DNA polymorphism and epigenetic marks modulate the affinity of a scaffold/matrix attachment region to the nuclear matrix

Eur J Hum Genet. 2014 Sep;22(9):1117-23. doi: 10.1038/ejhg.2013.306. Epub 2014 Jan 22.


Mechanisms that regulate attachment of the scaffold/matrix attachment regions (S/MARs) to the nuclear matrix remain largely unknown. We have studied the effect of simple sequence length polymorphism (SSLP), DNA methylation and chromatin organization in an S/MAR implicated in facioscapulohumeral dystrophy (FSHD), a hereditary disease linked to a partial deletion of the D4Z4 repeat array on chromosome 4q. This FSHD-related nuclear matrix attachment region (FR-MAR) loses its efficiency in myoblasts from FSHD patients. Three criteria were found to be important for high-affinity interaction between the FR-MAR and the nuclear matrix: the presence of a specific SSLP haplotype in chromosomal DNA, the methylation of one specific CpG within the FR-MAR and the absence of histone H3 acetylated on lysine 9 in the relevant chromatin fragment.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Acetylation
  • Adult
  • Base Sequence
  • Cell Line, Tumor
  • Cells, Cultured
  • Chromatin / metabolism
  • CpG Islands
  • DNA Methylation
  • Epigenesis, Genetic*
  • Female
  • Histones / metabolism
  • Humans
  • Male
  • Matrix Attachment Regions / genetics*
  • Microsatellite Repeats / genetics*
  • Middle Aged
  • Molecular Sequence Data
  • Muscular Dystrophy, Facioscapulohumeral / genetics*
  • Myoblasts / metabolism
  • Nuclear Matrix / metabolism*
  • Polymorphism, Genetic*
  • Protein Binding


  • Chromatin
  • Histones