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.

Public Health Relevance

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.

Agency
National Institute of Health (NIH)
Institute
National Institute of Allergy and Infectious Diseases (NIAID)
Type
Research Project (R01)
Project #
5R01AI085077-04
Application #
8515919
Study Section
Pathogenic Eukaryotes Study Section (PTHE)
Program Officer
Mcgugan, Glen C
Project Start
2010-09-15
Project End
2014-08-31
Budget Start
2013-09-01
Budget End
2014-08-31
Support Year
4
Fiscal Year
2013
Total Cost
$362,484
Indirect Cost
$107,470
Name
University of California Riverside
Department
Anatomy/Cell Biology
Type
Schools of Earth Sciences/Natur
DUNS #
627797426
City
Riverside
State
CA
Country
United States
Zip Code
92521
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
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
Bunnik, Evelien M; Le Roch, Karine G (2015) PfAlba1: master regulator of translation in the malaria parasite. Genome Biol 16:221
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
Ay, Ferhat; Bunnik, Evelien M; Varoquaux, Nelle et al. (2015) Multiple dimensions of epigenetic gene regulation in the malaria parasite Plasmodium falciparum: gene regulation via histone modifications, nucleosome positioning and nuclear architecture in P. falciparum. Bioessays 37:182-94
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
Ay, Ferhat; Bunnik, Evelien M; Varoquaux, Nelle et al. (2014) Three-dimensional modeling of the P. falciparum genome during the erythrocytic cycle reveals a strong connection between genome architecture and gene expression. Genome Res 24:974-88
Polishko, Anton; Bunnik, Evelien M; Le Roch, Karine G et al. (2014) PuFFIN--a parameter-free method to build nucleosome maps from paired-end reads. BMC Bioinformatics 15 Suppl 9:S11
Russell, Karen; Cheng, Chia-Ho; Bizzaro, Jeffrey W et al. (2014) Homopolymer tract organization in the human malarial parasite Plasmodium falciparum and related Apicomplexan parasites. BMC Genomics 15:848

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