Fig. 4
Methylation marks associated with specific genome features. A Log2(ChIP/input) enrichment of H3K27me and H3K18me across the coding region (CDS) of all genes in the genome (n = 5,602) scaled to the same size by computeMatrix. The 1.0 kb region upstream and downstream of the CDS is also depicted. B H3K4me2, H3K27me, and H3K18me ChIP tracks depicting log2(ChIP/input) for a representative chromosome. Regions where histone PTMs have higher enrichment in merozoites than other stages are indicated by black rectangles. Data range of ChIP tracks is indicated in brackets. C H3K4me2 log2(ChIP/input) tracks for early schizonts (40 hpi), merozoites, and early rings (4 hpi) highlighting the internal virulence gene cluster on chromosome 7. Data range for ChIP tracks is indicated in brackets. D H3K4me2 enrichment in merozoites compared to early schizonts (n = 178) shown across the coding sequence (CDS) and 1.0 kb up- and downstream of the gene. Genes were scaled to the same size by computeMatrix. E Types of genes with H3K4me2 enrichment in merozoites compared to early schizonts. Overrepresentation of var, rifin, stevor, exported proteins, and non-coding RNA was tested for statistical significance with Chi-squared test. F) Distribution of H3K27me and H3K18me across chromosome 7 (a representative chromosome). The level of histone marks is shown as counts per gene length (kb) normalized to input values. The two arms of the chromosome are scaled and depicted as the proportion of the distance from centromere with the centromere located at 0 and both telomeres located at 1. Line of best fit as determined by nonlinear regression analysis is indicated by solid blue (schizonts, 40 hpi) and red (merozoites) lines. The 95% confidence interval of the line of best fit is indicated by the outer red or blue lines. G) Immunofluorescence images of H3K18me staining in schizonts and rings. H) Western blots of H3K18me and H3K27me in nuclear fractions of P. falciparum rings (R), trophozoites (T), and schizonts (S). The red triangle indicates the H3K27me band. Total cell lysates of the human (Hs) cell line Expi293F and E. coli cells (Ec) were included as controls