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In vivo dissection of a clustered-CTCF domain boundary reveals developmental principles of regulatory insulation [Capture-C]

ABSTRACT: In vivo dissection of a clustered-CTCF domain boundary reveals developmental principles of regulatory insulation [Capture-C]

PROVIDER: PRJNA716993 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR14062141_1.fastq.gz	Fastqsanger.gz
	SRR14062141_2.fastq.gz	Fastqsanger.gz
	SRR14062142_1.fastq.gz	Fastqsanger.gz
	SRR14062142_2.fastq.gz	Fastqsanger.gz
	SRR14062143_1.fastq.gz	Fastqsanger.gz

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Similar Datasets

In vivo dissection of a clustered-CTCF domain boundary reveals developmental principles of regulatory insulation

Project description:In vivo dissection of a clustered-CTCF domain boundary reveals developmental principles of regulatory insulation

| PRJNA717002 | ENA

In vivo dissection of a clustered-CTCF domain boundary reveals developmental principles of regulatory insulation [ChIPmentation]

Project description:In vivo dissection of a clustered-CTCF domain boundary reveals developmental principles of regulatory insulation [ChIPmentation]

| PRJNA811239 | ENA

In vivo dissection of a clustered-CTCF domain boundary reveals developmental principles of regulatory insulation [ChIP-seq]

Project description:In vivo dissection of a clustered-CTCF domain boundary reveals developmental principles of regulatory insulation [ChIP-seq]

| PRJNA717009 | ENA

In vivo dissection of a clustered-CTCF domain boundary reveals developmental principles of regulatory insulation [ChIPmentation]

Project description:Vertebrate genomes organize into topologically associating domains (TADs), delimited by boundaries that insulate regulatory elements from non-target genes. However, how boundary function is established is not well understood. Here, we combine genome-wide analyses and transgenic mouse assays to dissect the regulatory logic of clustered-CTCF boundaries in vivo, interrogating their function at multiple levels: chromatin interactions, transcription and phenotypes. Individual CTCF binding sites (CBS) deletions revealed that the characteristics of specific sites can outweigh other factors like CBS number and orientation. Combined deletions demonstrated that CBS cooperate redundantly and provide boundary robustness. We show that divergent CBS signatures are not strictly required for effective insulation and that chromatin loops can be formed by non-canonically oriented sites, which suggests a loop interference mechanism. Further, we observe that insulation strength constitutes an effective modulator of gene expression and phenotypes. Our results highlight the modular nature of boundaries and their control over developmental processes.

2022-05-05 | GSE197629 | GEO

In vivo dissection of a clustered-CTCF domain boundary reveals developmental principles of regulatory insulation [ChIP-seq]

2022-05-05 | GSE169558 | GEO

In vivo dissection of a clustered-CTCF domain boundary reveals developmental principles of regulatory insulation [Capture-C]

2022-05-05 | GSE169548 | GEO

In vivo dissection of a clustered-CTCF domain boundary reveals developmental principles of regulatory insulation.

Project description:Vertebrate genomes organize into topologically associating domains, delimited by boundaries that insulate regulatory elements from nontarget genes. However, how boundary function is established is not well understood. Here, we combine genome-wide analyses and transgenic mouse assays to dissect the regulatory logic of clustered-CCCTC-binding factor (CTCF) boundaries in vivo, interrogating their function at multiple levels: chromatin interactions, transcription and phenotypes. Individual CTCF binding site (CBS) deletions revealed that the characteristics of specific sites can outweigh other factors such as CBS number and orientation. Combined deletions demonstrated that CBSs cooperate redundantly and provide boundary robustness. We show that divergent CBS signatures are not strictly required for effective insulation and that chromatin loops formed by nonconvergently oriented sites could be mediated by a loop interference mechanism. Further, we observe that insulation strength constitutes a quantitative modulator of gene expression and phenotypes. Our results highlight the modular nature of boundaries and their control over developmental processes.

| S-EPMC9279147 | biostudies-literature

Dissection of a CTCF topological boundary uncovers principles of enhancer-oncogene regulation

Project description:Dissection of a CTCF topological boundary uncovers principles of enhancer-oncogene regulation

| PRJNA1010760 | ENA

In vivo dissection of a clustered-CTCF domain boundary reveals developmental principles of regulatory insulation

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

2022-05-05 | GSE169561 | 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

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