ArticleBMC genomics2020
Refining the transcriptome of the human malaria parasite Plasmodium falciparum using amplification-free RNA-seq.
Article in BMC genomics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 72 papers.
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72 citing papers in PubMed.
- Inducible dCas12a system expands CRISPRi/a capabilities for functional genomics in malaria parasiteiScience · 2026Article
- Characterization of Sec14 Domain-Containing Proteins in the Malaria Parasite Plasmodium falciparum.Molecular microbiology · 2026Article
- New insights on Plasmodium gene expression from direct RNA sequencing.Trends in parasitology · 2026Review
- Revisiting Glutathione Transferases ofPharmaceuticals (Basel, Switzerland) · 2026Review
- Deciphering chromatin architecture and dynamics in Plasmodium falciparum using the nucDetective pipeline.PLoS computational biology · 2026Article
- Versatile, marker-free platform for life cycle-wide imaging of Plasmodium falciparum by integrating an exogenous gene cassette into a conserved intergenic locus.Scientific reports · 2026Article
- Dynamic regulation of long non-coding RNAs across asexual and gametocyte development inbioRxiv : the preprint server for biology · 2026Article
- Chromatin state dynamics during the Plasmodium falciparum intraerythrocytic development cycle.BMC genomics · 2026Article
- Genome-wide analysis of strand-specific transcription and DNA methylation inFrontiers in microbiology · 2026Article
- An essential adaptor for apicoplast fission and inheritance in malaria parasites.Nature communications · 2025Article
- Heterogeneous constraint and adaptation across the malaria parasite life cycle.Proceedings. Biological sciences · 2025Article
- An Essential Adaptor for Apicoplast Fission and Inheritance in Malaria Parasites.bioRxiv : the preprint server for biology · 2025Article
- Inner-mitochondrial membrane protein PfMPV17 is linked to P. falciparum in vitro resistance to the indoloquinolizidine alkaloid alstonine.The Journal of antimicrobial chemotherapy · 2025Article
- SUN-domain proteins of the malaria parasitemBio · 2025Article
- Pfs16: A Key Parasitophorous Vacuole Membrane Protein Crucial for Malaria Parasite Development and Transmission.The protein journal · 2025Review
- SIP2 is the master transcription factor ofScience advances · 2025Article
- Article
- Nucleotide-resolution Mapping of RNA N6-Methyladenosine (m6A) modifications and comprehensive analysis of global polyadenylation events in mRNA 3' end processing in malaria pathogenbioRxiv : the preprint server for biology · 2025Article
- Systematic in vitro evolution inScience (New York, N.Y.) · 2024Article
- AeLife · 2024Article
12 more citing papers are in PubMed but not listed here.
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8 authors.
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Abstract
backgroundPlasmodium parasites undergo several major developmental transitions during their complex lifecycle, which are enabled by precisely ordered gene expression programs. Transcriptomes from the 48-h blood stages of the major human malaria parasite Plasmodium falciparum have been described using cDNA microarrays and RNA-seq, but these assays have not always performed well within non-coding regions, where the AT-content is often 90-95%.
resultsWe developed a directional, amplification-free RNA-seq protocol (DAFT-seq) to reduce bias against AT-rich cDNA, which we have applied to three strains of P. falciparum (3D7, HB3 and IT). While strain-specific differences were detected, overall there is strong conservation between the transcriptional profiles. For the 3D7 reference strain, transcription was detected from 89% of the genome, with over 78% of the genome transcribed into mRNAs. We also find that transcription from bidirectional promoters frequently results in non-coding, antisense transcripts. These datasets allowed us to refine the 5' and 3' untranslated regions (UTRs), which can be variable, long (> 1000 nt), and often overlap those of adjacent transcripts.
conclusionsThe approaches applied in this study allow a refined description of the transcriptional landscape of P. falciparum and demonstrate that very little of the densely packed P. falciparum genome is inactive or redundant. By capturing the 5' and 3' ends of mRNAs, we reveal both constant and dynamic use of transcriptional start sites across the intraerythrocytic developmental cycle that will be useful in guiding the definition of regulatory regions for use in future experimental gene expression studies.
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