news and views The ribosomal RNAs (rRNA) of all organ- isms undergo many different covalent nucleotide modifications clustered around regions of key importance for translation. In eukaryotes and Archaea, the most common of these nucleotide modifications are methylation of the 2′-hydroxyl on the ribose (2′-O-methyla- tion) and conversion of uridine to pseudouridine (Ψ) by rotation of the base. Both of these modifications are directed by guide RNAs, termed small nucleolar RNAs (snoRNAs) in eukaryotes or small RNAs (sRNAs) in archaea 1–3 . These function in the form of RNA–pro- tein complexes termed snoRNPs or sRNPs. The RNAs that direct 2′-O-methy- lation are termed box C/D s(no)RNAs, based on the presence of two sequence elements (box C and box D) conserved among all members of this class (Fig. 1). Another group, the box H/ACA snoRNAs, selects sites of Ψ formation. In each class the RNA modifying enzyme is a component of the corresponding snoRNPs, and the site of modification is determined by base pairing of the snoRNA to the RNA substrate. In addi- tion, a small number of snoRNAs in each class are required for the cleavage of the pre-rRNA to generate mature rRNA. A key feature of these RNA modifica- tion systems is that no constraints are placed on the substrate beyond comple- mentarity to the guide RNA sequence. Thus, new sites of RNA modification can readily be targeted. In humans, both 2′-O-methylation and pseudouridine for- mation in the small nuclear RNA (snRNA) components of the mRNA splic- ing machinery are also directed by snoRNAs 4–7 . As in the rRNAs, these modi- fications are restricted to functionally important regions and contribute to the faithful function of the modified RNA. More exotically, numerous box C/D- like snoRNAs identified in mammals lack clear target sequences in either rRNAs or snRNAs and are detectably expressed only in brain 8 . One such snoRNA is predicted to methylate the serotonin C receptor mRNA at a residue that also undergoes functionally important A→U editing in the pre-mRNA 8 . Other brain-specific mRNAs are also likely to be 2′-O-methy- lated with important functional conse- quences. Notably, these snoRNAs are transcribed from gene clusters that lie in ‘imprinted’ regions. Either the paternal or Insights into the structure and function of a guide RNP Alessandro Fatica and David Tollervey Many different RNA species undergo nucleotide modifications at sites identified by guide small nucleolar ribonucleoprotein (snoRNP) particles. The co-crystal structure of two snoRNP proteins gives valuable clues into the workings of this system. nature structural biology • volume 10 number 4 • april 2003 237 Fig. 1 Schematic of the potential structures of archaeal and eukaryotic box C/D s(no)RNPs and model for methylation site selection. a, The archaeal sRNAs and eukaryotic s(no)RNAs generally contain both box C/D and related box-C’/D’ regions, each flanked by a modification guide sequence, giving a pseudo symmetric structure. Data from Aittaleb et al. 15 indicate that there is also symmetry in the protein structure. In archaeal sRNPs two copies of Nop5p homodimerize via a coiled-coil domain, linking the protein complexes at C/D and C’/D’. In eukaryotic snoRNPs a heterodimer between the closely related Nop5p and Nop56p proteins is predicted. In the free snoRNP, the modification guide sequences are envisaged to be bound across the Nop5p–Fibrillarin interface for presentation to potential substrates. b, The target RNA (red) is 2’-O-methylated at a site (indicated by a purple dot), which is determined solely by its position within a duplex formed with the guide s(no)RNA (black). For this system to work, the RNA duplex must be very accurately positioned relative to the active site in the Fibrillarin methyltransferase, indicated in (a). The snoRNA-target duplex is probably positioned by stacking onto stem II formed by the box C/D or C’/D’ elements (shown as sequences). Accurate positioning of stem II within the complex is likely to be assisted by binding of L7Ae/Snu13p to the sharp K-turn in the loop formed between boxes C and D. Binding of Nop5p to L7Ae/Snu13p and box C/D is envisaged to accurately position the active site of Fibrillarin for interaction with the RNA duplex. a b © 2003 Nature Publishing Group http://www.nature.com/naturestructuralbiology