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

ABSTRACT: 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.

ORGANISM(S): Drosophila melanogaster

PROVIDER: GSE198761 | GEO | 2022/07/19

REPOSITORIES: GEO

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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.

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

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

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

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

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M1BP cooperates with CP190 to activate transcription at TAD borders and promote chromatin insulator activity

Project description:Genome organization is driven by forces affecting transcriptional state, but the relationship between transcription and genome architecture remains unclear. Here, we identified the Drosophila transcription factor Motif 1 Binding Protein (M1BP) in physical association with the gypsy chromatin insulator core complex, including the universal insulator protein CP190. M1BP is required for enhancer-blocking and barrier activities of the gypsy insulator as well as its proper nuclear localization. Genome-wide, M1BP specifically colocalizes with CP190 at Motif 1-containing promoters, which are enriched at topologically associating domain (TAD) borders. M1BP facilitates CP190 chromatin binding at many shared sites and vice versa. Both factors promote Motif 1-dependent gene expression and transcription near TAD borders genome-wide. Finally, loss of M1BP reduces chromatin accessibility and increases both inter- and intra-TAD local genome compaction. Our results reveal physical and functional interaction between CP190 and M1BP to activate transcription at TAD borders and mediate chromatin insulator-dependent genome organization.

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

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

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M1BP cooperates with CP190 to activate transcription at TAD borders and promote chromatin insulator activity

Project description:In order to identify more gypsy insulator interactors, we performed immunoaffinity purification of Drosophila embryonic nuclear extracts using antibodies specific for CP190 and analyzed the eluates using quantitative mass spectrometry.

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