Combining Chromatin Immunoprecipitation and Oligonucleotide Tiling Arrays (ChIP-Chip) for Functional Genomic Studies

  • Jérôme Eeckhoute
  • Mathieu Lupien
  • Myles Brown
Part of the Methods in Molecular Biology™ book series (MIMB, volume 556)


Central to systems biology are genome-wide technologies and high-throughput experimental approaches. Completion of the sequencing of the human genome as well as those of a number of other higher eukaryotes now allows for the first time the mapping of all of the cis-regulatory regions of genes as well as the details of nucleosome position and modification. One approach to achieving this goal involves chromatin immunoprecipitation combined with DNA oligonucleotide tiling arrays (ChIP-chip). This allows for the identification of genomic regions bound by a given factor, its cistrome, or harboring a given epigenomic modification through hybridization on tiling arrays covering the entire genome or specific regions of interest. This technology offers an unbiased assessment of the potential biological function of any DNA associated factor or epigenomic mark. Through integration of ChIP-chip data with complementary genome-wide approaches including expression profiling, CGH and SNP arrays, novel paradigms of transcriptional regulation and chromatin structure are emerging.

Key words

Chromatin immunoprecipitation tiling arrays ChIP-chip epigenetic epigenomic genomic cistrome 



The authors are indebted to Drs. Jason Carroll and Timothy Geistlinger for advice on the ChIP-chip procedure.


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Copyright information

© Humana Press, a part of Springer Science+Business Media, LLC 2009

Authors and Affiliations

  • Jérôme Eeckhoute
    • 1
  • Mathieu Lupien
    • 1
  • Myles Brown
    • 1
  1. 1.Division of Molecular and Cellular OncologyHarvard Medical School, Dana-Farber Cancer InstituteBostonUSA

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