Fig. 3

H3K4me3 and H3R17me2 overlap genome-wide and are shifted into gene bodies in gametocytes. A Scatter plots showing the spearman correlation of mean H3K4me3 versus H3R17me2 coverage from two biological replicates in female day 6 gametocytes and ring stage parasites. B mean H3K4me3 or H3R17me2 coverage from two biological replicates in gametocytes versus ring stage parasites, respectively. The genome was divided into 150 bins and the average log₂-transformed ChIP/Input ratio was calculated. R², spearman correlation coefficient. C Piechart showing percentages of peaks intersecting intergenic regions, intragenic regions, or both (overlapping). D Violin plot of peak lengths. Peaks were called by MACS2 in female gametocytes and ring stage parasites. A two-sided student’s t-test showed for H3K4me3 peaks test statistic t = 17.505, degrees of freedom df = 19,404, p-value < 2.2e-16; and for H3R17me2 peaks test statistic t = 6.3903, degrees of freedom df = 17,222, p-value = 1.698e-10. E Profile plots and heatmap of log₂-tranformed ChIP/Input data from 2 kb upstream to 4 kb downstream of every gene centred on the ATG and sorted by gene length. The dashed line shows the STOP site of the respective genes. F Examples of H3K4me3 or H3R17me2 ChIPseq profiles for a selection of loci with differential peaks in female gametocytes and rings. Transcripts detected by RNA-Seq are shown in the bottom line (FPKM). SBP1, skeleton binding protein (ring specific expression), region shown from 65.5 kbp to 72 kbp; Pfs230, 6-cysteine protein P230 (gametocyte specific expression), region shown from 368.4 kbp to 381.16 kbp; AdoMetDC/ODC, S-adenosylmethionine decarboxylase/ornithine decarboxylase (upstream peaks in both stages), region shown from 1.324 Mbp to 1.332 Mbp. Genes are marked by orientation either green (+ genes) or orange (- genes), with introns marked in either light green or dark red. G Average log₂-transformed ChIP/Input coverage plots for H3K4me3 and H3R17me2 in day 6 female gametocytes and ring stage parasites over ookinete specifically expressed genes (defined by [48], available on PlasmoDB), oocyst specific genes (compared to blood stage genes, defined by [74], available on PlasmoDB), and all genes