Malaria remains one of the most deadly infectious diseases in the world. To identify new therapeutic strategies, we must gain a comprehensive understanding of how the malaria parasite regulates its complex life cycle. The goal of this proposal is to elucidate the mechanisms that orchestrate chromatin restructuring. More specifically, we explore whether nucleosome positioning, occupancy and turnover direct developmental programs over the course of the parasite infectious cycle. There is growing evidence that the epigenetic state of chromatin plays a role in parasite gene expression and pathogenicity. Whereas histone levels in most eukaryotes remain fairly constant across the cell cycle, we have found a """"""""histone crash"""""""" precisely at the most transcriptionally active stage of the parasite erythrocytic cycle. Accordingly, we hypothesize that the unique manner in which P. falciparum regulates histone turnover and positioning may control the parasite gene expression in a specific manner. Using two complementary methods, we will measure histone-free and histone-bound DNA content across the parasite life cycle. DNA-enriched regions will be analyzed using next generation sequencing technology (Illumina(R)). Results will generate maps of """"""""open"""""""" and """"""""closed"""""""" chromatin regions that will be correlated with steady state mRNA patterns. To determine whether histone post-translational modifications regulate histone turnover, we will use a mass spectrometry approach. Stage-specific histone marks will be validated by ChIP-seq experiments. Further mass spectrometry and functional genomic studies will then be used to determine the chromatin-remodeling complexes that are involved in regulating histone turnover. Using these independent data sets, we seek to explore a connection between histone positioning, histone post-translational modifications and the parasite transcriptome. Revealing the molecular mechanisms that control histone turnover will not only allow us to find new ways to interfere with waves of transcriptional expression but will also transform our perceptions of the molecular mechanisms controlling the parasite transcription at the chromatin level and provide signposts for new anti-malarial therapies.

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The goal of this proposal is to elucidate the mechanisms that orchestrate chromatin restructuring. The proposed research explores whether nucleosome positioning, occupancy and turnover direct developmental programs over the course of the parasite infectious cycle.

National Institute of Health (NIH)
National Institute of Allergy and Infectious Diseases (NIAID)
Research Project (R01)
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Pathogenic Eukaryotes Study Section (PTHE)
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Mcgugan, Glen C
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University of California Riverside
Anatomy/Cell Biology
Schools of Earth Sciences/Natur
United States
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Bunnik, Evelien M; Cook, Kate B; Varoquaux, Nelle et al. (2018) Changes in genome organization of parasite-specific gene families during the Plasmodium transmission stages. Nat Commun 9:1910
Batugedara, Gayani; Le Roch, Karine G (2018) Unraveling the 3D genome of human malaria parasites. Semin Cell Dev Biol :
Batugedara, Gayani; Lu, Xueqing M; Bunnik, Evelien M et al. (2017) The Role of Chromatin Structure in Gene Regulation of the Human Malaria Parasite. Trends Parasitol 33:364-377
Lu, Xueqing Maggie; Batugedara, Gayani; Lee, Michael et al. (2017) Nascent RNA sequencing reveals mechanisms of gene regulation in the human malaria parasite Plasmodium falciparum. Nucleic Acids Res 45:7825-7840
Saraf, Anita; Cervantes, Serena; Bunnik, Evelien M et al. (2016) Dynamic and Combinatorial Landscape of Histone Modifications during the Intraerythrocytic Developmental Cycle of the Malaria Parasite. J Proteome Res 15:2787-801
Bunnik, Evelien M; Batugedara, Gayani; Saraf, Anita et al. (2016) The mRNA-bound proteome of the human malaria parasite Plasmodium falciparum. Genome Biol 17:147
Daub, Mary Elisabeth; Prudhomme, Jacques; Le Roch, Karine et al. (2015) Synthesis and potent antimalarial activity of kalihinol B. J Am Chem Soc 137:4912-5
Lu, Xueqing Maggie; Bunnik, Evelien M; Pokhriyal, Neeti et al. (2015) Analysis of nucleosome positioning landscapes enables gene discovery in the human malaria parasite Plasmodium falciparum. BMC Genomics 16:1005
Bunnik, Evelien M; Le Roch, Karine G (2015) PfAlba1: master regulator of translation in the malaria parasite. Genome Biol 16:221
Fernandez, Edward B; Villarreal, Jason; Lonardi, Stefano et al. (2015) FHAST: FPGA-Based Acceleration of Bowtie in Hardware. IEEE/ACM Trans Comput Biol Bioinform 12:973-81

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