High-content and super-resolution microscopy reveals the dynamic nuclear architecture and mobile epigenetic marks in Plasmodium falciparum

The malaria-causing parasite Plasmodium falciparum 1s dependent on tightly regulated gene expression for its progression through the intra-erythrocytic life cycle, pathogenesis and establishment of persistent infection by evasion of the human host's immune system. Evidence points towards P. falciparum being unusually dependent on nuclear architecture and genomic organisation for the control of gene expression. Spatially defined nuclear regions of transcriptional activity have been detected and the spatial positioning of loci may determine their transcriptional potential. Additionally, a number of epigenetic markers have been shown to occupy spatially distinct subcompartments of the nuclear volume. Limitations of microscopic assays used until now have left us with a stereotyped and incomplete image of the organisation of the parasite nucleus and the transcriptional and epigenetic factors involved in the regulation of parasite gene expression, and the possible dynamics thereof. This work focused on the use of high-content and super-resolution fluorescent microscopy for the study and graphical representation of the spatial organisation of various nuclear factors involved in transcriptional regulation in P. falciparum parasites. The first objective (chapter 2) establishes P. falciparum parasite sample preparation and fluorescent labeling techniques for microscopy. Immunofluorescent labeling of var gene associated transcription repressive and permissive histone modifications, H3K9me3 and H3K9ac, respectively, as well as serine 2- phosphorylated RNA polymerase II and the putative transcription and splicing factor PfMyb2, was optimised. DNA fluorescent in situ hybridisation was also optimised for labeling of var gene exons. In the second objective (chapter 3), the assays established in the previous chapter are used for high-content combinatorial labeling in thousands of nuclei, followed by analysis using a bespoke computational algorithm for the detection and classification of different labeling patterns. This approach revealed a high level of diversity in the nuclear distributions of each assayed target. Superresolution stochastic optical reconstruction microscopy was used to further study the sub-diffraction organisation of selected labeling patterns. The data presented in this dissertation reveal that the complex spatial organisation of certain nuclear factors is subject to greater diversity within the nucleus of P. falciparum parasites than previously thought.