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Distribution of Drosophila insulator proteins after ecdysone treatment in Kc cells

ABSTRACT: Here we examine changes in the distribution of Drosophila insulator proteins during the ecdysone response. We performed ChIP-seq analysis in Kc cells at 0, 3, and 48 hours of ecdysone treatment with antibodies against CP190, Su(Hw), dCTCF, and BEAF-32B.

ORGANISM(S): Drosophila melanogaster

PROVIDER: GSE30740 | GEO | 2011/10/14

SECONDARY ACCESSION(S): PRJNA154553

REPOSITORIES: GEO

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Distribution of Drosophila insulator proteins after ecdysone treatment in Kc cells

Project description:Here we examine changes in the distribution of Drosophila insulator proteins during the ecdysone response. We performed ChIP-seq analysis in Kc cells at 0, 3, and 48 hours of ecdysone treatment with antibodies against CP190, Su(Hw), dCTCF, and BEAF-32B. Examination of 4 different insulator proteins at 3 time points of ecdysone treatment.

2011-10-13 | E-GEOD-30740 | biostudies-arrayexpress

Genome-wide binding profiles of Drosophila melanogaster insulator proteins in Kc and Mbn2 cells

Project description:ChIP-chip experiments with NimbleGen whole-genome tiling arrays to compare Su(Hw), dCTCF, BEAF, and CP190 localization on DNA in Kc and Mbn2 cells revealed that BEAF is a third subclass of CP190-containing insulators. The DNA binding proteins, Su(Hw), dCTCF, and BEAF show unique distribution patterns with respect to the location and expression level of genes, suggesting diverse roles for these three subclasses of insulators in genome organization. Notably, cell line specific localization sites for all three DNA binding proteins as well as CP190 indicate multiple levels at which insulators can be regulated to affect gene expression. Three replicates of Su(Hw), dCTCF, and CP190 ChIP-chip experiments in both Kc and Mbn2 cells as well as two replicates of BEAF ChIP-chip experiments in both Kc and Mbn2 cells were compared.

2010-05-19 | E-GEOD-15661 | biostudies-arrayexpress

Genome-wide binding profiles of Drosophila melanogaster insulator proteins in Kc and Mbn2 cells

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Distribution of Drosophila insulator proteins during interphase and mitosis

Project description:Here we compare the distribution of insulator proteins during interphase and mitosis. We performed ChIP-seq analysis on purified populations of interphase and mitotic Kc cells, using antibodies against CP190, dCTCF, BEAF, and Su(Hw).

2013-01-21 | GSE32584 | GEO

Distribution of Drosophila insulator proteins during interphase and mitosis

2013-01-21 | E-GEOD-32584 | biostudies-arrayexpress

Genomewide analysis of Insulator protein binding sites in Drosophila embryos at E0-12

Project description:Insulators are DNA sequences that control the interactions among genomic regulatory elements and act as chromatin boundaries. A thorough understanding of their location and function is necessary to address the complexities of metazoan gene regulation. We studied by ChIP-chip the genome-wide binding sites of 6 insulator-associated proteins – dCTCF, CP190, BEAF-32, Su(Hw), Mod(mdg4) and GAF – to obtain the first comprehensive map of insulator elements in Drosophila embryos. We identify over 14,000 putative insulators, including all previously known insulators. We find two major classes of insulators defined by dCTCF/CP190/BEAF-32 and Su(Hw) respectively. Distributional analyses of insulators revealed that particular sub-classes of insulator elements are excluded between cis-regulatory elements and their target promoters, divide differentially expressed, alternative, and divergent promoters, act as chromatin boundaries, are associated with chromosomal breakpoints among species, and are embedded within active chromatin domains. Together, these results provide a map demarcating the boundaries of gene regulatory units, and a framework for understanding insulator function during the development and evolution of Drosophila. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

2009-05-29 | GSE16245 | GEO

Genome-wide binding of two new insulator-like proteins Pita and ZIPIC

Project description:Insulators are multiprotein–DNA complexes that regulate nuclear architecture. The Drosophila CP190 protein is a common cofactor of two main insulator complexes formed by the DNA-binding proteins Su(Hw) and dCTCF. Here, we have identified two new DNA-binding proteins, Pita and ZIPIC, that interact with CP190. In vitro, CP190 interacts with Pita through the BTB domain and with ZIPIC through the centrosomal targeting domain. The artificial binding sites for Pita or ZIPIC partially block enhancers and protect gene expression from PRE-mediated silencing in transgenic lines. Pita binds adjacent to dCTCF in the well-studied Mcp insulator and is required for its activity, which indicates that two insulator proteins can cooperate in organizing a functional insulator. Pita and ZIPIC preferentially bind to the promoter regions and extensively colocalize with dCTCF and BEAF. These results suggest that insulator proteins can fulfill multiple functions in chromosome architecture and gene expression.

2014-10-01 | GSE54337 | GEO

Kc cells from Drosophila melanogaster during ecdysone treatment and CP190 knockdown

Project description:This SuperSeries is composed of the following subset Series: GSE30686: Gene expression analysis of Kc cells from Drosophila melanogaster during ecdysone treatment and CP190 knockdown GSE30740: Distribution of Drosophila insulator proteins after ecdysone treatment in Kc cells Refer to individual Series

2011-10-13 | E-GEOD-30741 | biostudies-arrayexpress

Gene expression analysis of Kc cells from Drosophila melanogaster during ecdysone treatment and CP190 knockdown

Project description:This study examines the changes in genes expression that occur in Drosophila melanogaster during the ecdysone response as well as during RNAi knockdown of the insulator protein, CP190. Analysis was performed in Kc cells after 0, 3, and 48 hours of ecdysone treatment in the presence of either control or CP190 knockdown.

2011-10-14 | GSE30686 | GEO

NURF301 contributes to gypsy chromatin insulator-mediated nuclear organization

Project description:Chromatin insulators are DNA-protein complexes that can prevent the spread of repressive chromatin and block communication between enhancers and promoters to regulate gene expression. In Drosophila, the gypsy chromatin insulator complex consists of three core proteins: CP190, Su(Hw), and Mod(mdg4)67.2. These factors concentrate at nuclear foci termed insulator bodies, and their normal localization is correlated with proper insulator function. Here, we identified NURF301/E(bx), a nucleosome remodeling factor, as a novel regulator of gypsy insulator body localization through a high-throughput RNAi imaging screen. NURF301 promotes gypsy-dependent insulator barrier activity and physically interacts with gypsy insulator proteins. Using ChIP-seq, we found that NURF301 co-localizes with insulator proteins genome-wide, and NURF301 promotes chromatin association of Su(Hw) and CP190 at gypsy insulator binding sites. These effects correlate with NURF301-dependent nucleosome repositioning. At the same time, CP190 and Su(Hw) are also required for recruitment of NURF301 to chromatin. Finally, Oligopaint FISH combined with immunofluorescence revealed that NURF301 promotes 3D contact between insulator bodies and gypsy binding site DNA, and NURF301 is required for proper nuclear positioning of gypsy binding sites. Our data provide new insights into how a nucleosome remodeling factor and insulator proteins cooperatively contribute to nuclear organization.

2022-10-14 | PXD032165 | Pride

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