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SnoBIRD: A tool to identify C/D box snoRNAs and refine their annotation across all eukaryotes

ABSTRACT: Small nucleolar RNAs (snoRNAs), a group of noncoding RNAs present amongst all eukaryotes, are known for their regulation of ribosome biogenesis and splicing. Despite their central cellular roles, current snoRNA annotations remain incomplete. Indeed, several eukaryote annotations contain few or no snoRNAs, and none distinguishes expressed snoRNAs from their pseudogenes—a recently characterized snoRNA subclass with distinct features and expression levels. To address this, we developed SnoBIRD, a BERT-based C/D box snoRNA predictor trained on snoRNAs spanning all eukaryote kingdoms. We show that SnoBIRD outperforms existing tools in a test set environment and is the only predictor capable of identifying snoRNA pseudogenes using biologically relevant signal. Applied on the fission yeast and human genomes, we demonstrate that only SnoBIRD scales well with genome size in terms of runtime, and we identify and experimentally validate several new SnoBIRD-predicted C/D box snoRNAs. By running SnoBIRD on multiple eukaryote genomes, we identify hundreds of novel C/D box snoRNA candidates and highlight SnoBIRD’s usefulness to determine the evolutionary paths of snoRNAs that share a common host locus but are distributed across different species. Overall, SnoBIRD represents a user‑friendly and efficient tool for reliably predicting C/D box snoRNAs and their pseudogenes across any eukaryote kingdom.

ORGANISM(S): Mus musculus Schizosaccharomyces pombe Saccharomyces cerevisiae Gallus gallus Macaca mulatta

PROVIDER: GSE290579 | GEO | 2025/07/30

REPOSITORIES: GEO

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Project description:ncRNA expression, including snoRNAs, across 11 tissues using polyA-neutral amplification Non-coding RNAs (ncRNAs) are an essential class of molecular species that have been difficult to monitor on high throughput platforms due to frequent lack of polyadenylation. Using a polyadenylation-neutral amplification protocol and next-generation sequencing, we explore ncRNA expression in eleven human tissues. ncRNAs 7SL, U2, 7SK, and HBII-52 are expressed at levels far exceeding mRNAs. C/D and H/ACA box snoRNAs are associated with rRNA methylation and pseudouridylation, respectively: spleen expresses both, hypothalamus expresses mainly C/D box snoRNAs, and testes show enriched expression of both H/ACA box snoRNAs and RNA telomerase TERC. Within the snoRNA 14q cluster, 14q(I-6) is expressed at much higher levels than other cluster members. More reads align to mitochondrial than nuclear tRNAs. Many lincRNAs are actively transcribed, particularly those overlapping known ncRNAs. Within the Prader-Willi syndrome loci, the snoRNA HBII-85 (group I) cluster is highly expressed in hypothalamus, greater than in other tissues and greater than group II or III. Additionally, within the disease locus we find novel transcription across a 400,000 nt span in ovaries. This genome-wide polyA-neutral expression compendium demonstrates the richness of ncRNA expression, their high expression patterns, their function-specific expression patterns, and is publicly available. ArrayExpress Release Date: 2010-07-05 Publication Title: ncRNA expression, including snoRNAs, across 11 tissues using polyA-neutral amplification Publication Author List: Matthew Biery,Heather Bouzek,Ronghua Chen,Stuart Jackson,Jason M. Johnson,Carol A. Rohl,Chris K. Raymond,David Haynor,Christopher D. Armour,John C. Castle Person Roles: submitter Person Last Name: Loewer Person First Name: Martin Person Mid Initials: Person Email: martin.loewer@tron-mainz.de Person Phone: +49 6131-720298-11 Person Address: TRON Translationale Onkologie gGmbH, Langenbeckstr. 8, D-55131 Mainz Person Affiliation: TRON

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SnoBIRD: A tool to identify C/D box snoRNAs and refine their annotation across all eukaryotes

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