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Pathogenicity of genomic duplications is determined by formation of novel chromatin domains (neo-TADs) (4C-seq)

ABSTRACT: Pathogenicity of genomic duplications is determined by formation of novel chromatin domains (neo-TADs) (4C-seq)

PROVIDER: PRJNA312529 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR3178080_1.fastq.gz	Fastqsanger.gz
	SRR3178080_2.fastq.gz	Fastqsanger.gz
	SRR3178090_1.fastq.gz	Fastqsanger.gz
	SRR3178090_2.fastq.gz	Fastqsanger.gz
	SRR3178081_1.fastq.gz	Fastqsanger.gz

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Pathogenicity of genomic duplications is determined by formation of novel chromatin domains (neo-TADs) (4C-seq)

Project description:Genome-scale methods have identified subchromosomal structures so-called topologically associated domains (TADs) that subdivide the genome into discrete regulatory units, establish with their target genes. By re-engineering human duplications at the SOX9 locus in mice combined with 4C-seq and Capture Hi-C experiments, we show that genomic duplications can result in the formation of novel chromatin domains (neo-TADs) and that this process determines their molecular pathology.

2016-10-06 | GSE78067 | GEO

Pathogenicity of genomic duplications is determined by formation of novel chromatin domains (neo-TADs) (RNA-seq)

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Pathogenicity of genomic duplications is determined by formation of novel chromatin domains (neo-TADs) [Hi-C]

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Pathogenicity of genomic duplications is determined by formation of novel chromatin domains (neo-TADs)

Project description:Pathogenicity of genomic duplications is determined by formation of novel chromatin domains (neo-TADs)

| PRJNA312621 | ENA

Pathogenicity of genomic duplications is determined by formation of novel chromatin domains (neo-TADs)

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

2016-10-06 | GSE78109 | GEO

Duplications disrupt chromatin architecture and rewire GPR101-enhancer communication in X-linked acrogigantism [4C]

Project description:X-linked acrogigantism (X-LAG) is the most severe form of pituitary gigantism and is characterized by aggressive growth hormone (GH)-secreting pituitary tumors that occur in early childhood. X-LAG is associated with chromosome Xq26.3 duplications (the X-LAG locus typically includes the VGLL1, CD40LG, ARGHEF6, RBMX, and GPR101 genes) that lead to massive pituitary tumoral expression of GPR101, a novel regulator of GH secretion. In this work, we aimed to unravel the mechanism by which the duplications lead to marked pituitary misexpression of GPR101 alone. Using 4C-seq, we characterized the normal chromatin structure at the X-LAG locus. Using GPR101, RBMX, and VGLL1 viewpoints, we showed that GPR101 is located within a topologically associating domain (TAD) delineated by a tissue-invariant border that separates it from centromeric genes and regulatory sequences. Then, we showed that the duplications in multiple patients led to ectopic interactions that crossed the invariant TAD border, indicating the existence of a similar and consistent mechanism of neo-TAD formation in X-LAG. Rewiring GPR101-enhancer interaction within the new regulatory unit is likely to cause the high levels of aberrant expression of GPR101 in X-LAG pituitary.

2022-02-23 | GSE193112 | GEO

Disruptions of Topological Chromatin Domains Causes Pathogenic Rewiring of Gene-Enhancer Interactions [4C-Seq-human]

Project description:Mammalian genomes are organized into megabase-scale topologically associated domains (TADs) that have been proposed to represent large regulatory units. Here we demonstrate that disruption of TADs can cause rewiring of long-range regulatory architecture and result in pathogenic phenotypes. We show that distinct human limb malformations are caused by deletions, inversions, or duplications altering the structure of the TAD-spanning WNT6/IHH/EPHA4/PAX3 locus. Using CRISPR/Cas genome editing, we generated mice with corresponding rearrangements. Both in mouse limb tissue and patient-derived fibroblasts, disease-relevant structural changes cause ectopic interactions between promoters and non-coding DNA, and a cluster of limb enhancers normally associated with Epha4 is misplaced relative to TAD boundaries and drives ectopic limb expression of another gene in the locus. Our results demonstrate the functional importance of TADs for orchestrating gene expression via genome architecture and indicate criteria for predicting the pathogenicity of human structural variants, particularly in non-coding regions of the human genome. Circular Chromosome Conformation Capture (4C seq) at the WNT6/IHH/EPHA4/PAX3 locus in human adult fibroblasts (HAF) of adult patients and controls

2015-05-08 | E-GEOD-66378 | biostudies-arrayexpress

Disruptions of Topological Chromatin Domains Causes Pathogenic Rewiring of Gene-Enhancer Interactions [4C-Seq-mouse]

Project description:Mammalian genomes are organized into megabase-scale topologically associated domains (TADs) that have been proposed to represent large regulatory units. Here we demonstrate that disruption of TADs can cause rewiring of long-range regulatory architecture and result in pathogenic phenotypes. We show that distinct human limb malformations are caused by deletions, inversions, or duplications altering the structure of the TAD-spanning WNT6/IHH/EPHA4/PAX3 locus. Using CRISPR/Cas genome editing, we generated mice with corresponding rearrangements. Both in mouse limb tissue and patient-derived fibroblasts, disease-relevant structural changes cause ectopic interactions between promoters and non-coding DNA, and a cluster of limb enhancers normally associated with Epha4 is misplaced relative to TAD boundaries and drives ectopic limb expression of another gene in the locus. Our results demonstrate the functional importance of TADs for orchestrating gene expression via genome architecture and indicate criteria for predicting the pathogenicity of human structural variants, particularly in non-coding regions of the human genome. Circular Chromosome Conformation Capture (4C seq) at the Wnt6/Ihh/Epha4/Pax3 locus in developing distal limbs of mutants and WT animals at E11.5

2015-05-08 | E-GEOD-66379 | biostudies-arrayexpress

Mus musculus

Project description:Pathogenicity of genomic duplications is determined by formation of novel chromatin domains (neo-TADs) (RNA-seq)

| PRJNA312623 | ENA

Mus musculus

Project description:Pathogenicity of genomic duplications is determined by formation of novel chromatin domains (neo-TADs) [Hi-C]

| PRJNA312607 | ENA