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Induction of a chromatin boundary in vivo upon insertion of a TAD border (Hi-C)

ABSTRACT: Induction of a chromatin boundary in vivo upon insertion of a TAD border (Hi-C)

PROVIDER: PRJNA701299 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR13681279_1.fastq.gz	Fastqsanger.gz
	SRR13681279_2.fastq.gz	Fastqsanger.gz
	SRR13681280_1.fastq.gz	Fastqsanger.gz
	SRR13681280_2.fastq.gz	Fastqsanger.gz
	SRR13681281_1.fastq.gz	Fastqsanger.gz

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Induction of a chromatin boundary in vivo upon insertion of a TAD border

Project description:Induction of a chromatin boundary in vivo upon insertion of a TAD border

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Induction of a chromatin boundary in vivo upon insertion of a TAD border (TLA)

Project description:Induction of a chromatin boundary in vivo upon insertion of a TAD border (TLA)

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Induction of a chromatin boundary in vivo upon insertion of a TAD border (ChIP-Seq)

Project description:Induction of a chromatin boundary in vivo upon insertion of a TAD border (ChIP-Seq)

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Induction of a chromatin boundary in vivo upon insertion of a TAD border (MinION-nCATS)

Project description:Induction of a chromatin boundary in vivo upon insertion of a TAD border (MinION-nCATS)

| PRJNA701303 | ENA

Induction of a chromatin boundary in vivo upon insertion of a TAD border (4C-Seq)

Project description:Induction of a chromatin boundary in vivo upon insertion of a TAD border (4C-Seq)

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Induction of a chromatin boundary in vivo upon insertion of a TAD border (Hi-C)

Project description:Mammalian genomes are partitioned into sub-megabase to megabase-sized units of preferential interactions called topologically associating domains or TADs, which are likely important for the proper implementation of gene regulatory processes. These domains provide structural scaffolds for distant cis regulatory elements to interact with their target genes within the three-dimensional nuclear space and architectural proteins such as CTCF as well as the cohesin complex participate in the formation of the boundaries between them. However, the importance of the genomic context in providing a given DNA sequence the capacity to act as a boundary element remains to be fully investigated. To address this question, we randomly relocated a topological boundary functionally associated with the mouse HoxD gene cluster and show that it can indeed act similarly outside its initial genomic context. In particular, the relocated DNA segment recruited the required architectural proteins and induced a significant depletion of contacts between genomic regions located across the integration site. The host chromatin landscape was re-organized, with the splitting of the TAD wherein the boundary had integrated. These results provide evidence that topological boundaries can function independently of their site of origin, under physiological conditions during mouse development.

2021-07-05 | GSE166578 | GEO

Induction of a chromatin boundary in vivo upon insertion of a TAD border (TLA)

2021-07-05 | GSE166581 | GEO

A TAD boundary is preserved upon deletion of the CTCF-rich Firre locus [HiC_mESC]

Project description:The binding of the transcriptional regulator CTCF to the genome has been implicated in the formation of topologically associated domains (TADs). However, the general mechanisms of folding the genome into TADs are not fully understood. Here, we tested the effects of deleting a CTCF-rich locus on TAD boundary formation. Using genome-wide chromosome conformation capture (Hi-C), we focus on one TAD boundary on chromosome X harboring ~15 CTCF binding sites, and located at the long non-coding RNA (lncRNA) locus Firre. Specifically, this TAD boundary is invariant across evolution, tissues, and temporal dynamics of X-chromosome inactivation. We demonstrate that neither the deletion of this locus, nor the ectopic insertion of Firre cDNA or its ectopic expression are sufficient to alter TADs in a sex-, or allele-specific manner. In contrast, Firre’s deletion disrupts the chromatin super-loop formation of the inactive X-chromosome. Collectively, our findings suggest that apart from CTCF binding, additional mechanisms can play roles in establishing TAD boundary formation.

2018-02-12 | GSE104814 | GEO

A TAD boundary is preserved upon deletion of the CTCF-rich Firre locus [HiC_MEF]

2018-02-12 | GSE104367 | GEO

A TAD boundary is preserved upon deletion of the CTCF-rich Firre locus

Project description:ABSTRACT The binding of the transcriptional regulator CTCF to the genome has been implicated in the formation of topologically associated domains (TADs). However, the general mechanisms of folding the genome into TADs are not fully understood. Here, we tested the effects of deleting a CTCF-rich locus on TAD boundary formation. Using genome-wide chromosome conformation capture (Hi-C), we focus on one TAD boundary on chromosome X harboring ~15 CTCF binding sites, and located at the long non-coding RNA (lncRNA) locus Firre. Specifically, this TAD boundary is invariant across evolution, tissues, and temporal dynamics of X-chromosome inactivation. We demonstrate that neither the deletion of this locus, nor the ectopic insertion of Firre cDNA or its ectopic expression are sufficient to alter TADs in a sex-, or allele-specific manner. In contrast, Firre’s deletion disrupts the chromatin super-loop formation of the inactive X-chromosome. Collectively, our findings suggest that apart from CTCF binding, additional mechanisms may play roles in establishing TAD boundary formation. This SuperSeries is composed of the SubSeries listed below.

2018-02-12 | GSE98632 | GEO

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