Nucleotide-resolution mapping of RNA N6-methyladenosine (m6A) modifications and comprehensive analysis of global polyadenylation events in mRNA 3’-end processing in the malaria pathogen Plasmodium falciparum
8 affiliations
- 1Department of Biological Sciences, University of North Carolina, Charlotte, Indiana, USA
- 2School of Integrative Biological and Chemical Sciences, University of Texas Rio Grande Valley, Edinburg, TX, USA
- 3Department of Biomedical Engineering and Informatics, Luddy School of Informatics, Computing and Engineering, Indiana University Indianapolis (IUI), Indianapolis, Indiana, USA
- 4Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina, USA
- 5Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY, USA
- 6Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, North Carolina, USA
- 7Department of Statistics, University of North Carolina, Charlotte, North Carolina, USA
- 8Klaus Tschira Institute for Integrative Computational Cardiology, University of Heidelberg, Heidelberg, Germany
Abstract
N6-methyladenosine (m6A) is the most abundant internal modification of eukaryotic mRNA, yet its distribution and potential involvement in mRNA 3′-end processing in the malaria parasite Plasmodium falciparum remain poorly understood. Here, we combined nucleotide resolution DART-seq, Nanopore DRS, MeRIP-seq and complementary 3′-end sequencing approaches to investigate the relationship between m6A deposition and mRNA 3′-end formation across the parasite transcriptome. DART-seq identified 2330 reproducible m6A sites in 1195 genes, revealing stage-associated differences in the epitranscriptome and preferential enrichment of m6A within 3′ UTRs. Independent MeRIP-seq analysis further supported the reproducibility of these methylation patterns. mRNA 3′-end mapping revealed that cleavage and polyadenylation frequently occur within exceptionally adenosine-rich sequence regions. Integration of Nanopore DRS-derived m6A stoichiometry with experimentally defined poly(A) sites revealed preferential m6A enrichment at canonical DRACH motifs approximately 30–50 nucleotides upstream of transcript cleavage sites. Notably, single-molecule DRS analysis demonstrated differential m6A occupancy at shared transcript positions between proximal and distal alternative polyadenylation isoforms of the same gene, with lower occupancy in distal isoforms near proximal cleavage sites. Moreover, m6A enrichment was consistently observed upstream of the utilized poly(A) site in individual transcripts, suggesting an association between m6A deposition and alternative 3′-end formation. Distinct spatial associations of RNA secondary structure and m6A with poly(A) site regions were observed. Together, these findings provide a transcriptome-wide and single-molecule view of m6A modification patterns in relation to native poly(A) sites in P. falciparum, and the data are consistent with a model in which m6A is associated with and may contribute to 3′-end processing.
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BibTeX
@article{catacalosgoad2026nucleotideresolution,
title = {{Nucleotide-resolution mapping of RNA N6-methyladenosine (m6A) modifications and comprehensive analysis of global polyadenylation events in mRNA 3’-end processing in the malaria pathogen Plasmodium falciparum}},
author = {Cassandra Catacalos-Goad and Manohar Chakrabarti and Doaa Hassan Salem and Carli Camporeale and Sahiti Somalraju and Matthew Tegowski and Kaitlin Klotz and Ashwini Shivakumar and Lichun Zhou and Ruchi Singh and Robert W. Reid and Daniel A. Janies and Shaoyu Li and Kate D. Meyer and Sarath Chandra Janga and Christoph Dieterich and Arthur G. Hunt and Kausik Chakrabarti},
journal = {RNA Biology},
year = {2026},
month = oct,
doi = {10.1080/15476286.2026.2753979},
url = {https://doi.org/10.1080/15476286.2026.2753979},
note = {CC BY-NC 4.0},
}
RIS
TY - JOUR
TI - Nucleotide-resolution mapping of RNA N6-methyladenosine (m6A) modifications and comprehensive analysis of global polyadenylation events in mRNA 3’-end processing in the malaria pathogen Plasmodium falciparum
AU - Cassandra Catacalos-Goad
AU - Manohar Chakrabarti
AU - Doaa Hassan Salem
AU - Carli Camporeale
AU - Sahiti Somalraju
AU - Matthew Tegowski
AU - Kaitlin Klotz
AU - Ashwini Shivakumar
AU - Lichun Zhou
AU - Ruchi Singh
AU - Robert W. Reid
AU - Daniel A. Janies
AU - Shaoyu Li
AU - Kate D. Meyer
AU - Sarath Chandra Janga
AU - Christoph Dieterich
AU - Arthur G. Hunt
AU - Kausik Chakrabarti
PY - 2026
DA - 2026/10/28
JO - RNA Biology
DO - 10.1080/15476286.2026.2753979
UR - https://doi.org/10.1080/15476286.2026.2753979
AB - N6-methyladenosine (m6A) is the most abundant internal modification of eukaryotic mRNA, yet its distribution and potential involvement in mRNA 3′-end processing in the malaria parasite Plasmodium falciparum remain poorly understood. Here, we combined nucleotide resolution DART-seq, Nanopore DRS, MeRIP-seq and complementary 3′-end sequencing approaches to investigate the relationship between m6A deposition and mRNA 3′-end formation across the parasite transcriptome. DART-seq identified 2330 reproducible m6A sites in 1195 genes, revealing stage-associated differences in the epitranscriptome and preferential enrichment of m6A within 3′ UTRs. Independent MeRIP-seq analysis further supported the reproducibility of these methylation patterns. mRNA 3′-end mapping revealed that cleavage and polyadenylation frequently occur within exceptionally adenosine-rich sequence regions. Integration of Nanopore DRS-derived m6A stoichiometry with experimentally defined poly(A) sites revealed preferential m6A enrichment at canonical DRACH motifs approximately 30–50 nucleotides upstream of transcript cleavage sites. Notably, single-molecule DRS analysis demonstrated differential m6A occupancy at shared transcript positions between proximal and distal alternative polyadenylation isoforms of the same gene, with lower occupancy in distal isoforms near proximal cleavage sites. Moreover, m6A enrichment was consistently observed upstream of the utilized poly(A) site in individual transcripts, suggesting an association between m6A deposition and alternative 3′-end formation. Distinct spatial associations of RNA secondary structure and m6A with poly(A) site regions were observed. Together, these findings provide a transcriptome-wide and single-molecule view of m6A modification patterns in relation to native poly(A) sites in P. falciparum, and the data are consistent with a model in which m6A is associated with and may contribute to 3′-end processing.
SN - 1547-6286
SN - 1555-8584
ER -