Identification of an RNA-binding region in 18S dimethyladenosine methyltransferase DIMT1 essential for proliferation of acute myeloid leukemia cells

Aberrant assembly and function of ribosomes are implicated in cancers, including acute myeloid leukemia (AML). Here, we find that 18S rRNA methyltransferase DIMT1 is essential for AML proliferation through a non-catalytic function. We demonstrate that a positively charged cleft on DIMT1 plays an important role in RNA binding. Mutations at the identified cleft (5mutA-DIMT1) significantly weakens binding of DIMT1 to rRNA in vitro and in cells. Strikingly, the RNA-binding deficient 5mutA-DIMT1 is predominantly located in the nucleoplasm, in contrast with the primarily nucleolar localization of wild-type DIMT1. Furthermore, we demonstrate that rRNA binding is required for DIMT1 to undergo liquid-liquid phase separation in vitro, which likely promotes DIMT1’s nucleolar localization and its role in rRNA processing in cells. Importantly, re-expression of wild-type but not 5mutA-DIMT1 supports AML proliferation in competition-based cell proliferation assays. These results highlight the importance of targeting the catalytically independent RNA-binding activity of DIMT1 for therapy of AML. Ribosome profiling followed by high-throughput sequencing (ribo-seq) in MOLM13C cells with DIMT1 or Rosa (a negative control) depletion.