ArticleNucleic acids research2011
RNA-Seq analysis of splicing in Plasmodium falciparum uncovers new splice junctions, alternative splicing and splicing of antisense transcripts.
Article in Nucleic acids research, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 85 papers.
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Who cites it
85 citing papers in PubMed.
- New insights on Plasmodium gene expression from direct RNA sequencing.Trends in parasitology · 2026Review
- Inhibition of PfCLK3 interferes with malaria parasite RNA splicing and explains the mechanism of action of a new class of antimalarial candidates.Antimicrobial agents and chemotherapy · 2026Article
- The UTRs of Leishmania donovani vary in length and are enriched in potential regulatory structures.PLoS pathogens · 2026Article
- NanoPrePro: a fully equipped, fast, and memory-efficient preprocessor for nanopore transcriptomic sequencing.Briefings in bioinformatics · 2026Article
- Epitranscriptomic sculpting: the role of mMedical oncology (Northwood, London, England) · 2025Review
- The UTRs of Leishmania donovani vary in length and are enriched in potential regulatory structures.bioRxiv : the preprint server for biology · 2025Article
- A tale of two parasites: a glimpse into the RNA methylome of patient-derived Plasmodium falciparum and Plasmodium vivax isolates.Malaria journal · 2025Article
- Population genomics and transcriptomics of Plasmodium falciparum in Cambodia and Vietnam uncover key components of the artemisinin resistance genetic background.Nature communications · 2024Article
- An axonemal intron splicing program sustains Plasmodium male development.Nature communications · 2024Article
- Proteome-Wide Identification of RNA-dependent proteins and an emerging role for RNAs in Plasmodium falciparum protein complexes.Nature communications · 2024Article
- Novel insights into the role of long non-coding RNA in the human malaria parasite, Plasmodium falciparum.Nature communications · 2023Article
- Characterization of GEXP15 as a Potential Regulator of Protein Phosphatase 1 inInternational journal of molecular sciences · 2023Article
- The role of long noncoding RNAs in malaria parasites.Trends in parasitology · 2023Review
- Chemogenomic Profiling of a Plasmodium falciparum Transposon Mutant Library Reveals Shared Effects of Dihydroartemisinin and Bortezomib on Lipid Metabolism and Exported Proteins.Microbiology spectrum · 2023Article
- CRISPR-Cas13 in malaria parasite: Diagnosis and prospective gene function identification.Frontiers in microbiology · 2023Review
- Epitranscriptomics in parasitic protists: Role of RNA chemical modifications in posttranscriptional gene regulation.PLoS pathogens · 2022Review
- A manually curated annotation characterises genomic features of P. falciparum lncRNAs.BMC genomics · 2022Article
- Emerging biology of noncoding RNAs in malaria parasites.PLoS pathogens · 2022Review
- Pervasive sequence-level variation in the transcriptome ofNAR genomics and bioinformatics · 2022Article
- Non-coding RNAs in malaria infection.Wiley interdisciplinary reviews. RNA · 2022Review
25 more citing papers are in PubMed but not listed here.
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3 authors.
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Abstract
Over 50% of genes in Plasmodium falciparum, the deadliest human malaria parasite, contain predicted introns, yet experimental characterization of splicing in this organism remains incomplete. We present here a transcriptome-wide characterization of intraerythrocytic splicing events, as captured by RNA-Seq data from four timepoints of a single highly synchronous culture. Gene model-independent analysis of these data in conjunction with publically available RNA-Seq data with HMMSplicer, an in-house developed splice site detection algorithm, revealed a total of 977 new 5' GU-AG 3' and 5 new 5' GC-AG 3' junctions absent from gene models and ESTs (11% increase to the current annotation). In addition, 310 alternative splicing events were detected in 254 (4.5%) genes, most of which truncate open reading frames. Splicing events antisense to gene models were also detected, revealing complex transcriptional arrangements within the parasite's transcriptome. Interestingly, antisense introns overlap sense introns more than would be expected by chance, perhaps indicating a functional relationship between overlapping transcripts or an inherent organizational property of the transcriptome. Independent experimental validation confirmed over 30 new antisense and alternative junctions. Thus, this largest assemblage of new and alternative splicing events to date in Plasmodium falciparum provides a more precise, dynamic view of the parasite's transcriptome.
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