DNA binding selectivity of MeCP2 due to a requirement for A/T sequences adjacent to methyl-CpG

Mol Cell. 2005 Sep 2;19(5):667-78. doi: 10.1016/j.molcel.2005.07.021.

Abstract

DNA methylation is interpreted by a family of methyl-CpG binding domain (MBD) proteins that repress transcription through recruitment of corepressors that modify chromatin. To compare in vivo binding of MeCP2 and MBD2, we analyzed immunoprecipitated chromatin from primary human cells. Genomic sites occupied by the two MBD proteins were mutually exclusive. As MeCP2 was unable to colonize sites vacated by depletion of MBD2, we tested the hypothesis that methyl-CpG alone is insufficient to direct MeCP2 binding. In vitro selection for MeCP2 bound DNA-enriched fragments containing A/T bases ([A/T] > or = 4) adjacent to methyl-CpG. [A/T] > or = 4 was found to be essential for high-affinity binding at selected sites and at known MeCP2 target regions in the Bdnf and Dlx6 genes. MBD2 binding, however, did not require an A/T run. The unexpected restriction of MeCP2 to a defined subset of methyl-CpG sites will facilitate identification of genomic targets that are relevant to Rett Syndrome.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adenine / chemistry
  • Base Sequence
  • Brain-Derived Neurotrophic Factor / genetics
  • Cell Line
  • Cell Line, Tumor
  • Chromosomal Proteins, Non-Histone / genetics
  • Chromosomal Proteins, Non-Histone / metabolism*
  • CpG Islands / genetics
  • DNA / metabolism*
  • DNA Methylation
  • DNA-Binding Proteins / genetics
  • DNA-Binding Proteins / metabolism*
  • Homeodomain Proteins / genetics
  • Humans
  • Methyl-CpG-Binding Protein 2
  • Mutation
  • Protein Binding
  • Repressor Proteins / genetics
  • Repressor Proteins / metabolism*
  • Thymine / chemistry

Substances

  • Brain-Derived Neurotrophic Factor
  • Chromosomal Proteins, Non-Histone
  • DLX6 protein, human
  • DNA-Binding Proteins
  • Homeodomain Proteins
  • MBD2 protein, human
  • MECP2 protein, human
  • Methyl-CpG-Binding Protein 2
  • Repressor Proteins
  • DNA
  • Adenine
  • Thymine