Fig. 2

Unique histone remodeling is associated with a subset of merozoite-expressed genes. A State emissions profile generated by ChromHMM analysis. B Heatmap depicting the frequency of each ChromHMM state in the promoters (1,000 bp region upstream of the gene ATG) of all genes (n = 5,602) in early schizonts (SZ, 40 hpi), merozoites (MZ), and early rings (R, 4 hpi). C H3K27ac, H3K9ac, and H3K4me3 ChIP tracks depicting a region of H3K4me3 depletion upstream of AP2-EXP (PF3D7_1466400) and corresponding ChromHMM states. Black rectangle indicates the region where an H3K4me3 depletion is flanked by enrichment of H3K9ac and H3K27ac in merozoites. At the bottom, the AP2-EXP gene body is indicated by a green box, while the region with the 1 – 5 – 1 ChromHMM state pattern is marked by the blue box (coordinates on chromosome 14: 2,719,800–2,722,200 bp). Data range of ChIP tracks is indicated in brackets on the right. Scale bar depicting 1,000 bp is shown. D Average ChIP/input of H3K27ac, H3K9ac, and H3K4me3 across 66 regions with H3K4me3 depletion flanked by enrichment of H3K9ac and H3K27ac. Regions were scaled to the same size by computeMatrix, and the enrichment 1.0 kb upstream and downstream of the regions was also graphed. E Heatmap depicting the frequency of each ChromHMM state in the promoter region (1.000 bp upstream of the gene ATG) of schizont-expressed genes, ring-expressed genes, and genes with H3K4me3 depletion in the upstream intergenic region in early schizonts (S, 40 hpi), merozoites (M), and early rings (R, 4 hpi). F Functions associated with genes with H3K4me3 depletion. Functions were assigned based on information available in PlasmoDB and a review of the literature and can be found in Additional file 2: Table S12. Genes annotated as ‘conserved with unknown function’ (n = 9) in PlasmoDB are not shown in the graph but were included in all analyses. G Heatmap depicting normalized gene expression in protein-coding genes with H3K4me3 depletion (n = 70). Four non-coding genes with H3K4me3 depletion are not plotted because these genes were excluded from the RNA-seq differential gene expression analysis. H Boxplots depicting average gene expression of the genes with H3K4me3 depletion (panel) and a set of randomly selected genes (n = 99). Gene expression differed between time points for the panel of genes with H3K4me3 depletion (Kruskal–Wallis test). P values indicated in the graph are from Dunn’s post hoc tests. **, P < 0.01; ***, P < 0.001; ****, P < 0.0001. I) DNA motif in the H3K4me3 depletion regions. J) DNA motif in the H3K4me3 depletion regions of genes associated with PTEX