The tRNA methyltransferase Dnmt2 is required for accurate polypeptide synthesis during haematopoiesis

Abstract

The Dnmt2 enzyme utilizes the catalytic mechanism of eukaryotic DNA methyltransferases to methylate several tRNAs at cytosine 38. Dnmt2 mutant mice, flies, and plants were reported to be viable and fertile, and the biological function of Dnmt2 has remained elusive. Here, we show that endochondral ossification is delayed in newborn Dnmt2-deficient mice, which is accompanied by a reduction of the haematopoietic stem and progenitor cell population and a cell-autonomous defect in their differentiation. RNA bisulfite sequencing revealed that Dnmt2 methylates C38 of tRNA AspGTC, GlyGCC, and ValAAC, thus preventing tRNA fragmentation. Proteomic analyses from primary bone marrow cells uncovered systematic differences in protein expression that are due to specific codon mistranslation by tRNAs lacking Dnmt2-dependent methylation. Our observations demonstrate that Dnmt2 plays an important role in haematopoiesis and define a novel function of C38 tRNA methylation in the discrimination of near-cognate codons, thereby ensuring accurate polypeptide synthesis.

Statistically robust methylation calling for whole-transcriptome bisulfite sequencing reveals distinct methylation patterns for mouse RNAs

“…RNA modifications are particularly enriched in tRNAs, where they are often linked to translational regulation (Agris 2008). In this context, it has been shown that m5C modification of tRNA plays an important role in tRNA stability and in the regulation of translational fidelity (Schaefer et al 2010;Tuorto et al 2012Tuorto et al , 2015. Furthermore, m5C is also a widely conserved modification of rRNA, where it is implied in the quality control of ribosome biogenesis (Sharma et al 2013;Bourgeois et al 2015;Schosserer et al 2015).…”

Post-transcriptional modifications in development and stem cells

“…In mammals, deposition of m 5 C by DNMT2 or NSUN2 protects tRNAs from endonucleolytic cleavage by preventing binding of the endonuclease angiogenin and cleavage into two small non-coding RNA fragments (Fig. 5A,B) (Blanco et al, 2014;Schaefer et al, 2010;Tuorto et al, 2015). Lack of NSUN2-mediated methylation causes accumulation of 5′ tRNA-derived fragments and decreases global protein translation in cells (Blanco et al, , 2014.…”

“…By contrast, loss of DNMT2-mediated methylation of tRNA Asp GTC , Gly GCC and Val AAC causes tRNA-specific fragmentation patterns, which leads to specific codon mistranslation (Fig. 5A,B) (Tuorto et al, 2015). Cytosine-5 methylation of vault non-coding RNAs alters their processing into Argonaute-associated small RNA fragments that can function as miRNAs and regulate the translation of targeted mRNAs (Fig.…”

“…Single deletion of Dnmt2 in mice, flies and plants does not impair viability or fertility (Goll et al, 2006). However, loss of Dnmt2 in new-born mice affects the differentiation of haematopoietic stem and progenitor cell populations (Tuorto et al, 2015). Likewise, morpholino-mediated loss of Dnmt2 in zebrafish specifically impairs liver, retina and brain differentiation (Rai et al, 2007).…”

The Expression of DNA Methyltransferase DNMT3a in Classical and Fibrolamellar Hepatocellular Carcinoma

“…The family of mammalian methyltransferases consists of five enzymes, of which three possess enzymatic activity for DNA methylation -the remaining member of the group, DNMT2 plays an important role in polypeptide synthesis through tRNA methylation, hence its alternative name: TRDMT1 (tRNA aspartic acid methyltransferase 1) [6].…”