Smchd1 in neural stem cells.
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA437965 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR6826380_1.fastq.gz | Fastqsanger.gz | |||
| SRR6826380_2.fastq.gz | Fastqsanger.gz | |||
| SRR6826390_1.fastq.gz | Fastqsanger.gz | |||
| SRR6826390_2.fastq.gz | Fastqsanger.gz | |||
| SRR6826400_1.fastq.gz | Fastqsanger.gz |
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Project description:We sought to examine whether the non-canonical SMC protein Smchd1 plays a role in chromosome conformation. We used in situ Hi-C to analyse chromosome conformation changes upon deletion of the epigenetic regulator Smchd1 in female neural stem cells. In parallel, we analysed nucleosome accessibility using ATAC-seq, gene expression using RNA-seq, chromatin marks H3K27me3 and H3K27ac and Ctcf binding using ChIP-seq. We additionally analysed Smchd1 binding genome-wide using ChIP-seq. Together, we find that deletion of Smchd1 alters chromosome conformation at Smchd1 target genes including the inactive X chromosome, Hox genes and imprinted loc. Smchd1 deletion results in gain in Ctcf binding and activation of enhancers. We propose Smchd1 functions by limiting Ctcf-mediated chromosome looping.
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