The Nucleosome Landscape of P. falciparum Reveals Chromatin Architecture and Dynamics of Regulatory Sequences. Plasmodium falciparum

In eukaryotes, the chromatin architecture has a pivotal role in regulating all DNA-related processes. For P. falciparum, the causative agent of human malaria, the nucleosome landscape of the extremely AT-rich intergenic regulatory regions is largely unexplored. With the aid of a highly controlled MNase-seq procedure we reveal how positioning of nucleosomes provides a structural and regulatory framework to the transcriptional unit. We observe strong positioning of nucleosomes around splice sites that could aid co-transcriptional splicing events. In addition, nucleosome depleted regions are apparent hallmarks of transcription start sites (TSSs) and may support pre-initiation complex assembly. Moreover, we reveal nucleosome occupancy dynamics on strong TSSs during intraerythrocytic development, which correlate with gene expression changes and we observe a characteristic nucleosome architecture of functional - but not inert - TGCATGCA DNA motifs. Collectively, these findings highlight the regulatory capacity of the nucleosome landscape of this deadly human pathogen. Overall design: Mnase-seq during the intra-erythrocytic asexual cycle of Plasmodium falciparum var2csa-panned 3D7 parasites for 8 time-points, every 5 hours starting from 5 hours post invasion until 40 hours post-invasion (T5-T40). Cycle length of these parasites is ~43 hours, synchronicity window is ~ 8 hours. T40 has 2 technical replicates (independent digestions; T40A, T40B). Additionally, pellet control sample (T15), histone H4-ChIP control (T40A) and sonicated and amplified genomic DNA. Chromatin was digested using a combined MNase + exonuclease III treatment. Libraries were prepared according to a Plasmodium-optimized library preparation procedure including KAPA polymerase-mediated PCR amplification. Strand-specific RNA-seq for expression quantification during the intra-erythrocytic asexual cycle of Plasmodium falciparum var2csa-panned 3D7 parasites for 8 time-points every 5 hours starting from 5 hours post invasion invasion until 40 hours post-invasion (T5-T40). Cycle length of these parasites is ~43 hours, synchronicity window is ~ 8 hours. These samples are originating from the exact same batch of parasites as are the MNase-Seq libraries. Libraries were prepared according to a Plasmodium-optimized library preparation procedure including KAPA polymerase-mediated PCR amplification.