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

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.

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.

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.

Figure 3

Association between histone H4 hyperacetylation and gene expression in human myoblasts and myotubes. For all pairs of SNP-array probes and gene transcription starts at a given distance range, the plot shows the ratio of hybridizing over non-hybridizing SNP-array probes, for genes detected as transcribed (filled circles), or not transcribed (empty circles). The centre of the graph indicates the start of transcription for a gene with negative distances representing the upstream region and positive distances representing the downstream region. The detection of histone H4 modification is markedly higher in the [-0.3 Mb, +0.3 Mb] distance range of the start of transcription of expressed genes indicating a positive association between histone H4 hyperacetylation and gene expression. Each data point is computed from all pairs of SNP-Array probe to DNA microarray probeset at the given distance range, always more than 100. The data is provided as Supplementary Table S3. HypAcH4: hyperacetylated histone H4; noHypAcH4: non-hyperacetylated histone H4; Mb: megabases.