Role of the Chromosome Architectural Factor SMCHD1 in X-Chromosome Inactivation, Gene Regulation, and Disease in Humans

Genetics. 2019 Oct;213(2):685-703. doi: 10.1534/genetics.119.302600. Epub 2019 Aug 16.


Structural maintenance of chromosomes flexible hinge domain-containing 1 (SMCHD1) is an architectural factor critical for X-chromosome inactivation (XCI) and the repression of select autosomal gene clusters. In mice, homozygous nonsense mutations in Smchd1 cause female-specific embryonic lethality due to an XCI defect. However, although human mutations in SMCHD1 are associated with congenital arhinia and facioscapulohumeral muscular dystrophy type 2 (FSHD2), the diseases do not show a sex-specific bias, despite the essential nature of XCI in humans. To investigate whether there is a dosage imbalance for the sex chromosomes, we here analyze transcriptomic data from arhinia and FSHD2 patient blood and muscle cells. We find that X-linked dosage compensation is maintained in these patients. In mice, SMCHD1 controls not only protocadherin (Pcdh) gene clusters, but also Hox genes critical for craniofacial development. Ablating Smchd1 results in aberrant expression of these genes, coinciding with altered chromatin states and three-dimensional (3D) topological organization. In a subset of FSHD2 and arhinia patients, we also found dysregulation of clustered PCDH, but not HOX genes. Overall, our study demonstrates preservation of XCI in arhinia and FSHD2, and implicates SMCHD1 in the regulation of the 3D organization of select autosomal gene clusters.

Keywords: HOX genes; SMCHD1; X-chromosome inactivation; chromatin; clustered protocadherin genes; epigenetics.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, N.I.H., Intramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Cadherins / genetics
  • Choanal Atresia / genetics*
  • Choanal Atresia / pathology
  • Chromosomal Proteins, Non-Histone / genetics*
  • Codon, Nonsense / genetics
  • Female
  • Genes, Lethal / genetics
  • Humans
  • Mice
  • Microphthalmos / genetics*
  • Microphthalmos / pathology
  • Muscular Dystrophy, Facioscapulohumeral / genetics*
  • Muscular Dystrophy, Facioscapulohumeral / pathology
  • Nose / abnormalities*
  • Nose / pathology
  • Protocadherins
  • Transcriptome / genetics
  • X Chromosome Inactivation / genetics*


  • Cadherins
  • Chromosomal Proteins, Non-Histone
  • Codon, Nonsense
  • PCDH1 protein, human
  • Pcdh1 protein, mouse
  • Protocadherins
  • SMCHD1 protein, human

Supplementary concepts

  • Arhinia, choanal atresia, and microphthalmia