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

McCann JA, Muro EM, Palmer C, Palidwor G, Porter CJ, Andrade-Navarro MA, Rudnicki MA - BMC Genomics (2007)

Bottom Line: 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.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.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Ottawa Health Research Institute, Regenerative Medicine Program, 501 Smyth Road, Ottawa, Ontario, K1H 8L6, Canada. jennifer_mccann@biomedcom.org

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.

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SNP-array and gene expression DNA microarray data mapped to chromosomal positions. Positions corresponding to the transcripts detected by the Affymetrix HGU133A/B expression microarray are plotted in green if they were detected and black if they were not detected; corresponding genomic positions of the Affymetrix 10 K SNP-Array probes are plotted in red if they hybridized to DNA in the ChIP on SNP-chip experiment (indicating the position of hyperacetylated histone H4), and grey if not. Ambiguous data points are not shown. All 22 autosomes and the X chromosome are represented. The Y chromosome is not considered in the SNP-Array used. Mb: megabases; SNP: Single Nucleotide Polymorphism.
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Figure 1: SNP-array and gene expression DNA microarray data mapped to chromosomal positions. Positions corresponding to the transcripts detected by the Affymetrix HGU133A/B expression microarray are plotted in green if they were detected and black if they were not detected; corresponding genomic positions of the Affymetrix 10 K SNP-Array probes are plotted in red if they hybridized to DNA in the ChIP on SNP-chip experiment (indicating the position of hyperacetylated histone H4), and grey if not. Ambiguous data points are not shown. All 22 autosomes and the X chromosome are represented. The Y chromosome is not considered in the SNP-Array used. Mb: megabases; SNP: Single Nucleotide Polymorphism.

Mentions: We assessed the genomic distribution of hyperacetylated histone H4 by ChIP with an antibody specific to the N-terminal tail of histone H4 acetylated at residues Lys5, Lys8, Lys12, and Lys16. Hybridization of the ChIP products to the Affymetrix 10 K SNP microarray produced reproducible results for 3,914 probes (1,817 hybridized and 2,097 not hybridized) in a sample of human myoblasts, and for 4,897 probes (2,510 hybridized and 2,387 not hybridized) in a sample of human myotubes (see Methods). An overview of the genomic distribution of these results is given in Figure 1.


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

McCann JA, Muro EM, Palmer C, Palidwor G, Porter CJ, Andrade-Navarro MA, Rudnicki MA - BMC Genomics (2007)

SNP-array and gene expression DNA microarray data mapped to chromosomal positions. Positions corresponding to the transcripts detected by the Affymetrix HGU133A/B expression microarray are plotted in green if they were detected and black if they were not detected; corresponding genomic positions of the Affymetrix 10 K SNP-Array probes are plotted in red if they hybridized to DNA in the ChIP on SNP-chip experiment (indicating the position of hyperacetylated histone H4), and grey if not. Ambiguous data points are not shown. All 22 autosomes and the X chromosome are represented. The Y chromosome is not considered in the SNP-Array used. Mb: megabases; SNP: Single Nucleotide Polymorphism.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2194786&req=5

Figure 1: SNP-array and gene expression DNA microarray data mapped to chromosomal positions. Positions corresponding to the transcripts detected by the Affymetrix HGU133A/B expression microarray are plotted in green if they were detected and black if they were not detected; corresponding genomic positions of the Affymetrix 10 K SNP-Array probes are plotted in red if they hybridized to DNA in the ChIP on SNP-chip experiment (indicating the position of hyperacetylated histone H4), and grey if not. Ambiguous data points are not shown. All 22 autosomes and the X chromosome are represented. The Y chromosome is not considered in the SNP-Array used. Mb: megabases; SNP: Single Nucleotide Polymorphism.
Mentions: We assessed the genomic distribution of hyperacetylated histone H4 by ChIP with an antibody specific to the N-terminal tail of histone H4 acetylated at residues Lys5, Lys8, Lys12, and Lys16. Hybridization of the ChIP products to the Affymetrix 10 K SNP microarray produced reproducible results for 3,914 probes (1,817 hybridized and 2,097 not hybridized) in a sample of human myoblasts, and for 4,897 probes (2,510 hybridized and 2,387 not hybridized) in a sample of human myotubes (see Methods). An overview of the genomic distribution of these results is given in Figure 1.

Bottom Line: 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.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.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Ottawa Health Research Institute, Regenerative Medicine Program, 501 Smyth Road, Ottawa, Ontario, K1H 8L6, Canada. jennifer_mccann@biomedcom.org

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.

Show MeSH