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Capturing the dynamic RNA landscape of the malaria parasite P. falciparum

ABSTRACT: To date, total mRNA analysis throughout intraerythrocytic development of the malaria parasite, Plasmodium falciparum, has only revealed abundance profiles of each gene at a given time. Here, we establish a new methodology in Plasmodium falciparum that enables biosynthetic labeleing and capture of sub-population mRNA. As a proof of principle for this novel method, we examine the mRNA dynamics of early gametocyte commitment.

ORGANISM(S): Plasmodium falciparum

PROVIDER: GSE72695 | GEO | 2015/09/04

SECONDARY ACCESSION(S): PRJNA294681

REPOSITORIES: GEO

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Capturing the dynamic RNA landscape of the malaria parasite P. falciparum

Project description:To date, total mRNA analysis throughout intraerythrocytic development of the malaria parasite, Plasmodium falciparum, has only revealed abundance profiles of each gene at a given time. Here, we establish a new methodology in Plasmodium falciparum that enables biosynthetic labeleing and capture of sub-population mRNA. As a proof of principle for this novel method, we examine the mRNA dynamics of early gametocyte commitment. Plasmodium falciparum strains 3D7, E5, and F12 were highly synchronized and, at 36 hours post invasion, incubated with 40um 4-TU for 12 hours followed immediately by Trizol total RNA extraction. Total RNA from each timepoint was then biotinylated via a thiol-group on any transcript that incorporated a thiol-modified UTP. Biotinylated transcripts were then separated from total RNA by Streptavidin magnetic beads resulting in a Labeled sample. Any mRNA that was not bound to the beads resulted in an Unlabeled sample. Every 12 hours, two samples were analyzed by Agilent P. falciparum DNA microarray, Unlabeled and Labeled, resulting in 48 individual DNA microarrays (4 for each sample type).

2015-09-04 | E-GEOD-72695 | biostudies-arrayexpress

Replication origin mapping in the malaria parasite P. falciparum

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Transcriptional profiling defines histone acetylation as a regulator of gene expression during human-to-mosquito transmission of the malaria parasite Plasmodium falciparum

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Whole genome transcriptome profiling of P. falciparum sexually comitted ring stage parasite from malaria patient's peripheral blood

Project description:Malaria is spread by the transmission of sexual stage parasites, called gametocytes. However, with Plasmodium falciparum, gametocytes can only be detected in peripheral blood when they are mature and transmissible to a mosquito, which complicates control efforts. Here, we identify the set of genes overexpressed in patient blood samples with high levels of gametocyte-committed ring stage parasites. Expression of all 18 genes was regulated by transcription factor AP2-G, which is required for gametocytogenesis. We selected three genes, not expressed in mature gametocytes, to develop as biomarkers. All three biomarkers were validated in vitro using 6 different parasite lines and an algorithm developed that predicted gametocyte production in ex vivo samples and volunteer infection studies. The biomarkers were also sensitive enough to monitor gametocyte production in asymptomatic P. falciparum carriers allowing early detection and treatment of infectious reservoirs, as well as the in vivo analysis of factors that modulate sexual conversion.

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Parasite in vivo blood transcriptomes from Malawian children with cerebral malaria

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2016-06-24 | E-GEOD-83667 | biostudies-arrayexpress

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Project description:ChIP-seq experiments were performed for the putative telomere repeat-binding factor (PfTRF) in the malaria parasite Plasmodium falciparum strain 3D7. The gene encoding this factor (PF3D7_1209300) was endogenously tagged with either a GFP- or a 3xHA-tag and these transgenic parasite lines were used in ChIP-sequencing experiments. Sequencing of the ChIP and input libraries showed enrichment of PfTRF at all telomere-repeat containing chromosome ends (reference genome Plasmodium falciparum 3D7 from PlasmoDB version 6.1) as well as in all upsB var promoters.In addition,PfTRF was enriched at seven additional, intra-chromosomal sites and called in the PfTRF-HA ChIP-seq only. Plasmodium falciparum 3D7 parasites were generated with -GFP or -3xHA C-terminal tagged TRF (PF3D7_1209300). Nuclei were isolated from formaldehyde cross-linked schizont-stage transgenic parasites and used to prepare chromatin. Chromatin immunoprecipitations were performed using mouse anti-GFP (Roche Diagnostics, #11814460001) or rat anti-HA 3F10 (Roche Diagnostics, #12158167001). Sequencing libraries were prepared according to a Plasmodium-optimized library preparation procedure including KAPA polymerase-mediated PCR amplification.

2016-07-15 | E-GEOD-76537 | biostudies-arrayexpress

Expression analysis of Plasmodium falciparum 3D7 delta-PfPuf2 mutant

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