Whole genome DNA methylation analysis based on high throughput sequencing technology

Methods. 2010 Nov;52(3):203-12. doi: 10.1016/j.ymeth.2010.04.009. Epub 2010 Apr 27.


There are numerous approaches to decipher a whole genome DNA methylation profile ("methylome"), each varying in cost, throughput and resolution. The gold standard of these methods, whole genome bisulfite-sequencing (BS-seq), involves treatment of DNA with sodium bisulfite combined with subsequent high throughput sequencing. Using BS-seq, we generated a single-base-resolution methylome in human peripheral blood mononuclear cells (in press). This BS-seq map was then used as the reference methylome to compare two alternative sequencing-based methylome assays (performed on the same donor of PBMCs): methylated DNA immunoprecipitation (MeDIP-seq) and methyl-binding protein (MBD-seq). In our analysis, we found that MeDIP-seq and MBD-seq are complementary strategies, with MeDIP-seq more sensitive to highly methylated, high-CpG densities and MDB-seq more sensitive to highly methylated, moderate-CpG densities. Taking into account the size of a mammalian genome and the current expense of sequencing, we feel 3gigabases (Gbp) 45bp paired-end MeDIP-seq or MBD-seq uniquely mapped reads is the minimum requirement and cost-effective strategy for methylome pattern analysis.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Antibodies, Monoclonal / immunology
  • DNA / chemistry
  • DNA / immunology
  • DNA / metabolism
  • DNA Methylation*
  • Genome, Human / genetics*
  • High-Throughput Nucleotide Sequencing / methods*
  • Humans
  • Immunoprecipitation / methods
  • Leukocytes, Mononuclear / chemistry
  • Male
  • Methyl-CpG-Binding Protein 2 / metabolism
  • Oligonucleotide Array Sequence Analysis / methods
  • Sulfites / chemistry


  • Antibodies, Monoclonal
  • Methyl-CpG-Binding Protein 2
  • Sulfites
  • DNA
  • sodium bisulfite