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.