Fig. 5
H2A.Z and H2B.Z mark active and silent genes. A. Average histone variant profiles at genes that are active or silent in tachyzoites stages based on RNA-seq data [31]. TSS (transcriptional start site) and TTS (transcriptional termination site) denote boundaries of genes, with 2 kb upstream and downstream flanking sequence. Gene boundaries as defined by genome annotation were used if experimental TSS and TTS were not available. ChIP-seq signals were normalized by scaling to library size. B. Genome browser view of H2A.Z, H2B.Z and H3K4me3 at an active (left panel) and a silent (right panel) gene. Peaks called using MACS2 are shown under read density profiles. C. Statistical approach for investigating link between histone variant gene coverage and stage-specific gene expression. Genes marked by histone variant ChIP peaks were split into groups depending on what percentage of the gene (starting at 5’UTR, to 3’UTR) is covered by a peak. Each group of genes was compared to predefined gene sets containing genes that are upregulated in different parasite stages [12, 29] and a measure of enrichment (p-value) was calculated using a hypergeometric distribution test. D. Plots showing -log2(p-value) of enrichment for genes with different amounts of H2A.Z, H2B.Z or H3K4me3 coverage compared to tachyzoite or bradyzoite gene sets. Genes with different levels of H2A.X or H3.3 coverage in tachyzoite or bradyzoites gene sets and significance of enrichment (−log2(p-value)) calculated are shown for comparison. p-value of < 0.05 in the hypergeometric test was considered significant and is indicated by the dotted grey line