SMCHD1 Is Dispensable for Repeat-Induced FMR1 Hypermethylation in Fragile X Pluripotent Stem Cells

Fragile X syndrome (FRAX) is caused by CGG repeat expansion in the FMR1 gene, which triggers aberrant DNA hypermethylation, chromatin condensation, and transcriptional gene silencing. However, the mechanism that underlies this repeat-induced epigenetic defect remains poorly understood. SMCHD1 is a chromatin regulator that promotes de novo DNA methylation and heterochromatin formation at long repetitive elements, including the D4Z4 macrosatellite repeat implicated in facioscapulohumeral muscular dystrophy (FSHD). Given the mechanistic parallels between FSHD and FRAX, we hypothesized that SMCHD1 contributes to repeat-induced FMR1 hypermethylation. To test this, we disrupted SMCHD1 in an XY FRAX human embryonic stem cell (hESC) line carrying a heavily methylated CGG-expanded FMR1 allele. Despite efficient loss of SMCHD1, FMR1 hypermethylation remained unchanged, indicating that SMCHD1 is dispensable for FMR1 gene silencing. We next combined SMCHD1 knockout with CRISPR-mediated CGG repeat contraction to determine whether removal of the pathogenic mutation could restore the aberrant methylation. Nevertheless, FMR1 hypermethylation was preserved in all edited clones. These findings demonstrate that, unlike D4Z4 silencing in FSHD, FMR1 repeat-induced hypermethylation does not depend on SMCHD1 activity. Moreover, correction of the underlying CGG expansion through repeat contraction is insufficient to restore the normal hypomethylated state of the FMR1 locus in pluripotent stem cells.