MBD-isolated Genome Sequencing provides a high-throughput and comprehensive survey of DNA methylation in the human genome

Nucleic Acids Res. 2010 Jan;38(2):391-9. doi: 10.1093/nar/gkp992. Epub 2009 Nov 11.


DNA methylation is an epigenetic modification involved in both normal developmental processes and disease states through the modulation of gene expression and the maintenance of genomic organization. Conventional methods of DNA methylation analysis, such as bisulfite sequencing, methylation sensitive restriction enzyme digestion and array-based detection techniques, have major limitations that impede high-throughput genome-wide analysis. We describe a novel technique, MBD-isolated Genome Sequencing (MiGS), which combines precipitation of methylated DNA by recombinant methyl-CpG binding domain of MBD2 protein and sequencing of the isolated DNA by a massively parallel sequencer. We utilized MiGS to study three isogenic cancer cell lines with varying degrees of DNA methylation. We successfully detected previously known methylated regions in these cells and identified hundreds of novel methylated regions. This technique is highly specific and sensitive and can be applied to any biological settings to identify differentially methylated regions at the genomic scale.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Cell Line, Tumor
  • DNA Methylation*
  • DNA-Binding Proteins / chemistry
  • Gene Silencing
  • Genome, Human*
  • Genomics / methods
  • Humans
  • Protein Structure, Tertiary
  • Sequence Analysis, DNA / methods*


  • DNA-Binding Proteins
  • MBD2 protein