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Open Access Highly Accessed Methodology article

ChIP on SNP-chip for genome-wide analysis of human histone H4 hyperacetylation

Jennifer A McCann1, Enrique M Muro1, Claire Palmer12, Gareth Palidwor1, Christopher J Porter1, Miguel A Andrade-Navarro1 and Michael A Rudnicki12*

Author Affiliations

1 Ottawa Health Research Institute, Regenerative Medicine Program, 501 Smyth Road, Ottawa, Ontario, K1H 8L6, Canada

2 Faculty of Health Sciences, McMaster University Hamilton, Ontario, L8S 4K1, Canada

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BMC Genomics 2007, 8:322  doi:10.1186/1471-2164-8-322

Published: 14 September 2007

Abstract

Background

SNP microarrays are designed to genotype Single Nucleotide Polymorphisms (SNPs). These microarrays report hybridization of DNA fragments and therefore can be used for the purpose of detecting genomic fragments.

Results

Here, we demonstrate that a SNP microarray can be effectively used in this way to perform chromatin immunoprecipitation (ChIP) on chip as an alternative to tiling microarrays. We illustrate this novel application by mapping whole genome histone H4 hyperacetylation in human myoblasts and myotubes. We detect clusters of hyperacetylated histone H4, often spanning across up to 300 kilobases of genomic sequence. Using complementary genome-wide analyses of gene expression by DNA microarray we demonstrate that these clusters of hyperacetylated histone H4 tend to be associated with expressed genes.

Conclusion

The use of a SNP array for a ChIP-on-chip application (ChIP on SNP-chip) will be of great value to laboratories whose interest is the determination of general rules regarding the relationship of specific chromatin modifications to transcriptional status throughout the genome and to examine the asymmetric modification of chromatin at heterozygous loci.