SnoRNA Evolution, Genomic Context and Mobility: The Role of Function and Host Gene Association

Small nucleolar RNAs (snoRNAs) are best known for guiding chemical modifications of ribosomal and spliceosomal RNAs. Most vertebrate snoRNAs are encoded within introns of host genes and therefore depend on the production and processing of host precursor RNAs for their biogenesis. Despite this close genomic association, how host-gene context is associated with snoRNA abundance and evolution remains poorly understood. Here, we combined human snoRNA annotations from snoDB, Ensembl gene annotations, snoRNA-sensitive abundance data across multiple tissues, and vertebrate orthology analyses to systematically characterize snoRNA-host-gene relationships. Host genes were grouped into functional classes to compare snoRNA genomic organization, abundance, and conservation across host contexts. We confirmed that snoRNAs are enriched in ribosome-related and lncRNA host genes. SnoRNAs embedded in ribosome-related host genes, particularly ribosomal protein genes, showed the highest abundance and were predominantly broadly detected across tissues, whereas snoRNAs in other host classes were generally less abundant and more tissue-restricted. Across vertebrates, snoRNA sequences were often widely conserved, but the exact host-gene association was less stable, showing that sequence conservation can persist despite changes in genomic embedding. Ribosome-related host classes nevertheless emerged as comparatively stable environments. Together, these results show that snoRNA-host-gene relationships vary across host contexts and evolutionary histories and are consistent with a conceptual continuum from functionally concordant associations to more independent passenger relationships.