Human DIMT1 generates N(2)(6,6)A-dimethylation–containing small RNAs

Dimethyladenosine transferase 1 (DIMT1) is an evolutionarily conserved RNA N(6,6)-dimethyladenosine (m(2)(6,6)A) methyltransferase. DIMT1 plays an important role in ribosome biogenesis, and the catalytic activity of DIMT1 is indispensable for cell viability and protein synthesis. A few RNA-modifying enzymes can install the same modification in multiple RNA species. However, whether DIMT1 can work on RNA species other than 18S rRNA is unclear. Here, we describe that DIMT1 generates m(2)(6,6)A not only in 18S rRNA but also in small RNAs. In addition, m(2)(6,6)A in small RNAs were significantly decreased in cells expressing catalytically inactive DIMT1 variants (E85A or NLPY variants) compared with cells expressing wildtype DIMT1. Both E85A and NLPY DIMT1 variant cells present decreased protein synthesis and cell viability. Furthermore, we observed that DIMT1 is highly expressed in human cancers, including acute myeloid leukemia. Our data suggest that downregulation of DIMT1 in acute myeloid leukemia cells leads to a decreased m(2)(6,6)A level in small RNAs. Together, these data suggest that DIMT1 not only installs m(2)(6,6)A in 18S rRNA but also generates m(2)(6,6)A-containing small RNAs, both of which potentially contribute to the impact of DIMT1 on cell viability and gene expression.