N-methyladenosine in poly(A) tails stabilize VSG transcripts.

RNA modifications are important regulators of gene expression. In Trypanosoma brucei, transcription is polycistronic and thus most regulation happens post-transcriptionally. N-methyladenosine (mA) has been detected in this parasite, but its function remains unknown. Here we found that mA is enriched in 342 transcripts using RNA immunoprecipitation, with an enrichment in transcripts encoding variant surface glycoproteins (VSGs). Approximately 50% of the mA is located in the poly(A) tail of the actively expressed VSG transcripts. mA residues are removed from the VSG poly(A) tail before deadenylation and mRNA degradation. Computational analysis revealed an association between mA in the poly(A) tail and a 16-mer motif in the 3' untranslated region of VSG genes. Using genetic tools, we show that the 16-mer motif acts as a cis-acting motif that is required for inclusion of mA in the poly(A) tail. Removal of this motif from the 3' untranslated region of VSG genes results in poly(A) tails lacking mA, rapid deadenylation and mRNA degradation. To our knowledge, this is the first identification of an RNA modification in the poly(A) tail of any eukaryote, uncovering a post-transcriptional mechanism of gene regulation.