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

ABSTRACT: 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

ORGANISM(S): Drosophila melanogaster

PROVIDER: GSE12749 | GEO | 2009/02/21

SECONDARY ACCESSION(S): PRJNA114155

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 CTCF and CP190 ChIP. 2 biological replicates per experiment. dye-swaps as indicated in sample description.

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

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

Project description:Chromatin insulators and Polycomb group (PcG) complexes control nuclear organization to effect changes in gene expression. In Drosophila, RNA silencing pathways influence long range interactions mediated by PcG proteins and nuclear localization of the gypsy insulator; however, the underlying mechanisms are unknown. Here, we identify a singular requirement for Argonaute2 (AGO2) for the activity of the CCCTC-binding factor (CTCF)/Centrosomal protein 190 (CP190) dependent Fab-8 insulator. AGO2 and CP190 interact physically, and genome wide localization of AGO2 by chromatin immunoprecipitation and sequencing (ChIP-seq) reveals extensive colocalization of AGO2 with insulators and Polycomb Response Elements (PREs) but minimal overlap with regions of endogenous small interfering RNA (endo-siRNA) production. Finally, depletion of either CTCF or CP190 results in loss of AGO2 association with insulators, PREs, and other cis-regulatory regions. Our findings suggest that Dicer-independent recruitment of AGO2 to chromatin by insulator proteins promotes the definition of transcriptional domains throughout the genome. ChIP-seq of AGO2 in two Drosophila cell types (S2 and S3)

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

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

Project description:CTCF and Cp190 proteins are implicated at many insulator elements throughout Drosophila genome. Here we compared Hi-C maps, transcriptomes and binding of multiple insulator proteins in cultured Drosophila cells derived from CTCF-KO, Cp190-KO and control embryos.

2022-07-19 | GSE198760 | GEO

Topological screen identifies hundreds of Cp190 and CTCF dependent Drosophila chromatin insulator elements [ChIP-seq]

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CTCF/CP190 and ISWI dependent regulation of nucleosome occupancy [ChIP-seq]

Project description:H3-ChIP-seq was performed in order to analyze changes in nucleosomal occupancy after depletion of CTCF/P190 and ISWI from Drosophila S2 cells Histone H3 ChIP-seq from Drosophila S2 cells after CTCF/CP190 or ISWI-specific RNAi treatment

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Chromatin immunoprecipitation of Drosophila embryos at NC14 to identify binding sites of Beaf-32, CP190, CTCF, Su(Hw) and GAF insulator proteins

Project description:ChIP-seq against Beaf-32, CP190, CTCF, Su(Hw) and GAF was performed in wild-type embryos collected between 2h10 and 2h40 after egg laying (corresponding to the stage NC14). For each protein, ChIP-seq was done in biological duplicates. Matched input controls were also generated. Sequencing was performed on Illumina NextSeq 500.

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CTCF is required to form regulatory and physical boundaries at limited sites in the Drosophila nervous system [ChIP-seq]

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2021-01-18 | GSE146749 | GEO

CTCF/CP190 and ISWI dependent regulation of nucleosome occupancy [MNase-seq]

Project description:MNase-seq was performed in order to analyze changes in nucleosomal occupancy after depletion of CTCF/P190 and ISWI from Drosophila S2 cells MNase-seq from Drosophila S2 nuclei after CTCF/CP190 or ISWI-specific RNAi treatment

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