PfSnf2L - an epigenetic regulator of just-in-time expression and gametocyte formation [MNase-Seq]

The complex life cycle of the malaria parasite Plasmodium falciparum (Pf) and the accompanying transcriptional variation is only explained in part by stage-specific transcription factors like the ApiAP2 family, as these factors are strongly under-represented in Pf. Global and local changes in chromatin structure during life cycle progression suggest the contribution of epigenetic mechanisms as a critical mechanism for fine-tuning gene regulation during malaria parasite development. Pf chromatin is largely unexplored and is distinct from other eukaryotes in many respects. This is likely to accommodate the highly A/T-rich genome which averages over 90% in non-coding regions, the highest of any known eukaryote. We characterized PF3D7_1104200 (PfSnf2L), an ATPase-containing protein that is related to ISWI-type chromatin remodeling enzymes (CREs). Using a conditional knockout (KO) system, we demonstrate that PfSnf2L is essential for parasite development, globally controls just-in-time transcription regulation, and specifically represses gametocyte-specific gene expression. Characterization of the enzymatic activity in vitro, combined with mapping chromatin organization in vivo revealed that PfSnf2L shapes the promotor architecture of stage-specific genes through its nucleosome remodeling activity, thereby influencing gene activation and repression. The unique properties of the Plasmodium Snf2L allowed screening and identification of a specific inhibitor that specifically kills the parasite, phenocopies the loss of correct gene expression timing, and inhibits the formation of gametocytes. Overall design: Comparative nucleosome profiling analysis of MNase-seq data of 3D7 parasites with PfSnf2L-KO induced vs. non induced, for two different induction timepoints.