Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Chromosome conformation capture on chip (4C) at the Fab7 polycomb response element in the bithorax complex of Drosophila

ABSTRACT: In Drosophila melanogaster, Hox genes are organized in an anterior and a posterior cluster, called Antennapedia complex and bithorax complex, located on the same chromosome arm and separated by 10 Mb of DNA. Both clusters are repressed by Polycomb group (PcG) proteins. Here, we show that genes of the two Hox complexes can interact within PcG bodies in the cell nucleus in tissues where they are corepressed. This colocalization increases during development and depends on PcG proteins. Hox gene contacts are part of a large gene interaction network that includes other PcG target genes. Moreover, they are conserved in the distantly related Drosophila virilis species, and mutations on one of the loci weaken silencing of genes in the other locus, resulting in the exacerbation of homeotic phenotypes in a sensitized genetic background. Thus, the three-dimensional organization of Polycomb target genes in the cell nucleus is an evolutionarily conserved phenomenon that stabilizes the maintenance of epigenetic gene silencing.

ORGANISM(S): Drosophila melanogaster

PROVIDER: GSE23887 | GEO | 2010/12/31

SECONDARY ACCESSION(S): PRJNA130453

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Chromosome conformation capture on chip (4C) at the Fab7 polycomb response element in the bithorax complex of Drosophila

Project description:In Drosophila melanogaster, Hox genes are organized in an anterior and a posterior cluster, called Antennapedia complex and bithorax complex, located on the same chromosome arm and separated by 10 Mb of DNA. Both clusters are repressed by Polycomb group (PcG) proteins. Here, we show that genes of the two Hox complexes can interact within PcG bodies in the cell nucleus in tissues where they are corepressed. This colocalization increases during development and depends on PcG proteins. Hox gene contacts are part of a large gene interaction network that includes other PcG target genes. Moreover, they are conserved in the distantly related Drosophila virilis species, and mutations on one of the loci weaken silencing of genes in the other locus, resulting in the exacerbation of homeotic phenotypes in a sensitized genetic background. Thus, the three-dimensional organization of Polycomb target genes in the cell nucleus is an evolutionarily conserved phenomenon that stabilizes the maintenance of epigenetic gene silencing. Chromosome Conformation Capture on Chip (4C) was used to establish chromosomal interactions involving the Fab7 polycomb response element from the bithorax complex of Drosophila melanogaster. Larval brain and anterior discs from 3rd instar larvae were dissected to produce 2 replicate experiments with wild-type (WT-r1, WT-r2) and Fab-712 (F12-r1, F12-r2) fly lines. The 3C was performed as previously described (Hagege et al., 2007; Miele and Dekker, 2009) with the main differences being the use of DpnII (New England Biolabs), a 4 bp cutter restriction enzyme, and a fixation in 3% para-formaldehyde for 30 min, maximizing sensitivity and resolution of contact detection. The 4C DNA and DpnII digested genomic DNA (Control) samples were hybridized using a tiling array mapping the whole chromosome 3R which includes the antenapedia and bithorax hox clusters.

2010-12-31 | E-GEOD-23887 | biostudies-arrayexpress

Comparative analysis of PRE DNA-binding factors interactomes: purification of Combgap, Zeste, Psq and Adf1 associated proteins

Project description:The Polycomb group (PcG) and Trithorax group (TrxG) proteins are key epigenetic regulators controlling silenced and active states of genes in multicellular organisms, respectively. In Drosophila PcG/TrxG proteins are recruited to chromatin via binding to specialized DNA-elements termed Polycomb Response Elements (PREs). While precise mechanisms of PcG/TrxG proteins recruitment remains unknown, the important role is suggested to belong to sequence specific DNA-binding factors. Here, using affinity purification coupled with high throughput mass spectrometry (IP/MS), we isolated factors associated with Combgap, Psq, Zeste and Adf1 PRE DNA-binding Drosophila proteins. As a control we used unspecific IgG. For affinity purification the nuclear extract from Drosophila S2 cells and polyclonal antibodies against Combgap, Psq, Zeste and Adf1 were used.

2024-05-22 | PXD029459 | Pride

4C-seq analysis of the BX-C in S2 cells and cells expressing wild type or SAM mutant Polyhomeotic

Project description:4C-seq analysis using three viewpoint sequences in the Drosophila Bithorax Complex of Hox genes. 4C contacts were compared among S2 cells and those expressing wild type or SAM mutant Ph.

2015-12-01 | GSE61115 | GEO

Variant Polycomb complexes in Drosophila consistent with ancient functional diversity

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

Identification of new regulators of the three dimensional Polycomb organization by a microscopy-based genome-wide RNAi screen

Project description:Polycomb group (PcG) proteins dynamically define cellular identities through epigenetic repression of key developmental genes. PcG target gene repression can be stabilized through the interaction in the nucleus at PcG foci. Here, we report the results of a high-resolution microscopy genome-wide RNAi screen that identifies 129 genes that regulate the nuclear organization of Pc foci. Candidate genes include PcG components and chromatin factors, as well as many novel protein-modifying enzymes, including components of the SUMOylation pathway. In the absence of SUMO Pc foci coagulate into larger aggregates. Conversely, loss of function of the SUMO peptidase velo disperses Pc foci. Moreover, SUMO and velo colocalize with PcG proteins at PREs and Pc SUMOylation affects its chromatin targeting, suggesting that the dynamic regulation of Pc SUMOylation regulates PcG-mediated silencing by modulating the kinetics of Pc binding to chromatin as well as its ability to form Polycomb foci. ChIP-Seq mapping of Polycomb (PC), SUMO and Velo on Drosophila Melanogaster

2014-04-03 | E-GEOD-55303 | biostudies-arrayexpress

Drosophila Polycomb and Pleiohomeotic genomic binding in 0-16h embryos and L3 larval discs (ChIP-on-chip)

Project description:We have studied the linkage between the binding of Polycomb Group (PcG) proteins and the developmental regulation of gene expression using whole-genome mapping to identify sites bound by the PcG proteins, Polycomb (Pc) and Pleiohomeotic (Pho), in the Drosophila embryo and in a more restricted tissue, the imaginal discs of the third thoracic segment. Our data provide considerable support for the idea that Pho is a general component of the maintenance machinery since the majority of Pc targets are also associated with Pho binding. We find, in general, considerable developmental stability of Pc and Pho binding at target genes and observe that Pc/Pho binding can be associated with both expressed and inactive genes. In particular, at the Hox complexes both active and inactive genes have significant Pc and Pho binding; however, in comparison to inactive genes the active Hox genes show reduced and altered binding profiles. Keywords: ChIP-on-chip, tissue-specific binding

2008-08-01 | GSE11006 | GEO

A Polycomb Repressive Complex 1 proteome from Drosophila cells

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

Polycomb Group proteins are retained at specific sites on chromatin in mitosis

2013-01-04 | GSE38166 | GEO

Polycomb Group proteins are retained at specific sites on chromatin in mitosis

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

The Hox protein Antennapedia orchestrates Drosophila adult flight muscle development

Project description:The Hox protein Antennapedia orchestrates Drosophila adult flight muscle development

| PRJNA1117832 | ENA