Pseudouridylation goes regulatory.

RNA modifications are omnipresent among non-coding RNAs, so much so that pseudouridine (an isomer of uridine) was originally designated the ‘fifth nucleoside’. Their role ranges from fine-tuning to being functionally essential to their target RNAs. Ever since their discovery some 60 years ago, RNA modifications were considered constitutive. In this issue of The EMBO Journal, however, Wu et al demonstrate that environmental stimuli induce pseudouridylation of spliceosomal small nuclear (sn) RNA U2 at novel sites impacting pre-mRNA splicing. After the regulatory modification of protein and of DNA, that of RNA now adds another level of complexity to the cellular signaling landscape. Well over 100 different modifications decorate nucleotides in cellular RNA (Czerwoniec et al, 2009). Such modifications are particularly prominent in non-coding RNAs such as tRNA, ribosomal RNA, and snRNAs. Pseudouridylation (Figure 1, inset) and 20-O-methylation far outnumber the other modifications. For example, mammalian ribosomal RNA contains about 100 (and U2 snRNA 13) pseudouridines at specific sites where they are important for proper biogenesis and function of the ribonucleoproteins (RNPs) defined by these RNAs (Yu et al, 1998; King et al, 2003). Relative to uridine, pseudouridine provides an additional opportunity for hydrogen bonding (Figure 1, inset, green) and renders the RNA backbone more rigid (Charette and Gray, 2000). Modifications are introduced right after synthesis at the polynucleotide level, coor post-transcriptionally, and are believed to remain part of the RNA for its lifetime. The cell uses two mechanisms for site-specific pseudouridylation, both relying on recognition of the nucleotides flanking the target uridine. In the first, single-polypeptide pseudouridine