Structural Maintenance of Chromosomes, Hinge Domain containing 1 (Smchd1) is critical for the maintenance of X Chromosome Inactivation (XCI), and transcriptional repression at a subset of autosomal loci. Gain and loss of function mutations in SMCHD1 underlie Bosma arhinia micropthalmia syndrome (BAMS) and Facioscapulohumoral muscular dystrophy 2 (FSHD2), respectively - two distinct developmental disorders. Currently little is known about molecular mechanisms underlying the involvement of Smchd1 in transcriptional repression or disease.
Evidence in the literature suggests that Smchd1 and the non-coding RNA Xist might interact directly. We have previously shown that the hinge domain of Smchd1 binds synthetic oligonucleotides in vitro. I was therefore interested in whether Smchd1 directly associates with endogenous nucleic acids, and whether such interactions could be important for Smchd1's localisation to the chromatin. To this end, I performed PAR-CLIP to determine whether Smchd1 binds endogenous RNAs genome-wide. I find Smchd1-RNA interactions to be non-specific, and are therefore unlikely to act as a targeting mechanism. I also find that while Smchd1 is dependent on Xist for its localisation to the Xi, this is not due to a direct protein-RNA interaction, but rather due to a dependency on the downstream HnrnpK-polycomb pathway.
There is evidence to suggest that Smchd1 may be involved in regulating higher order chromatin organisation. To investigate changes to the chromatin architecture in the absence of Smchd1, I performed in-situ Hi-C and ATAC-seq in Smchd1 wild-type and deleted neural stem cells. For the first time my data have demonstrated a role for Smchd1 in chromatin organisation of the Hox clusters, and the inactive X chromosome. Furthermore, I have identified that in the absence of Smchd1, Hox genes are dysregulated, implicating Smchd1 in Hox gene silencing via a role in chromatin conformation.