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2′‐ O ‐methylation of eukaryotic ribosomal RNA (r)RNA, essential for ribosome function, is catalysed by box C/D small nucleolar (sno)RNPs. The RNA components of these complexes (snoRNAs) contain one or two guide sequences, which, through base‐pairing, select the rRNA modification site. Adjacent to the guide sequences are protein‐binding sites (the C/D or C′/D′ motifs). Analysis of >2000 yeast box C/D snoRNAs identified additional conserved sequences in many snoRNAs that are complementary to regions adjacent to the rRNA methylation site. This ‘extra base‐pairing’ was also found in many human box C/D snoRNAs and can stimulate methylation by up to five‐fold. Sequence analysis, combined with RNA–protein crosslinking in  Saccharomyces cerevisiae , identified highly divergent box C′/D′ motifs that are bound by snoRNP proteins.  In vivo  rRNA methylation assays showed these to be active. Our data suggest roles for non‐catalytic subunits (Nop56 and Nop58) in rRNA binding and support an asymmetric model for box C/D snoRNP organization. The study provides novel insights into the extent of the snoRNA–rRNA interactions required for efficient methylation and the structural organization of the snoRNPs.

Box C/D snoRNP catalysed methylation is aided by additional pre‐rRNA base‐pairing