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Three-dimensional chromatin interactions remain stable upon CAG/CTG repeat expansion

ABSTRACT: Three-dimensional chromatin interactions remain stable upon CAG/CTG repeat expansion

PROVIDER: PRJNA623390 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR11490500.fastq.gz	Fastqsanger.gz
	SRR11490700_1.fastq.gz	Fastqsanger.gz
	SRR11490700_2.fastq.gz	Fastqsanger.gz
	SRR11490501.fastq.gz	Fastqsanger.gz
	SRR11490601_1.fastq.gz	Fastqsanger.gz

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Three-dimensional chromatin interactions remain stable upon CAG/CTG repeat expansion

Project description:Expanded CAG/CTG repeats underlie thirteen neurological disorders, including myotonic dystrophy type 1 (DM1) and Huntington’s disease (HD). Upon expansion, CAG/CTG repeat loci acquire heterochromatic characteristics. This observation raises the hypothesis that repeat expansion provokes changes to higher-order chromatin conformation and thereby affects both gene expression in cis and the genetic instability of the repeat tract. Here we tested this hypothesis directly by performing 4C sequencing at the DMPK and HTT loci from DM1 and HD patient-derived cells. Surprisingly, chromatin contacts remain unchanged upon repeat expansion at both loci. This was true for expanded alleles with different DNA methylation levels and CTCF binding. Repeat tract sizes ranging from 15 to 1,700 repeats displayed strikingly similar chromatin interaction profiles. Moreover, the ectopic insertion of an expanded CAG repeat tract did not change the three-dimensional chromatin conformation of the surrounding genomic region. Our findings argue that extensive changes in heterochromatic properties are not enough to alter chromatin conformation at expanded CAG/CTG repeat loci. We conclude that 3D chromatin conformation is unlikely to drive repeat expansions or changes in gene expression in expanded CAG/CTG repeat disorders. This SuperSeries is composed of the SubSeries listed below.

2020-04-07 | GSE148185 | GEO

Three-dimensional chromatin interactions remain stable upon CAG/CTG repeat expansion.

Project description:Expanded CAG/CTG repeats underlie 13 neurological disorders, including myotonic dystrophy type 1 (DM1) and Huntington's disease (HD). Upon expansion, disease loci acquire heterochromatic characteristics, which may provoke changes to chromatin conformation and thereby affect both gene expression and repeat instability. Here, we tested this hypothesis by performing 4C sequencing at the DMPK and HTT loci from DM1 and HD-derived cells. We find that allele sizes ranging from 15 to 1700 repeats displayed similar chromatin interaction profiles. This was true for both loci and for alleles with different DNA methylation levels and CTCF binding. Moreover, the ectopic insertion of an expanded CAG repeat tract did not change the conformation of the surrounding chromatin. We conclude that CAG/CTG repeat expansions are not enough to alter chromatin conformation in cis. Therefore, it is unlikely that changes in chromatin interactions drive repeat instability or changes in gene expression in these disorders.

| S-EPMC7334000 | biostudies-literature

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Project description:Three-dimensional chromatin interactions remain stable upon CAG/CTG repeat expansion

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