Opposing changes in H2A.Z and acH2A.Z occupancy is a potential mechanism of transcriptional (de)regulation. (A) Line plots of acH2A.Z/H2A.Z changes in LNCaP compared to PrEC. Top 25% up-regulated genes (red line) and top 25% down-regulated genes (blue line), across the promoter region, −2000 bp to +1500 bp highlighted in hatched boxes. “Up”: top up-regulated genes show a gain of acH2A.Z /H2A.Z. “Down”: top down-regulated genes show a loss of acH2A.Z/H2A.Z. (B) Box plots display the significance of change between H2A.Z and acH2A.Z levels. y-axis: distributions of t-statistics (H2A.Z and acH2A.Z) with change in expression. x-axis: “NC” (no change in expression, gray boxes); “Down” (down-regulated genes, blue boxes); “Up” (up-regulated genes, red boxes). The P-values of significance of differences between box plots were obtained with the limma function geneSetTest where (*) means a P-value of <0.05. (C) (Top) Microarray hybridization signals for mRNA expression levels in LNCaP (red) and PrEC (green) of three representative oncogenes from Table 1 (left), and three tumor suppressor genes (TSG) from Table 2 (right). Gray background highlights signals below detection (<5.0). UCSC Genome Browser tracks (bottom) for H2A.Z (green background), acH2A.Z (yellow background), and acH2A.Z/H2A.Z (gray background). Enrichment over input status and differential pattern shown. Pr (green tracks): PrEC; LN (red tracks): LNCaP; LN-Pr (black tracks): LNCaP minus PrEC. TSS for each gene shown as an arrow, genomic coordinates are indicated and CpG islands are depicted by green boxes. The scale of UCSC tracks is represented as the distance in kilobases (kb) upstream of “−” and downstream from “+“ the TSS.
