Multiple hierarchies of Polycomb targeting to Drosophila genome (Part2)
Ontology highlight
ABSTRACT:
ORGANISM(S): Drosophila melanogaster
PROVIDER: GSE70744 | GEO | 2016/09/15
SECONDARY ACCESSION(S): PRJNA289468
REPOSITORIES: GEO
Similar Datasets
Project description:PcG proteins are critical epigenetic regulators of development. Here we compared genomic distribution of E(z) protein in cultured Drosophila cells lacking Psc/Su(z)2 proteins to that of the wild type.
2016-09-15 | GSE65566 | GEO
Project description:Polycomb group (PcG) proteins are critical epigenetic regulators of development. Here we compared genomic distribution of Polycomb (Pc) protein in cultured Drosophila cells lacking Su(z)12 protein to that of the wild type.
2016-09-15 | GSE83247 | GEO
Project description:Epigenetic regulation of gene expression, including by Polycomb Group (PcG) proteins, may depend on heritable chromatin states but how these states can be propagated through mitosis is unclear. Using immunofluorescence and biochemical fractionation, we find PcG proteins associated with mitotic chromosomes in Drosophila S2 cells. Genome-wide sequencing of chromatin immunoprecipitations (ChIP-SEQ) from mitotic cells indicates that Posterior Sex Combs (PSC) and Polyhomeotic (PH) are not present at well-characterized PcG targets including Hox genes in mitosis, but do remain at 11% of their interphase sites. 26% of interphase PSC sites overlap with recently described chromatin domain borders (Sexton et al., 2012), which are genomic regions characterized by low levels of long range contacts. PSC and PH are preferentially retained at these sites in mitosis, including borders flanking both Hox gene clusters. We hypothesize that disruption of long range chromatin contacts in mitosis contributes to PcG protein release from most sites, while persistent binding at sites with minimal long range contacts may nucleate re-establishment of PcG binding and chromosome organization after mitosis.
2013-01-04 | GSE38166 | GEO
Project description:Epigenetic regulation of gene expression, including by Polycomb Group (PcG) proteins, may depend on heritable chromatin states but how these states can be propagated through mitosis is unclear. Using immunofluorescence and biochemical fractionation, we find PcG proteins associated with mitotic chromosomes in Drosophila S2 cells. Genome-wide sequencing of chromatin immunoprecipitations (ChIP-SEQ) from mitotic cells indicates that Posterior Sex Combs (PSC) and Polyhomeotic (PH) are not present at well-characterized PcG targets including Hox genes in mitosis, but do remain at 11% of their interphase sites. 26% of interphase PSC sites overlap with recently described chromatin domain borders (Sexton et al., 2012), which are genomic regions characterized by low levels of long range contacts. PSC and PH are preferentially retained at these sites in mitosis, including borders flanking both Hox gene clusters. We hypothesize that disruption of long range chromatin contacts in mitosis contributes to PcG protein release from most sites, while persistent binding at sites with minimal long range contacts may nucleate re-establishment of PcG binding and chromosome organization after mitosis. Drosophila S2 cells were colchicine-treated and stained with anti-H3S10p antibody and FACS sorted to give mitotic samples. In parallel asynchronous Drosophila S2 cell cultures were stained for anti-H3 antibody and FACS sorted to give control samples. Chromatin from each of these sorted populations was immunoprecipitated using biotinylated antibodies against PSC. Two replicates of these samples are included. A stable Drosophila S2 cell line expressing biotin-tagged PH was also FACS sorted as above to give mitotic and control samples, and streptavidin-coated beads were used to pulldown biotinlyated PH. Inputs are included for each sample.
2013-01-04 | E-GEOD-38166 | biostudies-arrayexpress
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:Transcription regulation involves enzyme-mediated changes in chromatin structure. Here, we describe a novel mode of histone crosstalk during gene silencing, in which histone H2A monoubiquitylation is coupled to the removal of histone H3 Lys 36 dimethylation (H3K36me2). This pathway was uncovered through the identification of dRING-associated factors (dRAF), a novel Polycomb group (PcG) silencing complex harboring the histone H2A ubiquitin ligase dRING, PSC and the F-box protein, and demethylase dKDM2. In vivo, dKDM2 shares many transcriptional targets with Polycomb and counteracts the histone methyltransferases TRX and ASH1. Importantly, cellular depletion and in vitro reconstitution assays revealed that dKDM2 not only mediates H3K36me2 demethylation but is also required for efficient H2A ubiquitylation by dRING/PSC. Thus, dRAF removes an active mark from histone H3 and adds a repressive one to H2A. These findings reveal coordinate trans-histone regulation by a PcG complex to mediate gene repression. Microarray analysis of dKDM2, dRING, PC, PH and PSC target genes in Drosophila S2 cells Expression profiles of Drosophila S2 cells RNAi depleted (KD) for dKDM2, dRING, PC, PH or PSC were compared with expression profile of untreated S2 cells (Mock)
2011-12-13 | E-GEOD-34390 | biostudies-arrayexpress
Project description:Transcription regulation involves enzyme-mediated changes in chromatin structure. Here, we describe a novel mode of histone crosstalk during gene silencing, in which histone H2A monoubiquitylation is coupled to the removal of histone H3 Lys 36 dimethylation (H3K36me2). This pathway was uncovered through the identification of dRING-associated factors (dRAF), a novel Polycomb group (PcG) silencing complex harboring the histone H2A ubiquitin ligase dRING, PSC and the F-box protein, and demethylase dKDM2. In vivo, dKDM2 shares many transcriptional targets with Polycomb and counteracts the histone methyltransferases TRX and ASH1. Importantly, cellular depletion and in vitro reconstitution assays revealed that dKDM2 not only mediates H3K36me2 demethylation but is also required for efficient H2A ubiquitylation by dRING/PSC. Thus, dRAF removes an active mark from histone H3 and adds a repressive one to H2A. These findings reveal coordinate trans-histone regulation by a PcG complex to mediate gene repression. Microarray analysis of dKDM2, dRING, PC, PH and PSC target genes in Drosophila S2 cells
2011-12-13 | GSE34390 | GEO
Project description:Polycomb Group (PcG) proteins regulate gene expression by modifying chromatin. A key PcG complex, PRC1, has two activities: a ubiquitin ligase activity for histone H2A, and a chromatin compacting/nucleosome bridging activity that can inhibit transcription and chromatin remodeling. In Drosophila, the Posterior Sex Combs (PSC) subunit of PRC1 is central to both activities. The N-terminal homology region (HR) of PSC partners with dRING to form the ubiquitin ligase, while its intrinsically disordered C-terminal region (PSC-CTR) compacts chromatin, and inhibits chromatin remodeling and transcription in vitro. Both the HR and the PSC-CTR are essential in vivo. To understand how these two activities may be coordinated in PRC1, we used cross-linking mass spectrometry (XL-MS) to analyze the conformations of the PSC-CTR in PRC1 and how they change on binding DNA. XL-MS identifies interactions between the PSC-CTR and the core of PRC1, including the PSC HR. New contacts and overall more compacted PSC-CTR conformations are induced by DNA binding. We used chemical acetylation of accessible lysines for MS-based protein footprinting of the PSC-CTR. Protein footprinting reveals an extended, bipartite candidate DNA/chromatin binding surface. Our data suggest a model in which DNA (or chromatin) follows a long path on the flexible PSC-CTR. Intramolecular interactions of the PSC-CTR detected by XL-MS can bring the high affinity DNA/chromatin binding region close to the core of PRC1 without disrupting the interface between the ubiquitin ligase and the nucleosome. Our approach may be applicable to understanding the global organization of other large IDRs that bind nucleic acids.
2020-05-15 | MSV000085418 | MassIVE
Project description:The Polycomb group (PcG) proteins are fundamental epigenetic regulators that control the repressive state of target genes in multicellular organisms. One of the open questions is defining the mechanisms of PcG recruitment to chromatin. In Drosophila, the crucial role in PcG recruitment is thought to belong to DNA-binding proteins associated with Polycomb response elements (PREs). However, current data suggests that not all PRE-binding factors have been identified. Here, we report the identification of the transcription factor Crooked legs (Crol) as a novel PcG recruiter. Crol is a C2H2-type Zinc Finger protein that directly binds to poly(G)-rich DNA sequences. Mutation of Crol binding sites as well as crol CRISPR/Cas9 knockout diminish the repressive activity of PREs in transgenes. Like other PRE-DNA binding proteins, Crol co-localizes with PcG proteins inside and outside of H2K27me3 domains. Crol knockout impairs the recruitment of the PRC1 subunit Polyhomeotic and the PRE-binding protein Combgap at a subset of sites. The decreased binding of PcG proteins is accompanied by dysregulated transcription of target genes. Overall, our study identified Crol as a new important player in PcG recruitment and epigenetic regulation.
2023-04-19 | GSE202832 | GEO
Project description:The Polycomb group (PcG) proteins are fundamental epigenetic regulators that control the repressive state of target genes in multicellular organisms. One of the open questions is defining the mechanisms of PcG recruitment to chromatin. In Drosophila, the crucial role in PcG recruitment is thought to belong to DNA-binding proteins associated with Polycomb response elements (PREs). However, current data suggests that not all PRE-binding factors have been identified. Here, we report the identification of the transcription factor Crooked legs (Crol) as a novel PcG recruiter. Crol is a C2H2-type Zinc Finger protein that directly binds to poly(G)-rich DNA sequences. Mutation of Crol binding sites as well as crol CRISPR/Cas9 knockout diminish the repressive activity of PREs in transgenes. Like other PRE-DNA binding proteins, Crol co-localizes with PcG proteins inside and outside of H2K27me3 domains. Crol knockout impairs the recruitment of the PRC1 subunit Polyhomeotic and the PRE-binding protein Combgap at a subset of sites. The decreased binding of PcG proteins is accompanied by dysregulated transcription of target genes. Overall, our study identified Crol as a new important player in PcG recruitment and epigenetic regulation.
2023-04-19 | GSE202870 | GEO