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Biochemistry students of my generation had the RNA story relatively straight: ribosomal RNAs (rRNAs), transfer RNAs (tRNAs), and messenger RNAs (mRNAs) appeared to do everything expected of RNA in the cell at that time. In the last two decades or so, the situation has changed dramatically. In addition to rRNAs and tRNAs, hundreds of other non-protein-coding RNAs have emerged, having a diverse range of functions, from structural through regulatory to catalytic (1, 2). Particularly exciting recent examples of regulatory RNAs include Xist and roX RNAs, involved in chromosome dosage compensation in mammals and Drosophila, respectively (3), and tmRNA, which directs tagging of incomplete proteins for degradation in bacteria (4). By its nature—a potential to base-pair—the recognition of sequences in other nucleic acids is an RNA molecule's major asset. Indeed, several spliceosomal small nuclear (sn) RNAs (e.g., U1, U2, and U6) base-pair with short sequences in pre-mRNAs to delineate regions to be spliced out (5, 6). Other RNAs, which identify their targets by base-pairing, include editing guide RNAs in the mitochondria of kinetoplastid protozoans (7), and lin-4 and let-7, the 21-nucleotide (nt) long mini-RNAs, which regulate timing of early developmental decisions in Caenorhabditis elegans by hybridizing to the 3′ untranslated regions of their target mRNAs (8); let-7 functions also in other bilaterian animals, from molluscs to mammals (9). The class of noncoding RNAs that—at least in terms of numbers—is currently dominating the field is small nucleolar (sno) RNAs, which act as guides to direct pseudouridylation and 2′-O-ribose methylation in rRNA (10–14). In vertebrates, each of these modifications is found at about 100 sites per ribosome. Since a single guide snoRNA specifies one, at most two, modifications (Fig. 1A), the number of these RNAs may approach 200. Guide snoRNAs also operate in …

Imprinted expression of small nucleolar RNAs in brain: Time for RNomics