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TLA: Targeted Locus Amplification interaction libraries from TLA viewpoints in the GFP construct from GFP(CAG) cells.

ABSTRACT: TLA: Targeted Locus Amplification interaction libraries from TLA viewpoints in the GFP construct from GFP(CAG) cells.

PROVIDER: PRJNA623395 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR11490756_1.fastq.gz	Fastqsanger.gz
	SRR11490756_2.fastq.gz	Fastqsanger.gz
	SRR11490757_1.fastq.gz	Fastqsanger.gz
	SRR11490757_2.fastq.gz	Fastqsanger.gz

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TLA: Targeted Locus Amplification interaction libraries from TLA viewpoints in the GFP construct from GFP(CAG) cells.

Project description:We performed Targeted Locus Amplification (TLA) to map the insertion site of a stably integrated, hemizygous ectopic locus that contains CAG repeats (15 or 270 repeats) in clonal populations of HEK293-derived cells (GFP(CAG)15 or GFP(CAG)270).

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4C-seq: Three-dimensional chromatin interactions of FMR1, HTT, DMPK, and GFP viewpoints.

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4C-seq: Three-dimensional chromatin interactions of FMR1, HTT, DMPK, and GFP viewpoints.

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.

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