Work

FTO does not function as an m 6 A eraser in AML: a reassessment using direct RNA nanopore sequencing

Year: 2025

Type: preprint

Abstract: SUMMARY A central concept in epitranscriptomics is that the RNA demethylase FTO acts as a site-selective eraser of N 6 -methyladenosine (m 6 A) in specific mRNAs. This is most well-established in acute myeloid leukemia (AML), where demethylation of MYC is thought to promote leukemogenesis. Using nanopore direct RNA sequencing to quantify m 6 A transcriptome-wide, we find that m 6 A stoichiometry, including at MYC -specific sites, remains unaffected by FTO knockdown or pharmacologic inhibition in AML. Conversely, levels of N 6 -2’-O-dimethyladenosine (m 6 Am) are markedly increased in snRNAs, indicating that m 6 Am, not m 6 A, is the major substrate of FTO in AML. We extend these results outside the AML context in FTO knockout brain and HEK293T cells, detecting no selective increases in mRNA m 6 A but widespread increases in snRNA m 6 Am levels following FTO depletion. These findings suggest that FTO has minimal ability to erase m 6 A in mRNA. Instead, the reported biological effects of FTO are likely mediated by demethylation of m 6 Am.

Source: bioRxiv (Cold Spring Harbor Laboratory)

DOI: 10.1101/2025.10.22.681652