Snf2L drives Plasmodium just-in-time gene expression and gametocytogenesis

The complex life cycle of the malaria parasite Plasmodium falciparum (Pf) involves the differentiation into multiple distinct forms, requiring a tight and dynamic control of gene expression at each stage. However, the full range of variation cannot solely be explained by stage-specific transcription factors, such as ApiAP2-family members, as they are strongly under-represented in Pf. Huge changes in chromatin structure and epigenetic modifications during life cycle progression suggest a central role of these mechanisms in regulating the transcriptional program for parasite development. Pf chromatin is distinct from other eukaryotes with an extraordinarily high AT-content (>80 %) and highly divergent histones lacking typical DNA packaging properties. In addition, the chromatin remodelers, key in shaping chromatin structure, are not conserved and unexplored in Pf. We identified PfSnf2L (PF3D7_1104200) as ISWI-related ATPase actively repositioning Pf nucleosomes in vitro. Knockout studies demonstrate that PfSnf2L is essential, regulating asexual development and sexual differentiation. It globally controls just-in-time transcription by spatiotemporally determining nucleosome positioning at promoters of stage-specific genes. The unique sequence and functional properties of PfSnf2L allows the identification of an inhibitor that specifically kills Plasmodium falciparum, phenocopies the loss of correct gene expression timing, and inhibits the formation of gametocytes. Two biological replicates (with a single paired no-epitope negative control sample) of chromatin immunoprecipitation followed by sequencing (ChIP-seq) across four asexual blood stage timepoints (Early Ring, Late Ring, Trophozoite, and Schizont) was used to identify the genome-wide binding sites of chromatin-assocaited factor, PfSNF2L (gene ID: PF3D7_1104200), Plasmodium falciparum parasite line with a C-terminal 3xHA tag.