Transcriptome-wide dynamics of extensive m6A mRNA methylation during Plasmodium falciparum blood-stage development

Malaria pathogenesis results from the asexual replication of Plasmodium falciparum within human red blood cells, which relies on a precisely timed cascade of gene expression over a 48-hour life cycle. However, post-transcriptional control of this hardwired program has been largely unexplored. To this end, we performed a comprehensive characterization of m6A mRNA methylation during the different developmental stages. Using mass spectrometry and parallel m6A and RNA sequencing, we show that m6A is developmentally regulated and present at higher levels (>4-fold) than in other organisms investigated. Knockdown of the m6A methyltransferase by CRISPR interference leads to increased levels of transcripts that normally contain m6A. In accordance, we find an inverse correlation between m6A status and mRNA half-life or translational efficiency. Our data demonstrate the crucial function of extensive m6A mRNA methylation in dynamically fine-tuning the transcriptional program of a unicellular eukaryote and reveal a new ‘epitranscriptomic’ layer of gene regulation in malaria parasites. Characterization of m6A mRNA methylation dynamics during Plasmodium falciparum blood stage development. The m6A methyltransferase was knocked out using CRISRP interference and the dCas9 binding site was identified by dCas9 ChIP-seq. m6A-seq was performed in two replicates of the knock-down (gPfMT-A70 ) and control (gControl) parasite cell line at 12, 24 and 36 hours post infection (hpi). BioProject accession: PRJNA473770