Principles and challenges of genomewide DNA methylation analysis

Nat Rev Genet. 2010 Mar;11(3):191-203. doi: 10.1038/nrg2732.


Methylation of cytosine bases in DNA provides a layer of epigenetic control in many eukaryotes that has important implications for normal biology and disease. Therefore, profiling DNA methylation across the genome is vital to understanding the influence of epigenetics. There has been a revolution in DNA methylation analysis technology over the past decade: analyses that previously were restricted to specific loci can now be performed on a genome-scale and entire methylomes can be characterized at single-base-pair resolution. However, there is such a diversity of DNA methylation profiling techniques that it can be challenging to select one. This Review discusses the different approaches and their relative merits and introduces considerations for data analysis.

Publication types

  • Comparative Study
  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Review

MeSH terms

  • Animals
  • Chromatin Immunoprecipitation
  • Computational Biology
  • CpG Islands
  • DNA Methylation / genetics*
  • DNA Restriction Enzymes
  • Epigenesis, Genetic
  • Gene Expression Profiling
  • Genetic Techniques* / statistics & numerical data
  • Genomics
  • Humans
  • Nucleic Acid Amplification Techniques
  • Reproducibility of Results
  • Sequence Analysis, DNA
  • Sulfites


  • Sulfites
  • DNA Restriction Enzymes
  • sodium bisulfite