Epigenomic profiling using microarrays

Biotechniques. 2003 Aug;35(2):346-50, 352-4, 356-7. doi: 10.2144/03352rv01.


Genes occupy only a minor fraction of genomes such as ours; however, histone and nonhistone chromosomal proteins and methylated DNA bases are distributed over both genic and nongenic regions. These widespread "epigenomic" features can be mapped and characterized by alternative applications of the same microarray technologies that have been used for conventional transcriptional profiling. Here we describe diverse microarray-based strategies for profiling patterns of DNA methylation, DNA replication, DNA binding, and chromatin-associated proteins and histone modifications. The rapid progress that is being made in developing and applying epigenomic profiling methods and the increasing availability of microarrays mean that epigenomic profiling is likely to become a standard research tool for understanding chromatin structure and gene expression during development.

Publication types

  • Research Support, Non-U.S. Gov't
  • Review

MeSH terms

  • Animals
  • Chromatin / metabolism
  • DNA Methylation
  • DNA Replication
  • DNA-Binding Proteins / metabolism
  • Epigenesis, Genetic*
  • Gene Expression Profiling*
  • Gene Expression Regulation, Developmental
  • Genome*
  • Histones / chemistry
  • Humans
  • Models, Genetic
  • Oligonucleotide Array Sequence Analysis*


  • Chromatin
  • DNA-Binding Proteins
  • Histones