Fig. 3

H3K4me3 depletion region upstream of genes in P. berghei hepatic merozoites. A Distribution of H3K4me3 and H3K9ac in hepatic merozoites (68–75 hpi) shown as log₂(ChIP/input) across all coding sequences (CDS) in the genome, 1.0 kb upstream, and 0.5 kb downstream of the genes. All genes (n = 5,042) were scaled to the same size by computeMatrix. Enrichment of each mark for individual genes is depicted in the heatmap. Genes are sorted by expression level in hepatic merozoites. B Gene expression (log₁₀FPKM) plotted against H3K4me3 or H3K9ac enrichment (log₂(ChIP/input)) in the promoter region (1,000 bp upstream of the gene ATG). Line of best fit as determined by linear regression analysis is depicted by red line. The 95% confidence interval of the line of best fit is indicated by dashed red lines. C H3K9ac and H3K4me3 ChIP tracks depicting a region of H3K4me3 depletion upstream of PBANKA_0605700. Gene coding sequence is indicated by the green box. The black rectangle indicates the region of H3K4me3 depletion. Scale bar depicting 500 bp is shown. D Average enrichment of H3K9ac and H3K4me3 in hepatic merozoites depicted as log₂(ChIP/input) across 58 regions with H3K4me3 depletion. These regions were scaled to the same size by computeMatrix, and the enrichment 1.0 kb upstream and downstream of the regions is displayed. E Functions associated with genes belonging to the H3K4me3 depletion panel. Functions were assigned based on a literature review and can be found in Additional file 2: Table S19. Genes annotated as ‘conserved with unknown function’ (n = 10) in PlasmoDB are not shown but are included in all analyses. F Heatmap depicting DESeq2 normalized gene expression of H3K4me3 depletion panel genes (n = 64) in 48 hpi hepatic schizonts (48 hpi SZ, n = 2), 54 hpi hepatic schizonts (54 hpi SZ; n = 2), 60 hpi hepatic schizonts (60 hpi SZ; n = 2), hepatic merozoites/DCs (MZ; 69 hpi, n = 2), and erythrocytic early rings (4 hpi, n = 2). G Boxplots depicting the average gene expression of genes with H3K4me3 depletion (Panel, n = 64) and a set of randomly selected genes (Random, n = 147). Gene expression did not differ between time points for the panel of genes with H3K4me3 depletion (Kruskal–Wallis test). H) DNA motif in the H3K4me3 depletion regions