The posttranscriptional modification of messenger RNA (mRNA) and transfer RNA (tRNA) provides an additional layer of regulatory complexity during gene expression. Here, we show that a tRNA methyltransferase, TRMT10A, interacts with an mRNA demethylase FTO (ALKBH9), both in vitro and inside cells. TRMT10A installsN1-methylguanosine (m1G) in tRNA, and FTO performs demethylation onN6-methyladenosine (m6A) andN6,2′-O-dimethyladenosine (m6Am) in mRNA. We show that TRMT10A ablation not only leads to decreased m1G in tRNA but also significantly increases m6A levels in mRNA. Cross-linking and immunoprecipitation, followed by high-throughput sequencing results show that TRMT10A shares a significant overlap of associated mRNAs with FTO, and these mRNAs have accelerated decay rates potentially through the regulation by a specific m6A reader, YTHDF2. Furthermore, transcripts with increased m6A upon TRMT10A ablation contain an overrepresentation of m1G9-containing tRNAs codons read by tRNAGln(TTG), tRNAArg(CCG), and tRNAThr(CGT). These findings collectively reveal the presence of coordinated mRNA and tRNA methylations and demonstrate a mechanism for regulating gene expression through the interactions between mRNA and tRNA modifying enzymes.

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DEAD‐box helicases play a crucial role in the metabolism of cellular RNAs. One key member of this family is the helicase DDX3X, which is encoded on the X chromosome. Recently, the Y chromosome‐encoded homolog of DDX3X, DDX3Y, has been shown to be expressed at the protein level in several tissues, such as in the heart and in nervous tissue. Herein, we provide the first measurements of the catalytic activity of DDX3Y as it compares to DDX3X. Using both continuous and single time point ATPase measurements, we found DDX3Y to be a less active ATPase than DDX3X. Furthermore, using truncated forms of both proteins, we find that the intrinsically disordered regions (IDRs) of both proteins affect their ATPase activities to different degrees. Because the ATPase activity of DEAD‐box proteins is known to be RNA‐triggered, we also assayed the RNA binding propensity of these proteins. We found that, in agreement with our ATPase data, DDX3Y binds double stranded RNA less tightly than DDX3X. These findings may prove important to human health and disease, given that nearly half the population has a Y chromosome and thus expresses some amount of DDX3Y protein.