FTO controls reversible m 6 Am RNA methylation during snRNA biogenesis.

Small nuclear RNAs (snRNAs) are core spliceosome components and mediate pre-mRNA splicing. Here we show that snRNAs contain a regulated and reversible nucleotide modification causing them to exist as two different methyl isoforms, m ₁ and m ₂ , reflecting the methylation state of the adenosine adjacent to the snRNA cap. We find that snRNA biogenesis involves the formation of an initial m ₁ isoform with a single-methylated adenosine (2'-O-methyladenosine, Am), which is then converted to a dimethylated m ₂ isoform (N ⁶ ,2'-O-dimethyladenosine, m ⁶ Am). The relative m ₁ and m ₂ isoform levels are determined by the RNA demethylase FTO, which selectively demethylates the m ₂ isoform. We show FTO is inhibited by the oncometabolite D-2-hydroxyglutarate, resulting in increased m ₂ -snRNA levels. Furthermore, cells that exhibit high m ₂ -snRNA levels show altered patterns of alternative splicing. Together, these data reveal that FTO controls a previously unknown central step of snRNA processing involving reversible methylation, and suggest that epitranscriptomic information in snRNA may influence mRNA splicing.