Investigation of the Role of SMCHD1 in X-Chromosome Inactivation

Abstract

X-chromosome inactivation (XCI) silences one of the two X chromosomes in female mammals to equalize dosage of X-linked genes between sexes. This process is controlled by the long noncoding Xist RNA, which triggers gene silencing by recruiting various repressive factors to the inactive X chromosome (Xi). During XCI, the Xi also undergoes refolding into a unique 3D architecture. Whereas other chromosomes are folded into an active A compartment and an inactive B compartment, these compartments are lost on the Xi. How the Xi folds into this “compartment-less” structure is unclear. One of the factors enriched on the Xi is structural-maintenance-of-chromosomes hinge domain containing 1 (SMCHD1). SMCHD1 shares similarity with SMC proteins, a protein family critical for chromosome architecture. I therefore tested the hypothesis that SMCHD1 controls the folding of the Xi. In cells lacking SMCHD1, I found that the Xi becomes partitioned into two large compartments. These unique compartments, dubbed as “S1” and “S2” compartments, are distinct from A/B compartments. During XCI, A/B compartments are first remodeled into S1/S2 compartments. SMCHD1 then merges S1/S2 to create the “compartment-less” Xi. Furthermore, in the absence of SMCHD1, S1/S2 compartments persist, coinciding with defective silencing of Xi genes. Thus, the Xi compartments are folded in a stepwise manner, a process critical for gene silencing. To dissect the stepwise folding mechanism, I examined the relationship between S1/S2 compartments and Xist. Intriguingly, partitioning into S1/S2 compartments requires Xist. Furthermore, Xist does so by enriching Polycomb repressive complex 1 (PRC1), a self-associating protein complex, in the S1 compartment. PRC1 then facilitates SMCHD1 recruitment to continue Xi remodeling. Thus, the stepwise folding is mediated by the collaboration between PRC1 and SMCHD1. In humans, heterozygous SMCHD1 mutations are associated with facioscapulohumeral muscular dystrophy type 2 (FSHD2) and Bosma arhinia microphthalmia syndrome (BAMS). However, it is unclear if these mutations affect XCI. I reanalyzed published RNA-seq data and found that X-linked genes are not dysregulated in female FSHD2 and BAMS patients. Thus, disease-associated SMCHD1 mutations do not impair XCI, consistent with the absence of a sex bias in disease incidence or clinical severity in patients with FSHD2 and BAMS.