Drosophila melanogaster
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA94489 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Our proteomics anaylsis in Drosophila embryos revealed alternative forms of PRC2 and several distinct variant PRC1 types which are similar to polycomb complexes in mammals
2022-10-15 | PXD033615 | Pride
Project description:Polycomb group (PcG) proteins are evolutionarily conserved epigenetic regulators that maintain transcriptional states during development and are frequently misregulated in disease. Here, we generated a comprehensive collection of endogenously HA-tagged alleles for the core components of Polycomb Repressive Complex 1 (PRC1) and additional chromatin regulators in Drosophila melanogaster using CRISPR/Cas9-mediated genome engineering. We show that endogenous HA tagging preserves protein expression, chromatin localization, and genome-wide binding profiles, enabling direct comparison using a common, commercially available antibody to analyze distinct PcG subunits. Proteomic analyses recovered known components of canonical and non-canonical PRC1 and PRC2 complexes and identified additional PcG-associated factors. Notably, multiple components of the nuclear pore complex (NPC) were detected as PcG interactors, and genetic analyses confirmed a functional interaction between them. This resource provides a platform for standardized analysis of Polycomb function and chromatin regulation that can readily be extended to other chromatin regulatory complexes and applied across different developmental stages.
2026-08-17 | GSE338848 | GEO
Project description:Polycomb group (PcG) proteins are evolutionarily conserved epigenetic regulators that maintain transcriptional states during development and are frequently misregulated in disease. Here, we generated a comprehensive collection of endogenously HA-tagged alleles for the core components of Polycomb Repressive Complex 1 (PRC1) and additional chromatin regulators in Drosophila melanogaster using CRISPR/Cas9-mediated genome engineering. We show that endogenous HA tagging preserves protein expression, chromatin localization, and genome-wide binding profiles, enabling direct comparison using a common, commercially available antibody to analyze distinct PcG subunits. Proteomic analyses recovered known components of canonical and non-canonical PRC1 and PRC2 complexes and identified additional PcG-associated factors. Notably, multiple components of the nuclear pore complex (NPC) were detected as PcG interactors, and genetic analyses confirmed a functional interaction between them. This resource provides a platform for standardized analysis of Polycomb function and chromatin regulation that can readily be extended to other chromatin regulatory complexes and applied across different developmental stages.
2026-08-17 | GSE338847 | GEO
Project description:Polycomb Repressive Complexes PRC1 and PRC2 play a crucial role in silencing lineage-specific genes during early embryogenesis. To provide new insights in polycomb biology, we profiled the proximal interactome (proxeome) of the catalytic subunits RNF2 (PRC1) and EZH2 (PRC2) in mouse embryonic stem cells (mESCs). This revealed >100 proteins proximal to PRC2 and PRC1, which mainly comprise transcription factors, transcriptional regulators and RNA binding proteins. Interestingly, the EZH2 proxeome included both PRC complexes, while the RNF2 proxeome only identified PRC1 subunits. More than half of the PRC2 proximal proteins are shared with PRC1, revealing the molecular constitution of polycomb chromatin domains. We identified several pluripotency-associated transcription factors, including NANOG, for which we confirmed genomic co-localisation with PRC2. Upon PRC2 disruption, NANOG redistributes to specific sites containing its DNA binding motif. Finally, we compared PRC2 proximal interactomes between naïve mESCs, serum-cultured mESCs and embryoid bodies, altogether providing a comprehensive resource in different cellular contexts that may help to further decipher Polycomb biology.
2025-02-25 | PXD058327 | Pride
Project description:Polycomb Repressive Complexes PRC1 and PRC2 play a crucial role in silencing lineage-specific genes during early embryogenesis. To provide new insights in polycomb biology, we profiled the proximal interactome (proxeome) of the catalytic subunits RNF2 (PRC1) and EZH2 (PRC2) in mouse embryonic stem cells (mESCs). This revealed >100 proteins proximal to PRC2 and PRC1, which mainly comprise transcription factors, transcriptional regulators and RNA binding proteins. Interestingly, the EZH2 proxeome included both PRC complexes, while the RNF2 proxeome only identified PRC1 subunits. More than half of the PRC2 proximal proteins are shared with PRC1, revealing the molecular constitution of polycomb chromatin domains. We identified several pluripotency-associated transcription factors, including NANOG, for which we confirmed genomic co-localisation with PRC2. Upon PRC2 disruption, NANOG redistributes to specific sites containing its DNA binding motif. Finally, we compared PRC2 proximal interactomes between naïve mESCs, serum-cultured mESCs and embryoid bodies, altogether providing a comprehensive resource in different cellular contexts that may help to further decipher Polycomb biology.
2025-02-25 | PXD047569 | Pride
Project description:Polycomb group proteins form two main complexes, PRC2 and PRC1, which generally coregulate their target genes. Here, we show that PRC1 components act as neoplastic tumor suppressors independently of PRC2 function. By mapping the distribution of PRC1 components and the histone H3K27me3 mark, we identify genes that acquire PRC1 and H3K27me3 in larvae, and a much larger set of genes bound by PRC1 in the absence of H3K27me3 in larval tissues. These genes massively outnumber canonical targets and they are preeminently involved in the regulation of cell proliferation, signaling and polarity. Mutation in PRC1 components specifically deregulates this set of genes, whereas canonical targets are derepressed in both PRC1 and PRC2 mutants. In human ES cells, PRC1 components colocalize with H3K27me3 like in Drosophila embryos, whereas they are selectively recruited to a large set of proliferation and signaling-associated genes in differentiated cell types, showing that the redeployment of PRC1 components during development is evolutionarily conserved. Comparative study of Polycomb group proteins and histon marks during development with ChIP-Seq and RNA-Seq data in eye discs and wing discs (L3 stage) in Drosophila
2016-07-18 | E-GEOD-74080 | biostudies-arrayexpress
Project description:Polycomb repressive complexes 1 and 2 (PRC1 and PRC2) are highly conserved epigenetic factors that collaborate at multiple levels to maintain their target genes in a repressed state. However, recent reports suggest that PRC1 binds a subset of active promoters and enhancers devoid of the PRC2-mediated H3K27me3 repressive mark in both Drosophila and mammals. Here, we characterize the 3D epigenome of Drosophila Eye-antennal imaginal discs (EDs) and identify a large set of PRC1-bound promoters and enhancers that show preferential interactions in 3D. These PRC1-centered contacts are generally not pre-formed in embryos and coincide with increased PRC1 binding at the larval stage, a concomitant increase in expression during development and mis-regulation in PRC1 mutants. A detailed analysis of the dachshund locus indicates that PRC1-anchored chromatin loops are not only repressive structures, but might also be required for gene activation. Finally, a meta-analysis of RING1B binding profiles and 3D contacts during mouse neural differentiation suggests that this function might be conserved in mammals. These data suggest that, in addition to its known function in gene silencing, PRC1 binding to enhancers and promoters favors stage-specific 3D contacts to facilitate transcription of key developmental genes.
2020-01-12 | GSE126985 | GEO
Project description:Polycomb group (PcG) mutants were first identified in Drosophila based on their failure to maintain proper Hox gene repression during development. The proteins encoded by the corresponding fly genes mainly assemble into one of two discrete Polycomb Repressive Complexes: PRC1 or PRC2. However, biochemical analyses in mammals have revealed alternative forms of PRC2, and multiple distinct types of non-canonical or variant PRC1. Through a series of proteomic analyses, we identify analogous PRC2 and variant PRC1 complexes in Drosophila, as well as a broader repertoire of interactions implicated in early development. Our data provide strong support for the ancient diversity of PcG complexes, and a framework for future analysis in a longstanding and versatile genetic system.
2022-04-29 | GSE201842 | GEO
Project description:Polycomb Group (PcG) proteins regulate gene expression through changes to chromatin structure and are essential for development. PcG proteins function together with the Trithorax Group (TrxG) proteins, which affect diverse steps in transcription activation. The PcG and TrxG are genetically and functionally antagonistic, and current understanding suggests a balance of their activities can maintain a wide range of transcription states. PcG and TrxG proteins assemble into a series of complexes. How these complexes work together, how PcG complexes are recruited to target genes, and whether other proteins are involved in their regulation of gene expression remain open questions. We carried out tandem affinity purification followed by mass spectrometry (TAP-MS) on two core components of Drosophila Polycomb Repressive Complex 1 (PRC1). Our data reveal a network of interactions among PcG complexes, and extensive co-purification of TrxG complexes with PRC1. We co-purified >50 transcription factors with PRC1 that were not previously linked to the PcG. Finally, we identify novel co-purifying complexes, including HP1c and PCNA handling complexes. Our resource of candidate PRC1 interacting proteins generate new hypotheses for PRC1 function.
2023-04-20 | MSV000091759 | MassIVE
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