FMR1 epigenetic silencing commonly occurs in undifferentiated fragile X-affected embryonic stem cells

Stem Cell Reports. 2014 Nov 11;3(5):699-706. doi: 10.1016/j.stemcr.2014.09.001. Epub 2014 Oct 3.


Fragile X syndrome (FXS) is the most common heritable form of cognitive impairment. It results from epigenetic silencing of the X-linked FMR1 gene by a CGG expansion in its 5'-untranslated region. Taking advantage of a large set of FXS-affected human embryonic stem cell (HESC) lines and isogenic subclones derived from them, we show that FMR1 hypermethylation commonly occurs in the undifferentiated state (six of nine lines, ranging from 24% to 65%). In addition, we demonstrate that hypermethylation is tightly linked with FMR1 transcriptional inactivation in undifferentiated cells, coincides with loss of H3K4me2 and gain of H3K9me3, and is unrelated to CTCF binding. Taken together, these results demonstrate that FMR1 epigenetic gene silencing takes place in FXS HESCs and clearly highlights the importance of examining multiple cell lines when investigating FXS and most likely other epigenetically regulated diseases.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • 5' Untranslated Regions / genetics
  • Blotting, Western
  • Cell Line
  • DNA Methylation
  • Embryonic Stem Cells / metabolism*
  • Epigenesis, Genetic*
  • Fragile X Mental Retardation Protein / genetics*
  • Fragile X Mental Retardation Protein / metabolism
  • Fragile X Syndrome / genetics*
  • Fragile X Syndrome / pathology
  • Gene Expression
  • Gene Silencing*
  • Histones / metabolism
  • Humans
  • Lysine / metabolism
  • Methylation
  • Octamer Transcription Factor-3 / genetics
  • Reverse Transcriptase Polymerase Chain Reaction
  • SOXB1 Transcription Factors / genetics
  • Sequence Analysis, DNA
  • Trinucleotide Repeat Expansion / genetics
  • X Chromosome Inactivation


  • 5' Untranslated Regions
  • FMR1 protein, human
  • Histones
  • Octamer Transcription Factor-3
  • POU5F1 protein, human
  • SOX2 protein, human
  • SOXB1 Transcription Factors
  • Fragile X Mental Retardation Protein
  • Lysine