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

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

PROVIDER: PRJNA611807 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR11283144_1.fastq.gz	Fastqsanger.gz
	SRR11283144_2.fastq.gz	Fastqsanger.gz
	SRR11283145_1.fastq.gz	Fastqsanger.gz
	SRR11283145_2.fastq.gz	Fastqsanger.gz
	SRR11283146_1.fastq.gz	Fastqsanger.gz

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CTCF is required to form regulatory and physical boundaries at limited sites in the Drosophila nervous system

Project description:CTCF is required to form regulatory and physical boundaries at limited sites in the Drosophila nervous system

| PRJNA611806 | ENA

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

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

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

Project description:CTCF is required to form regulatory and physical boundaries at limited sites in the Drosophila nervous system [Hi-C]

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

2021-01-18 | GSE146750 | GEO

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

Project description:CCCTC-binding factor (CTCF) is a conserved protein able to block communication between regulatory elements and gene promoters in flies and mammals. Here, we studied CTCF function in the Drosophila central nervous system (CNS) in which we find CTCF plays a vital role. RNA-sequencing of CNSs of CTCF[0] mutants that completely lack CTCF identified putative targets that are expressed in altered patterns. We find that CTCF recruits Centrosomal protein 190 kDa (Cp190) to CTCF's binding sites to co-regulate a substantial fraction of common genes that we find are also altered in CNSs of Cp190[KO] mutants carrying a CRISPR/Cas9-mediated deletion of the Cp190 open reading frame.

2021-01-18 | GSE146751 | GEO

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

Project description:CCCTC-binding factor (CTCF) is a conserved protein able to block communication between regulatory elements and gene promoters in flies and mammals. Here, we studied CTCF function in the Drosophila central nervous system (CNS) in which we find CTCF plays a vital role. Chromatin immunoprecipitation (ChIP)-sequencing of CTCF and its partner protein Centrosomal protein 190 kDa (Cp190) in CNSs of wildtype (WT), CTCF[0] mutants completely lacking CTCF and Cp190[KO] mutants with a CRISPR/Cas9-mediated deletion of the Cp190 open reading frame identified CTCF and Cp190 peaks defined as enriched in WT relative to each respective mutant control. These experiments also revealed that CTCF recruits Cp190 to CTCF's binding sites, but Cp190 is dispensable for CTCF binding to most of CTCF's sites.

2021-01-18 | GSE146749 | GEO

CTCF is required to form regulatory and physical boundaries at limited sites in the Drosophila nervous system

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

2021-01-18 | GSE146752 | GEO

Essential role of Cp190 in physical and regulatory boundary formation in Drosophila

Project description:Animal genomes fold into contact domains defined by enhanced internal contact frequencies with debated functions in establishing independent gene regulatory domains. A large fraction of contact domains in mammals are formed by stalling of chromosomal loop-extruding cohesin by CTCF at domain boundaries. 90% of domain boundaries in Drosophila form CTCF-independently, and other proteins were proposed to form chromosomal loops with dual functions of segregating promoters from inappropriate regulatory elements and connecting distal regulatory elements to their correct targets. Here, we genetically ablate the ubiquitous boundary-associated factor Cp190 and assess impacts on genome folding and transcriptional regulation in embryos. Our results reveal that Cp190 is a major factor required for contact domain boundary formation and gene insulation in Drosophila.

2022-05-30 | PXD027795 | Pride

Essential role of Cp190 in physical and regulatory boundary formation in Drosophila [HiC]

Project description:While Drosophila has widespread contact domains, most domain boundaries are formed independently of CTCF by unclear mechanisms. We genetically ablate the ubiquitous boundary-associated factor Cp190 and examine impacts on genome folding and developmental gene regulation in Drosophila embryos. We find that Cp190 is widely required to form fly domain boundaries that are distal from transcribed gene promoters, while promoter proximal boundaries are unaffected by Cp190 loss.

2022-05-12 | GSE180375 | GEO

Essential role of Cp190 in physical and regulatory boundary formation in Drosophila [ChIP-seq]

2022-05-12 | GSE180374 | GEO