Interactions among Polycomb domains are guided by chromosome architecture
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ABSTRACT:
ORGANISM(S): Drosophila melanogaster
PROVIDER: GSE23166 | GEO | 2011/05/09
SECONDARY ACCESSION(S): PRJNA142699
REPOSITORIES: GEO
Similar Datasets
Project description:Polycomb group (PcG) proteins bind and regulate hundreds of genes. Previous evidence has suggested that long-range chromatin interactions may contribute to the regulation of PcG target genes. Here, we adapted the Chromosome Conformation Capture on Chip (4C) assay to systematically map chromosomal interactions in Drosophila melanogaster larval brain tissue. Our results demonstrate that PcG target genes interact extensively with each other in nuclear space. These interactions are highly specific for PcG target genes, because non-target genes with either low or high expression show distinct interactions. Notably, interactions are mostly limited to genes on the same chromosome arm, and we demonstrate that a topological rather than a sequence-based mechanism is responsible for this constraint. Our results demonstrate that many interactions among PcG target genes exist, and that these interactions are guided by overall chromosome architecture. We applied Chromosome Conformation Capture on Chip (4C) to map long-range chromatin interactions among PcDs on a genome-wide scale. Moreover, we implemented a modification of the 4C protocol in which the 4C PCR products are further amplified in a linear fashion using a T7 RNA amplification procedure. Finally, we fluorescently labeled the amplified products with dye and hybridized them to a specially designed microarray, which covers approximately 92% of the non-repetitive fly genome. In this way, we could identify all fragments that are in close contact with a chosen locus with limited material from a single fly tissue (i.e. larval brain).
2011-05-09 | E-GEOD-23166 | biostudies-arrayexpress
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
Project description:Hox genes are essential regulators of embryonic development. They are activated in a temporal sequence following their topological order within their genomic clusters. Subsequently, states of activity are fine-tuned and maintained to translate into domains of progressively overlapping gene products. While the mechanisms underlying such temporal and spatial progressions begin to be understood, many of their aspects remain unclear. We have systematically analyzed the 3D chromatin organization of Hox clusters in vivo, during their activation using high-resolution circular chromosome conformation capture (4C-seq). Initially, Hox clusters are organized as single 3D chromatin compartments decorated with bivalent chromatin marks. Their progressive transcriptional activation is associated with a dynamic bi-modal 3D organization, whereby the genes switch one after the other, from an inactive to an active 3D compartment. These local 3D dynamics occur within a larger constitutive framework of interactions within the surrounding Topological Associated Domains, which confirms previous results that regulation of this process in primarily cluster intrinsic. The local step-wise progression in time can be stopped and memorized at various body levels and hence it may accounts for the various chromatin architectures previously described at different anterior to posterior body levels for the same embryo at a later stage. Circular Chromosome Conformation Capture (4C-seq) samples from mouse ES cells and mouse embryonic samples at different stages of development. Data based on 41 biological samples.
2014-04-28 | E-GEOD-55342 | biostudies-arrayexpress
Project description:We developed a targeted chromosome conformation capture (4C) approach that uses unique molecular identifiers (UMI) to derive high complexity quantitative chromosome contact profiles with controlled signal to noise ratios. We demonstrate that the method improves the sensitivity and specificity for detection of long-range chromosomal interactions, and that it allows the design of interaction screens with predictable statistical power. UMI-4C robustly quantifies contact intensity changes between cell types and conditions, opening the way toward incorporation of long-range interactions in quantitative models of gene regulation.
2016-06-15 | GSE76763 | GEO
Project description:We developed a targeted chromosome conformation capture (4C) approach that uses unique molecular identifiers (UMI) to derive high complexity quantitative chromosome contact profiles with controlled signal to noise ratios. We demonstrate that the method improves the sensitivity and specificity for detection of long-range chromosomal interactions, and that it allows the design of interaction screens with predictable statistical power. UMI-4C robustly quantifies contact intensity changes between cell types and conditions, opening the way toward incorporation of long-range interactions in quantitative models of gene regulation.
2016-09-23 | GSE87209 | GEO
Project description:We developed a targeted chromosome conformation capture (4C) approach that uses unique molecular identifiers (UMI) to derive high complexity quantitative chromosome contact profiles with controlled signal to noise ratios. We demonstrate that the method improves the sensitivity and specificity for detection of long-range chromosomal interactions, and that it allows the design of interaction screens with predictable statistical power. UMI-4C robustly quantifies contact intensity changes between cell types and conditions, opening the way toward incorporation of long-range interactions in quantitative models of gene regulation. We constructed UMI-4C profiles of 13 different genomic loci (viewpoints) in five different cell lines, in order to study the 3D chromatin contact maps of these selected loci. The coordinates for these viewpoints are: G1p1 chrX:48646542; baitG1_3_5kb chrX:48641393; bait_50kb chrX:48595987; bait_165kb chrX:48476525; ANK1 chr8:41654693; hbb_3HS chr11:5221346; hbb_HBB chr11:5248714; hbb_HBBP1_G1 chr11:5266532; HBB_HBE chr11:5292159; HBB_HS2 chr11:5301345; HBB_HS3 chr11:5306690; HBB_HS5 chr11:5313539; HBB_HBD chr11:5256597
2016-06-15 | E-GEOD-76763 | biostudies-arrayexpress
Project description:The spatial organization of DNA in the cell nucleus is an emerging key contributor to genomic function. We have developed 4C technology, or 3C-on-chip, which allows for an unbiased genome-wide search for DNA loci that contact a given locus in the nuclear space. We demonstrate here that active and inactive genes are engaged in many long-range intrachromosomal interactions and can also form interchromosomal contacts. The active b-globin locus in fetal liver contacts mostly transcribed, but not necessarily tissue-specific, loci elsewhere on chromosome 7, while the inactive locus in fetal brain contacts different, transcriptionally silent, loci. A housekeeping gene in a gene dense region on chromosome 8 forms long-range contacts predominantly with other active gene clusters, both in cis and in trans, and many of these intra- and interchromosomal interactions are conserved between the tissues analyzed. Our data demonstrate that chromosomes fold into areas of active chromatin and areas of inactive chromatin and establish 4C technology as a powerful tool to study nuclear architecture. Keywords: 4C technology
2006-09-22 | GSE5891 | GEO
Project description:The ability to correlate chromosome conformation and gene expression gives a great deal of information regarding the strategies used by a cell to properly regulate gene activity. 4C-seq is a relatively new and increasingly popular technology where the set of genomic interactions generated by a single point in the genome can be determined. 4C-seq experiments generate large, complicated datasets and it is imperative that signal is properly distinguished from noise. Currently there are a limited number of methods for analyzing 4C-seq data. Here, we present a new method, fourSig, which, in addition to being simple to use and as precise as current methods, also includes a new feature to prioritize significantly enriched interactions and predict their reproducibility among experimental replicates. Here, we demonstrate the efficacy of fourSig with previously published and novel 4C-seq datasets and show that our significance prioritization correlates with the ability to reproducibly detect interactions amongst replicates. The datasets provided include those generated from allele-specific 4C-Seq with a viewpoint of the TSS for the gene Ibtk on mouse Chromosome 9. FASTQ files, text files containing genomic coordiantes and read counts, and bedGraph formats for UCSC Genome Browser tracks are provided. All sequences were mapped relative to mouse genome build mm9. Sequencing of circular chromosome conformation capture (4C-Seq) was performed at the transcription start site (TSS) for the gene Ibtk for three replicates in F1 hybrid mouse trophoblast stem (TS) cells. Experiment was designed to detect allele specific patterns using SNP differences between the inbred lines mated to produce the TS cells (C57Bl/6 and CAST/EiJ)
2014-02-22 | E-GEOD-50907 | biostudies-arrayexpress
Project description:Hox genes are required for the development of the intestinal caecum, a major organ of species eating plants. We have analysed the transcriptional regulation of Hoxd genes in caecal buds and show that they are controlled by a series of enhancers located in a gene desert telomeric to the HoxD cluster. The start site of two neighboring and opposite long non-coding RNAs, Hotdog and Twin of Hotdog, specifically transcribed in the caecum, contacts the expressed Hoxd genes in the framework of a topological domain, a large domain of interactions, which ensures a robust transcription of these genes during caecum budding. We show that hedgehogs have kept this regulatory potential despite the absence of caecum, suggesting that these enhancers are used in other developmental situations. In this context, we discuss some striking similarities between the caecum and the limb buds, suggesting the implementation of a common budding tool-kit. Chromosome Conformation Capture (4C seq) at the HoxD locus in developing caeca at E13.5
2013-10-23 | E-GEOD-44360 | biostudies-arrayexpress
Project description:Hox genes are required for the development of the intestinal caecum, a major organ of species eating plants. We have analysed the transcriptional regulation of Hoxd genes in caecal buds and show that they are controlled by a series of enhancers located in a gene desert telomeric to the HoxD cluster. The start site of two neighboring and opposite long non-coding RNAs, Hotdog and Twin of Hotdog, specifically transcribed in the caecum, contacts the expressed Hoxd genes in the framework of a topological domain, a large domain of interactions, which ensures a robust transcription of these genes during caecum budding. We show that hedgehogs have kept this regulatory potential despite the absence of caecum, suggesting that these enhancers are used in other developmental situations. In this context, we discuss some striking similarities between the caecum and the limb buds, suggesting the implementation of a common budding tool-kit. Chromosome Conformation Capture-on-chip analysis (4C) at the Hoxd locus in developing caeca at E13.5, Array data were quantile normalized within 4C/input replicate groups and scaled to medial feature intensity of 100 using TAS software (Affymetrix). For each genomic position, a data set was generated consisting of all (PM-MM) pairs mapping within a sliding window of 250 bp.
2013-10-23 | E-GEOD-44357 | biostudies-arrayexpress