Non-coding RNAs (ncRNAs) are a subset of RNAs that do not code for protein. They are divided into a number of different groups based on their function and targets. Small nucleolar RNAs (snoRNAs) are ncRNAs that have long been known to function as guides for ribosomal RNA (rRNA) modifying enzymes. They are classified into two major groups: box C/D snoRNAs and box H/ACA snoRNAs. Most box C/D snoRNAs direct the 2'-O-methylation of rRNA substrates, but some lack known targets and are therefore termed 'orphan snoRNAs'. Studies have implicated orphan snoRNAs in pre-mRNA processing and stability, but the functional consequence of snoRNA binding to mRNAs has not been fully determined. Saccharomyces cerevisiae had two orphan snoRNAs, snR4 and snR45, with no known function in ribosome synthesis. This project aimed to determine the targets of these snoRNAs, and investigate the effects of snoRNA binding to non-canonical target RNAs, as well as the underlying mechanism. Synthetic gene array screens with deletions of the SNR4 and SNR45 genes identified multiple positive and negative genetic interactions. In particular, deletion of either snoRNA gene was synthetic-lethal with mutation of the snoRNA-associated methyltransferase, Nop1 (Fibrillarin in humans), demonstrating that both have important functions. CLASH analyses of RNA-RNA interactions showed that these snoRNAs bind multiple mRNAs, while RNA sequencing and RT-qPCR revealed that snoRNA deletion altered mRNA abundance. Both orphan snoRNAs were well conserved between fungi, with a region of high conservation indicating a potential binding site. Associations were identified between snR4 and snR45 and multiple sequences within rRNA, including two recently identified sites of 18S rRNA acetylation. Work elsewhere showed that snR4 and snR45 function as guides for the acetyltransferase Kre33 using the region of high conservation, removing their 'orphan' status. Orphan snoRNAs have been implicated in human diseases, such as Prader Willi Syndrome and cancers. The work discussed in this thesis helps to elucidate the RNA interactions of yeast orphan snoRNAs. It has provided a greater understanding of the mechanisms involved, and may inform future work in combatting human disease.

Background: Small nucleolar RNAs (snoRNAs) are one of the most ancient families amongst non-protein-coding RNAs. They are ubiquitous in Archaea and Eukarya but absent in bacteria. Their main function is to target chemical modifications of ribosomal RNAs. They fall into two classes, box C/D snoRNAs and box H/ACA snoRNAs, which are clearly distinguished by conserved sequence motifs and the type of chemical modification that they govern. Similarly to microRNAs, snoRNAs appear in distinct families of homologs that affect homologous targets. In animals, snoRNAs and their evolution have been studied in much detail. In plants, however, their evolution has attracted comparably little attention. Results: In order to chart the phylogenetic distribution of individual snoRNA families in plants, we applied a sophisticated approach for identifying homologs of known plant snoRNAs across the plant kingdom. In response to the relatively fast evolution of snoRNAs, information on conserved sequence boxes, target sequences, and secondary structure is combined to identify additional snoRNAs. We identified 296 families of snoRNAs in 24 species and traced their evolution throughout the plant kingdom. Many of the plant snoRNA families comprise paralogs. We also found that targets are well-conserved for most snoRNA families. Conclusions: The sequence conservation of snoRNAs is sufficient to establish homologies between phyla. The degree of this conservation tapers off, however, between land plants and algae. Plant snoRNAs are frequently organized in highly conserved spatial clusters. As a resource for further investigations we provide carefully curated and annotated alignments for each snoRNA family under investigation.

Background: Small nucleolar RNAs (snoRNAs) are one of the most ancient families amongst non-protein-coding RNAs. They are ubiquitous in Archaea and Eukarya but absent in bacteria. Their main function is to target chemical modifications of ribosomal RNAs. They fall into two classes, box C/D snoRNAs and box H/ACA snoRNAs, which are clearly distinguished by conserved sequence motifs and the type of chemical modification that they govern. Similarly to microRNAs, snoRNAs appear in distinct families of homologs that affect homologous targets. In animals, snoRNAs and their evolution have been studied in much detail. In plants, however, their evolution has attracted comparably little attention. Results: In order to chart the phylogenetic distribution of individual snoRNA families in plants, we applied a sophisticated approach for identifying homologs of known plant snoRNAs across the plant kingdom. In response to the relatively fast evolution of snoRNAs, information on conserved sequence boxes, target sequences, and secondary structure is combined to identify additional snoRNAs. We identified 296 families of snoRNAs in 24 species and traced their evolution throughout the plant kingdom. Many of the plant snoRNA families comprise paralogs. We also found that targets are well-conserved for most snoRNA families. Conclusions: The sequence conservation of snoRNAs is sufficient to establish homologies between phyla. The degree of this conservation tapers off, however, between land plants and algae. Plant snoRNAs are frequently organized in highly conserved spatial clusters. As a resource for further investigations we provide carefully curated and annotated alignments for each snoRNA family under investigation.