Processing of snoRNAs as a new source of regulatory non-coding RNAs: snoRNA fragments form a new class of functional RNAs

Abstract

Recent experimental evidence suggests that most of the genome is transcribed into non-coding RNAs. The initial transcripts undergo further processing generating shorter, metabolically stable RNAs with diverse functions. Small nucleolar RNAs (snoRNAs) are non-coding RNAs that modify rRNAs, tRNAs, and snRNAs that were considered stable. We review evidence that snoRNAs undergo further processing. High-throughput sequencing and RNase protection experiments showed widespread expression of snoRNA fragments, known as snoRNA-derived RNAs (sdRNAs). Some sdRNAs resemble miRNAs, these can associate with argonaute proteins and influence translation. Other sdRNAs are longer, form complexes with hnRNPs and influence gene expression. C/D box snoRNA fragmentation patterns are conserved across multiple cell types, suggesting a processing event, rather than degradation. The loss of expression from genetic loci that generate canonical snoRNAs and processed snoRNAs results in diseases, such as Prader-Willi Syndrome, indicating possible physiological roles for processed snoRNAs. We propose that processed snoRNAs acquire new roles in gene expression and represent a new class of regulatory RNAs distinct from canonical snoRNAs.

Figure 1. Generation of non-coding RNAs from longer precursors

rRNAs: ribosomal RNAs are embedded in a larger precursor RNAs from which they are released through a series of endo and exo-nuclease activities [66]. tRNAs: transfer RNAs are generated from precursors that often contains introns, that are released through nuclease cleavage [67]. snRNAs: a primary pol II transcript is cleaved at the 3' end [68,69]. snoRNAs: in vertebrates, small nucleolar RNAs are located in introns from which they are released after lariat opening and exonuclease trimming [68]. miRNAs: microRNAs reside in double stranded structures, which are cleaved by Drosha/DGCR8 and later DICER [4]. endosiRNAs: endogenous siRNAs are cleaved by DICER [70,71]. Stars indicate base modifications that have been well documented for rRNA [66], tRNA, snRNA [67] and snoRNA [72]. The dotted arrow indicates the generation of miRNAs from snoRNAs. It is currently not clear at what stage this further processing occurs.

Figure 2. Function and biogenesis of snoRNA derived RNAs (sdRNAs)

A: Most mammalian snoRNAs reside in introns from which they are released during the splicing reaction. After lariat opening, the intron is degraded by exonucleases (yellow). Proteins assembling on the snoRNA prevent its further degradation and mature snoRNAs accumulate in the nucleolus (B). It is currently unclear whether sdRNAs originate from a common precursor RNA (C) or are generated from snoRNAs through further processing (D). E: snoRNA give rise to psnoRNAs and miRNAs that together form snoRNA derived RNAs (sdRNAs). F: psnoRNAs influence gene expression and (G) alternative splicing. H: snoRNA derived miRNAs act in translational regulation. I: Canonical snoRNAs can accumulate in the cytosol under stress conditions.

Figure 3. Schematic alignment of psnoRNAs to a generic C/D box snoRNA

On the top is a hypothetical, generic C/D box snoRNA. The RNA is artificially set to 100 nt in length, which allows alignment of the functional motifs found in various snoRNAs of different lengths. The RNA elements are colored. C: C-box, D: D-box, D’ and C’: D’ and C’ boxes, AS: Antisense box. The yellow boxes at the end reflect the terminal stem structures. The psnoRNAs listed in Supplemental Table 1 are indicated schematically by showing the RNA elements they contain. These sequences were experimentally validated. Note that most include C and D boxes and lack the stems. The numbers indicate the occurrence of each form listed in Supplemental Table 1. More sequences have been identified in deep sequencing experiments [32].