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Genome-wide binding of the insulator factors CTCF and CP190

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

OTHER RELATED OMICS DATASETS IN: PRJNA114125PRJNA114155PRJNA114127PRJNA111023

ORGANISM(S): Drosophila melanogaster

PROVIDER: GSE12765 | GEO | 2009/02/20

SECONDARY ACCESSION(S): PRJNA111023

REPOSITORIES: GEO

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Analysis of genome-wide binding of the insulator factors CTCF and CP190

Project description:We identified about 3000 CTCF sites in the genome. In addition to binding to CTCF sites we found CP190 to bind to transcriptional start sites of actively transcribed genes where it inversely correlates with nucleosome occupancy. Keywords: ChIP-chip

2009-02-21 | GSE12749 | GEO

Analysis of genome-wide binding of the insulator factors CTCF and CP190

2010-05-05 | E-GEOD-12749 | biostudies-arrayexpress

Topological screen identifies hundreds of Cp190 and CTCF dependent Drosophila chromatin insulator elements

Project description:This SuperSeries is composed of the SubSeries listed below.

2022-07-19 | GSE198763 | GEO

RNAi-independent role for Argonaute2 in CTCF/CP190 chromatin insulator function.

Project description:A major role of the RNAi pathway in Schizosaccharomyces pombe is to nucleate heterochromatin, but it remains unclear whether this mechanism is conserved. To address this question in Drosophila, we performed genome-wide localization of Argonaute2 (AGO2) by chromatin immunoprecipitation (ChIP)-seq in two different embryonic cell lines and found that AGO2 localizes to euchromatin but not heterochromatin. This localization pattern is further supported by immunofluorescence staining of polytene chromosomes and cell lines, and these studies also indicate that a substantial fraction of AGO2 resides in the nucleus. Intriguingly, AGO2 colocalizes extensively with CTCF/CP190 chromatin insulators but not with genomic regions corresponding to endogenous siRNA production. Moreover, AGO2, but not its catalytic activity or Dicer-2, is required for CTCF/CP190-dependent Fab-8 insulator function. AGO2 interacts physically with CTCF and CP190, and depletion of either CTCF or CP190 results in genome-wide loss of AGO2 chromatin association. Finally, mutation of CTCF, CP190, or AGO2 leads to reduction of chromosomal looping interactions, thereby altering gene expression. We propose that RNAi-independent recruitment of AGO2 to chromatin by insulator proteins promotes the definition of transcriptional domains throughout the genome.

| S-EPMC3165934 | biostudies-literature

Genome-wide binding of posterior HOXA/D transcription factors reveals subgrouping and association with CTCF

Project description:This SuperSeries is composed of the SubSeries listed below.

2016-12-31 | GSE86089 | GEO

CTCF/CP190 and ISWI dependent regulation of nucleosome occupancy

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2014-08-11 | E-GEOD-51600 | biostudies-arrayexpress

The Drosophila insulator proteins CTCF and CP190 link enhancer blocking to body patterning.

Project description:Insulator sequences guide the function of distantly located enhancer elements to the appropriate target genes by blocking inappropriate interactions. In Drosophila, five different insulator binding proteins have been identified, Zw5, BEAF-32, GAGA factor, Su(Hw) and dCTCF. Only dCTCF has a known conserved counterpart in vertebrates. Here we find that the structurally related factors dCTCF and Su(Hw) have distinct binding targets. In contrast, the Su(Hw) interacting factor CP190 largely overlapped with dCTCF binding sites and interacts with dCTCF. Binding of dCTCF to targets requires CP190 in many cases, whereas others are independent of CP190. Analysis of the bithorax complex revealed that six of the borders between the parasegment specific regulatory domains are bound by dCTCF and by CP190 in vivo. dCTCF null mutations affect expression of Abdominal-B, cause pharate lethality and a homeotic phenotype. A short pulse of dCTCF expression during larval development rescues the dCTCF loss of function phenotype. Overall, we demonstrate the importance of dCTCF in fly development and in the regulation of abdominal segmentation.

| S-EPMC2230845 | biostudies-literature

Topological screen identifies hundreds of Cp190- and CTCF-dependent <i>Drosophila</i> chromatin insulator elements.

Project description:Drosophila insulators were the first DNA elements found to regulate gene expression by delimiting chromatin contacts. We still do not know how many of them exist and what impact they have on the Drosophila genome folding. Contrary to vertebrates, there is no evidence that fly insulators block cohesin-mediated chromatin loop extrusion. Therefore, their mechanism of action remains uncertain. To bridge these gaps, we mapped chromatin contacts in Drosophila cells lacking the key insulator proteins CTCF and Cp190. With this approach, we found hundreds of insulator elements. Their study indicates that Drosophila insulators play a minor role in the overall genome folding but affect chromatin contacts locally at many loci. Our observations argue that Cp190 promotes cobinding of other insulator proteins and that the model, where Drosophila insulators block chromatin contacts by forming loops, needs revision. Our insulator catalog provides an important resource to study mechanisms of genome folding.

| S-EPMC9897668 | biostudies-literature

CTCF binding polarity determines chromatin looping

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2015-10-29 | E-GEOD-72720 | biostudies-arrayexpress

The binding sites for the chromatin insulator protein CTCF map to DNA methylation-free domains genome-wide.

Project description:All known vertebrate chromatin insulators interact with the highly conserved, multivalent 11-zinc finger nuclear factor CTCF to demarcate expression domains by blocking enhancer or silencer signals in a position-dependent manner. Recent observations document that the properties of CTCF include reading and propagating the epigenetic state of the differentially methylated H19 imprinting control region. To assess whether these findings may reflect a universal role for CTCF targets, we identified more than 200 new CTCF target sites by generating DNA microarrays of clones derived from chromatin-immunopurified (ChIP) DNA followed by ChIP-on-chip hybridization analysis. Target sites include not only known loci involved in multiple cellular functions, such as metabolism, neurogenesis, growth, apoptosis, and signalling, but potentially also heterochromatic sequences. Using a novel insulator trapping assay, we also show that the majority of these targets manifest insulator functions with a continuous distribution of stringency. As these targets are generally DNA methylation-free as determined by antibodies against 5-methylcytidine and a methyl-binding protein (MBD2), a CTCF-based network correlates with genome-wide epigenetic states.

| S-EPMC509268 | biostudies-literature

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