Centromeric non-coding RNAs and antigenic variation gene regulatory elements in Plasmodium falciparum

Many basic biological processes, such as mitosis and gene regulation, have been well-characterized in model eukaryotes, but certain aspects of these mechanisms are very divergent in Plasmodium falciparum, the parasite that causes malaria. Chromatin structure and function is important in both mitosis and gene regulation, and studying how P. falciparum chromatin differs from that of model organisms could prove useful in identifying drug targets as well as in understanding the evolution of these basic cellular functions. In this dissertation, I present the discovery of the RNA component of centromeric chromatin followed by a study of the interaction of DNA gene regulatory elements and their effect on epigenetic gene silencing.;Non-coding RNAs can influence chromosome organization and gene expression by directing specific chromatin modifications to targeted regions of the genome. We examined the role of ncRNAs in the assembly of chromatin at the centromeres of P. falciparum. We show that centromeric regions within the Plasmodium genome contain bi-directional promoter activity driving the expression of short ncRNAs that are localized within the nucleus and that appear to associate with the centromeres themselves, strongly suggesting that they are central characters in epigenetic maintenance and function of centromeric chromatin.;Antigenic variation in the human malaria parasite, Plasmodium falciparum, depends on the epigenetic transcriptional regulation of the var gene family, with gene activation and silencing under strict control. Whether the silencing is set at the level of entire chromosomal regions via heterochromatin spreading or at the level of individual var promoters by a silencing element within each var intron has been debated. Here we consider both possibilities using clonal parasite lines carrying chromosomally integrated transgenes. Our results provide more evidence for the hypothesis that var genes are primarily silenced at the level of an individual gene, rather than by heterochromatin spreading, though both mechanisms are involved in var gene regulation. We also found that an intron is capable of silencing in either direction and that once established, a var promoter/intron pair is stably maintained through many generations, suggesting a possible role in epigenetic memory.