Control of box C/D snoRNP assembly by N⁶-methylation of adenine

N6-methyladenine is the most widespread mRNA modification. A sub-set of human box C/D snoRNA species have target GAC sequences that lead to formation of N6-methyladenine at a key trans Hoogsteen-sugar A•G basepair, of which half are methylated in vivo. The GAC target is conserved only in those that are methylated. Methylation prevents binding of the 15.5 kDa protein and the induced folding of the RNA. Thus the assembly of the box C/D snoRNP could in principle be regulated by RNA methylation at its critical first stage. Crystallography reveals that N6-methylation of adenine prevents the formation of trans Hoogsteen-sugar A•G basepairs, explaining why the box C/D RNA cannot adopt its kinked conformation. More generally, our data indicate that sheared A•G basepairs (but not Watson-Crick basepairs) are more susceptible to disruption by N6mA methylation and are therefore possible regulatory sites. The human signal recognition particle RNA and many related Alu retrotransposon RNA species are also methylated at N6 of an adenine that forms a sheared basepair with guanine and mediates a key tertiary interaction.