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The N<jats:sup>6<\/jats:sup>-methyl adenosine (m6A) is an important epigenetic modification primarily present on mRNA that controls the levels of transcripts and efficiency of translation in eukaryotes. Recently, the dynamics of m6A on mRNAs at all three developmental stages of <jats:italic>P. falciparum<\/jats:italic> in RBCs have been profiled; however, the proteins that regulate the m6A containing mRNAs in the parasites are unknown.<\/jats:p>\n<\/jats:sec><jats:sec>\n<jats:title>Results<\/jats:title>\n<jats:p>Using sequence analysis, we computationally identified that the <jats:italic>P. falciparum<\/jats:italic> genome encodes two putative YTH (YT521-B Homology) domain-containing proteins, which could potentially bind to m6A containing mRNA. We developed a modified methylated RNA immunoprecipitation (MeRIP) assay using PfYTH2 and find that it binds selectively to m6A containing transcripts. The PfYTH2 has a conserved aromatic amino acid cage that forms the methyl-binding pocket. Through site-directed mutagenesis experiments and molecular dynamics simulations, we show that F98 residue is important for m6A binding on mRNA. Fluorescence depolarization assay confirmed that PfYTH2 binds to methylated RNA oligos with high affinity. Further, MeRIP sequencing data revealed that PfYTH2 has more permissive sequence specificity on target m6A containing mRNA than other known eukaryotic YTH proteins. Taken together, here we identify and characterize PfYTH2 as the major protein that could regulate m6A containing transcripts in <jats:italic>P. falciparum<\/jats:italic>.<\/jats:p>\n<\/jats:sec><jats:sec>\n<jats:title>Conclusion<\/jats:title>\n<jats:p><jats:italic>Plasmodium<\/jats:italic> spp. lost the canonical m6A-specific demethylases in their genomes, however, the YTH domain-containing proteins seem to be retained. This study presents a possibility that the YTH proteins are involved in post-transcriptional control in <jats:italic>P. falciparum<\/jats:italic>, and might orchestrate the translation of mRNA in various developmental stages of <jats:italic>P. falciparum<\/jats:italic>. This is perhaps the first characterization of the methyl-reading function of YTH protein in any parasites.<\/jats:p>\n<\/jats:sec>","DOI":"10.1186\/s13072-020-00355-7","type":"journal-article","created":{"date-parts":[[2020,8,31]],"date-time":"2020-08-31T10:03:10Z","timestamp":1598868190000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":25,"title":["N6-Adenosine methylation on mRNA is recognized by YTH2 domain protein of human malaria parasite Plasmodium falciparum"],"prefix":"10.1186","volume":"13","author":[{"given":"Gayathri","family":"Govindaraju","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rajashekar Varma","family":"Kadumuri","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Devadathan Valiyamangalath","family":"Sethumadhavan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"C. 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Healthy volunteers provided written consent for the collection of blood to obtain the RBCs from healthy volunteers at RGCB Molecular Diagnostic facility.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"Not applicable.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"The authors declare that they have no competing interests.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"33"}}