ATAC-seq in Smchd1 wild-type and Smchd1 deleted neural stem cells.

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. Overall design: n=3 Smchd1del/del vs n=3 Smchd1fl/fl female neural stem cell lines + n=2 Smchd1del/del vs n=2 Smchd1fl/fl male neural stem cell lines, ATAC-seq in all. Comparisons made between del/del and fl/fl for females alone, or females+males together.