Transcriptional activity and regulation of gene expression during the intraerythrocytic developmental cycle of Plasmodium falciparum

Plasmodium falciparum , the apicomplexan parasite responsible for the most deadly form of malaria, undergoes complex cellular changes during its 48h intraerythrocytic developmental cycle (IDC) in the human host. Microarray studies report that at the steady-state mRNA level, most genes are periodic, peaking once during each progression through the morphological stages and tying differential gene expression to the cellular development of the IDC. Although the common eukaryotic components of gene regulation at the levels of chromatin structure, transcriptional activation and elongation, and RNA stability are encoded in the P. falciparum genome, the interplay between mechanisms that control mRNA expression during the IDC remains poorly understood. This dissertation addresses the role of transcriptional activity in the expression of genes during the IDC. RNA synthesis was examined independently from downstream processes using radiolabeling nuclear run-on. At the level of total transcriptional activity--the composite of the whole transcriptome--parasites of each morphological stage contribute differentially to the transcriptional activity of the population due to both increased numbers of nuclei and variable transcriptional activity per nucleus, suggesting links between cellular development and overall regulation of transcriptional activity. Characterizing differential total transcriptional activity over the IDC allowed quantitative analysis of the absolute transcriptional activities of specific genes from nuclear run-on hybridizations. Subsequent analysis validated the use of comparing transcriptional activity and steady-state RNA levels to deduce changes in RNA stability in P. falciparum and revealed variation in both magnitude and timing of sense-strand transcriptional activity among the genes. Genes PFI1755c and PFB0120w, which interchanged sense- and antisense-strand transcriptional dominance during the IDC, were found to support distinct models of strand-specific transcriptional regulation. Together, these studies provide unique, strand-specific quantitative data on a large set of transcriptionally uncharacterized genes across the IDC and reveal links between the morphological stages, cell cycle, and regulation of transcriptional activity. This work provides a model for analysis of stage-specific phenomena, demonstrates the multifaceted utility of comparing transcriptional activity to steady-state RNA, and revisits the enigma of sense- and antisense-strand regulation in P. falciparum .