Comparative Heterochromatin Profiling Reveals Conserved and Unique Epigenome Signatures Linked to Adaptation and Development of Malaria Parasites

Abstract

Heterochromatin-dependent gene silencing is central to the adaptation and survival of Plasmodium falciparum malaria parasites, allowing clonally variant gene expression during blood infection in humans. By assessing genome-wide heterochromatin protein 1 (HP1) occupancy, we present a comprehensive analysis of heterochromatin landscapes across different Plasmodium species, strains, and life cycle stages. Common targets of epigenetic silencing include fast-evolving multi-gene families encoding surface antigens and a small set of conserved HP1-associated genes with regulatory potential. Many P. falciparum heterochromatic genes are marked in a strain-specific manner, increasing the parasite's adaptive capacity. Whereas heterochromatin is strictly maintained during mitotic proliferation of asexual blood stage parasites, substantial heterochromatin reorganization occurs in differentiating gametocytes and appears crucial for the activation of key gametocyte-specific genes and adaptation of erythrocyte remodeling machinery. Collectively, these findings provide a catalog of heterochromatic genes and reveal conserved and specialized features of epigenetic control across the genus Plasmodium.

Keywords: HP1; Plasmodium; antigenic variation; epigenetics; gametocytes; gene silencing; heterochromatin; host-parasite interaction; malaria; sexual differentiation.

Graphical abstract

Figure 1

HP1 Localization and Genome-wide HP1 Occupancy in Six Different Plasmodium Species (A) IFAs showing HP1 localization (green) in P. falciparum (α-PfHP1 antibodies), P. vivax, and P. knowlesi (α-PvHP1 antibodies), and P. chabaudi, P. berghei, and P. yoelii (α-PbHP1 antibodies) trophozoites. Nuclei were stained with DAPI (blue). Scale bars, 2.5 μm. (B) Log₂-transformed ChIP/input ratio tracks from schizont stages of six Plasmodium species. Coding sequences are shown as blue (sense strand) and red (antisense strand) boxes. (C) Relative composition of heterochromatic genes in six Plasmodium species, classified into multi-gene families or groups of “unknown,” “unknown exported,” and “other.” Numbers indicate the total number of high-confidence heterochromatic genes. See also Figures S1–S3; Tables S1 and S2.

Figure 2

Conserved Single-Copy Genes Associated with HP1 in More Than One Species (A) HP1 enrichment values for conserved syntenic orthologs in six Plasmodium species. Asterisks denote high-confidence heterochromatic genes (p > 0.99999). (B) HP1 enrichment tracks over the ap2-g locus in six Plasmodium species. Coding sequences are shown as blue (sense strand) and red (antisense strand) boxes. (C) HP1 enrichment tracks over the cap380 locus in six Plasmodium species. See also Tables S1 and S2.

Figure 3

Genes Differentially Marked by PkHP1 in P. knowlesi Parasites Invading Human or Macaque RBCs (A) HP1 enrichment tracks over the six genes showing >2.5-fold increased HP1 occupancy in P. knowlesi A1-H.1 compared with A1-C.1. Coding sequences are shown as blue (sense strand) and red (antisense strand) boxes. (B) HP1 enrichment tracks over the six genes showing >2.5-fold increased HP1 occupancy in P. knowlesi clone A1-C.1 compared with A1-H.1. See also Table S3.

Figure 4

Strain-Specific Differences in Heterochromatin Organization in P. falciparum Schizonts (A) Log2-transformed ChIP/Input ratio tracks from P. falciparum strains Pf2004, NF135, NF54 and 3D7 schizonts. Chromosome 8 and zoom-ins of its proximal end and the distal end of chromosome 12 are depicted as representative examples. Coding sequences are shown as blue (sense strand) and red (antisense strand) boxes. (B) Heatmap based on k-means clustering of Z-score-transformed ChIP/input ratios calculated for each gene. Clusters containing genes with variable HP1 occupancy are marked in turquoise. Chromosome maps depict the position of variably marked genes (turquoise) in relation to HP1-demaracted heterochromatin (brown tracks; average Z-score-transformed ChIP/input ratios across the strains calculated in 1,000-bp windows). (C) Relative composition of invariably marked heterochromatic genes (clusters 1–4), classified into multi-gene families or groups of “unknown exported” and “other.” (D) Relative composition of variably marked heterochromatic genes (clusters 5–11), classified into multi-gene families and groups of “unknown exported” and “other.” See also Figure S4 and Table S4.

Figure 5

Genome-wide PfHP1 Localization Is Invariable across the IDC (A) Log₂-transformed ChIP/Input ratio tracks from P. falciparum 3D7 ring, trophozoite, and schizont stages. Chromosome 3 is depicted as a representative example. Coding sequences are shown as blue (sense strand) and red (antisense strand) boxes. (B) Pairwise comparisons of PfHP1 coverage of individual genes between the three IDC stages. r, Pearson correlation values. (C) Scatterplots displaying for each gene the maximum transcript level during the IDC (Kensche et al., 2016) (gray dots) in relation to HP1 occupancy in schizonts (green dots). Genes were sorted according to HP1 occupancy. Genes with clonally variant expression (Rovira-Graells et al., 2012) are marked with a red circle. var genes are indicated as blue dots. See also Table S5.

Figure 6

Differences in Heterochromatin Organization between Asexual and Sexual P. falciparum Blood Stage Parasites (A) Log₂-transformed ChIP-seq ChIP/input ratio tracks from P. falciparum Pf2004 schizonts and stage II/III and stage IV/V gametocytes. The proximal end of chromosome 2 is depicted as an example for an expanded heterochromatic domain in gametocytes. Genes involved in knob formation (kahsp40, PF3D7_0201800; pfemp3, PF3D7_0201900; kahrp, PF3D7_0202000) are marked in orange. Early gametocyte markers PF3D7_1476500, PF3D7_1476600, PF3D7_1477300 (pfg14_744/phist), PF3D7_1477400 (phist), PF3D7_1477700 (pfg14_748/phista), and PF3D7_1478000 (gexp17) at the distal end of chromosome 14 have reduced PfHP1 occupancy in gametocytes and are marked in purple. (B) Heatmap based on k-means clustering of Z-score-transformed ChIP/input ratios calculated for each gene. Examples of genes with reduced (cluster 5) or increased (clusters 6–8) HP1 occupancy in gametocytes are highlighted in purple and orange, respectively. Chromosome maps depict the position of genes with reduced (purple) or increased (orange) HP1 occupancy in gametocytes in relation to PfHP1-demarcated heterochromatin (green tracks and blue inverted tracks are Z-score-transformed ChIP/input ratios in schizonts and stage IV/V gametocytes, respectively, calculated in 1,000-bp windows). See also Figure S5 and Table S6.