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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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Genomic correlation of histone H4 hyperacetylation and gene expression. (A) For all pairs of SNP-array probes detecting genomic sites separated a given distance range, the plots show (for myoblasts (top) and myotubes (bottom)) the fraction of pairs where both probes are hybridized (left), and both probes are not hybridized (right). For pairs of SNP-probes at distances below 0.3 Mb (full circles) the fraction of those where both detect histone H4 hyperacetylation is significantly above the average for those at larger distances (horizontal discontinuous line). Each data point was computed from all the SNP-probe pairs at the corresponding distance range (more than 500 and 700 for myoblasts and myotubes, respectively). The data is provided as Supplementary Table S1. (B) For all pairs of Affymetrix DNA microarray HGU133A/B probesets detecting transcripts with transcription starts at a given distance range, the plot shows (for myoblasts (top) and myotubes (bottom)) the fraction of pairs where both probesets are hybridized (left), and both probesets are not hybridized (right). Note that the Affymetrix DNA microarray HGU133A/B includes often multiple probesets for the same transcript or for alternative splice variants of the same transcript that start at the same position; these probesets explain the higher than random values for the gene expression plot at near-zero distance. All data points were computed using all the pairs of probesets at the distance range, which were more than 30,000 except for the lowest range point (pairs at less than 2 Kb; 7,093 probeset pairs). The data is provided as Supplementary Table S2. Apart from this sort range effect, which is related to probeset design, no other effect can be observed indicating any correlation of gene expression between proximal genes. HypAcH4: hyperacetylated histone H4; Mb: megabases; exp: expressed genes; no exp: not expressed genes.
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Figure 2: Genomic correlation of histone H4 hyperacetylation and gene expression. (A) For all pairs of SNP-array probes detecting genomic sites separated a given distance range, the plots show (for myoblasts (top) and myotubes (bottom)) the fraction of pairs where both probes are hybridized (left), and both probes are not hybridized (right). For pairs of SNP-probes at distances below 0.3 Mb (full circles) the fraction of those where both detect histone H4 hyperacetylation is significantly above the average for those at larger distances (horizontal discontinuous line). Each data point was computed from all the SNP-probe pairs at the corresponding distance range (more than 500 and 700 for myoblasts and myotubes, respectively). The data is provided as Supplementary Table S1. (B) For all pairs of Affymetrix DNA microarray HGU133A/B probesets detecting transcripts with transcription starts at a given distance range, the plot shows (for myoblasts (top) and myotubes (bottom)) the fraction of pairs where both probesets are hybridized (left), and both probesets are not hybridized (right). Note that the Affymetrix DNA microarray HGU133A/B includes often multiple probesets for the same transcript or for alternative splice variants of the same transcript that start at the same position; these probesets explain the higher than random values for the gene expression plot at near-zero distance. All data points were computed using all the pairs of probesets at the distance range, which were more than 30,000 except for the lowest range point (pairs at less than 2 Kb; 7,093 probeset pairs). The data is provided as Supplementary Table S2. Apart from this sort range effect, which is related to probeset design, no other effect can be observed indicating any correlation of gene expression between proximal genes. HypAcH4: hyperacetylated histone H4; Mb: megabases; exp: expressed genes; no exp: not expressed genes.

Mentions: Analysis of the hybridization reported by SNP-array probes indicates that there is a tendency for probes detecting H4 hyperacetylation to cluster in nearby genomic positions (Figure 2A, Additional file 1). This tendency is significant up to a range of 300 kb meaning that histone H4 hyperacetylation occurs in clusters that can span 300 kb. In contrast, non-hybridized probes do not cluster (Figure 2A). It is unlikely that the clustering effect is due to ChIP'd DNA fragments hybridizing to multiple probes in the SNP-array, since the DNA is digested with XbaI, which cuts once every 4 kb in the human genome, on average.


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)

Genomic correlation of histone H4 hyperacetylation and gene expression. (A) For all pairs of SNP-array probes detecting genomic sites separated a given distance range, the plots show (for myoblasts (top) and myotubes (bottom)) the fraction of pairs where both probes are hybridized (left), and both probes are not hybridized (right). For pairs of SNP-probes at distances below 0.3 Mb (full circles) the fraction of those where both detect histone H4 hyperacetylation is significantly above the average for those at larger distances (horizontal discontinuous line). Each data point was computed from all the SNP-probe pairs at the corresponding distance range (more than 500 and 700 for myoblasts and myotubes, respectively). The data is provided as Supplementary Table S1. (B) For all pairs of Affymetrix DNA microarray HGU133A/B probesets detecting transcripts with transcription starts at a given distance range, the plot shows (for myoblasts (top) and myotubes (bottom)) the fraction of pairs where both probesets are hybridized (left), and both probesets are not hybridized (right). Note that the Affymetrix DNA microarray HGU133A/B includes often multiple probesets for the same transcript or for alternative splice variants of the same transcript that start at the same position; these probesets explain the higher than random values for the gene expression plot at near-zero distance. All data points were computed using all the pairs of probesets at the distance range, which were more than 30,000 except for the lowest range point (pairs at less than 2 Kb; 7,093 probeset pairs). The data is provided as Supplementary Table S2. Apart from this sort range effect, which is related to probeset design, no other effect can be observed indicating any correlation of gene expression between proximal genes. HypAcH4: hyperacetylated histone H4; Mb: megabases; exp: expressed genes; no exp: not expressed genes.
© Copyright Policy - open-access
Related In: Results  -  Collection

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Figure 2: Genomic correlation of histone H4 hyperacetylation and gene expression. (A) For all pairs of SNP-array probes detecting genomic sites separated a given distance range, the plots show (for myoblasts (top) and myotubes (bottom)) the fraction of pairs where both probes are hybridized (left), and both probes are not hybridized (right). For pairs of SNP-probes at distances below 0.3 Mb (full circles) the fraction of those where both detect histone H4 hyperacetylation is significantly above the average for those at larger distances (horizontal discontinuous line). Each data point was computed from all the SNP-probe pairs at the corresponding distance range (more than 500 and 700 for myoblasts and myotubes, respectively). The data is provided as Supplementary Table S1. (B) For all pairs of Affymetrix DNA microarray HGU133A/B probesets detecting transcripts with transcription starts at a given distance range, the plot shows (for myoblasts (top) and myotubes (bottom)) the fraction of pairs where both probesets are hybridized (left), and both probesets are not hybridized (right). Note that the Affymetrix DNA microarray HGU133A/B includes often multiple probesets for the same transcript or for alternative splice variants of the same transcript that start at the same position; these probesets explain the higher than random values for the gene expression plot at near-zero distance. All data points were computed using all the pairs of probesets at the distance range, which were more than 30,000 except for the lowest range point (pairs at less than 2 Kb; 7,093 probeset pairs). The data is provided as Supplementary Table S2. Apart from this sort range effect, which is related to probeset design, no other effect can be observed indicating any correlation of gene expression between proximal genes. HypAcH4: hyperacetylated histone H4; Mb: megabases; exp: expressed genes; no exp: not expressed genes.
Mentions: Analysis of the hybridization reported by SNP-array probes indicates that there is a tendency for probes detecting H4 hyperacetylation to cluster in nearby genomic positions (Figure 2A, Additional file 1). This tendency is significant up to a range of 300 kb meaning that histone H4 hyperacetylation occurs in clusters that can span 300 kb. In contrast, non-hybridized probes do not cluster (Figure 2A). It is unlikely that the clustering effect is due to ChIP'd DNA fragments hybridizing to multiple probes in the SNP-array, since the DNA is digested with XbaI, which cuts once every 4 kb in the human genome, on average.

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