Identification of discrete classes of small nucleolar RNA featuring different ends and RNA binding protein dependency.
Bottom Line: The results indicate that C/D snoRNAs are expressed as two distinct forms differing in their ends with respect to boxes C and D and in their terminal stem length.Analysis of the potential secondary structure of both forms indicates that the k-turn motif required for binding of NOP58 is less stable in short forms which are thus less likely to mature into a canonical snoRNP.Taken together the data suggest that C/D snoRNAs are divided into at least two groups with distinct maturation and functional preferences.
Affiliation: Département de biochimie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada.Show MeSH
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Mentions: Box C/D snoRNAs are 50–100 nucleotides (nt)-long transcripts featuring conserved box C (RUGAUGA where R is a purine) and box D (CUGA) motifs that align to form a characteristic structural motif called the kink-turn or K-turn motif (4,7,9–11), as illustrated in Figure 1A. K-turn motifs are widespread in many classes of RNA and involve non-canonical G–A base pairing causing a tight kink in the axis of double-stranded RNA (12,13). The k-turn motif is typically flanked by a 5’ canonical stem composed of regular base pairs and by a 3’ non-canonical stem consisting of the G–A base pairs (11,13). The minor grooves of the canonical and non-canonical stems can interact, coordinated by metal ions or binding proteins, stabilizing the structure (11). In box C/D snoRNAs, constrained by the sequences of the boxes C and D, the non-canonical G–A stem is typically followed by one pair of U–U mismatched nucleotides and two canonical base pairs (Figure 1A). Both the canonical stem and the extended non-canonical stem appear to be important for proper processing of the snoRNA (14) and assembly of the snoRNP complex. In vertebrates, most snoRNAs are encoded in introns and co-transcribed from the promoter of their host genes. The assembly of the pre-snoRNP complex typically occurs on spliced and debranched introns and is initiated by the recognition of the k-turn structure by the core binding protein 15.5K (15–20). The binding of 15.5K to the k-turn provides a scaffold for the assembly of the box C/D snoRNP complex which includes additional core binding proteins NOP56, NOP58 and the methyltransferase fibrillarin (15,21–26). The resulting pre-snoRNPs are exonucleolytically trimmed from both the 5′ and 3′ ends, generating mature snoRNPs (19,20,27). The binding of the core proteins likely protects the snoRNAs from further trimming and determines their exact termini (14). Disruption of the k-turn and flanking stems prevents stable accumulation of snoRNAs (14,22), underlining the importance of these motifs for the appropriate processing and the stability of C/D snoRNAs and the proper structure and assembly C/D snoRNPs.
Affiliation: Département de biochimie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada.