:Polycomb group (PcG) proteins maintain the silenced state of key developmental genes in animals, but how these proteins are recruited to specific regions of the genome is still poorly understood. In Drosophila, PcG proteins are recruited to Polycomb response elements (PREs) that include combinations of sites for sequence specific DNA binding “PcG recruiters,” including Pho, Cg, and Spps. To understand their roles in PcG recruitment, we compared Pho-, Cg-, and Spps-binding sites against H3K27me3 and key PcG proteins by ChIP-seq in wild-type and mutant third instar larvae. H3K27me3 in canonical Polycomb domains is decreased after the reduction of any recruiter. Reduction of Spps and Pho, but not Cg, causes the redistribution of H3K27me3 to heterochromatin. Regions with dramatically depleted H3K27me3 after Spps knockout are usually accompanied by decreased Pho binding, suggesting their cooperative binding. PcG recruiters, the PRC2 component E(z), and the PRC1 components Psc and Ph cobind thousands of active genes outside of H3K27me3 domains. This study demonstrates the importance of distinct PcG recruiters for the establishment of unique Polycomb domains. Different PcG recruiters can act both cooperatively and independently at specific PcG target genes, highlighting the complexity and diversity of PcG recruitment mechanisms.

2018-03-07 | GSE102339 | GEO

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 (Fruit Fly)

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Differentiating Drosophila female germ cells initiate Polycomb silencing by regulating PRC2-interacting proteins

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Genomic binding profiling upon expression of AbdA in S2 cells

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Chromatin immunoprecipitation of mouse polycomb group (PcG) proteins in embryonic stem cells

Project description:Polycomb group (PcG) proteins are highly conserved from flies to mammals and many of these factors have essential roles in early embryonic development. PcG proteins comprise two multimeric complexes, the Polycomb Repressive complexes 1 and 2 (PRC1 and 2), which have been shown to repress transcription through epigenetic modification of chromatin structure. To gain insight into the role of Polycomb in early development, we have identified PRC1 and PRC2 target genes in mouse embryonic stem (ES) cells using genome-scale location analysis. We found that PRC2 occupies many genes that encode key regulators of development including those encoding transcription factors and components of signaling pathways. These genes are repressed and contain nucleosomes methylated at lysine 27 on histone H3. The majority of PRC2 bound and methylated target genes are co-occupied by PRC1 indicating that these complexes function at a similar set of genes in ES cells. Lack of PRC1 or PRC2 subunits in ES cells results in derepression of target genes and loss of pluripotency. These results provide insight into how PcG proteins contribute to the maintenance of stem cell identity.

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Context dependent role of Pho binding sites in Polycomb complex recruitment in Drosophila

Project description:Polycomb group (PcG) proteins maintain the silenced state of key developmental genes, but how these proteins are recruited to specific regions of the genome is still not completely understood. In Drosophila, PcG proteins are recruited to Polycomb response elements (PREs) comprised of a flexible array of sites for sequence-specific DNA binding proteins, “PcG recruiters”, including Pho, Spps, Cg, GAF and many others. Pho is thought to play a central role in PcG recruitment. Early data showed that mutation of Pho binding sites in PREs in transgenes abrogated the ability of those PREs to repress gene expression. In contrast, genome-wide experiments in pho mutants or by Pho knockdown showed that PcG proteins can bind to PREs in the absence of Pho. Here we directly addressed the importance of Pho binding sites in two engrailed (en) PREs at the endogenous locus and in transgenes. Our results show that Pho binding sites are required for PRE activity in transgenes with a single PRE. In a transgene, two PREs together lead to stronger, more stable repression and confer some resistance to the loss of Pho binding sites. Making the same mutation in Pho binding sites has little effect on PcG-protein binding at the endogenous en gene. Overall, our data support the model that Pho is important for PcG binding but emphasize how multiple PREs and chromatin environment increase the ability of PREs to function in the absence of Pho.

2023-05-08 | GSE227553 | GEO

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