Trypanosome small nuclear RNAs contain the largest repertoire of pseudouridines known so far and are guided by dual function small nucleolar RNA

The parasite Trypanosoma brucei cycles between an insect and a mammalian host,and is the causative agent of sleeping sickness. Here we performed the first genome-wide mapping of pseudouridines (Ψs) on the small RNome. The analysis revealed thepresence of 85 Ψs on small nuclear RNAs (snRNA), the highest number reported thusfar. The Ψs were found at sites of RNA-RNA interactions, but strikingly also on RNA-protein interaction domains. The modifications on the snRNAs are guided by smallnuclear or nucleolar RNAs (sn(o)RNAs) that are localized both within and outside thenucleolus. A trypanosome protein homologue to WDR79, the binding protein of Cajal-body RNA (scaRNA), is essential for guiding Ψ on snRNAs, using flexible guiding rules. Silencing of a single sn(o)RNA eliminated the Ψs on both rRNA and snRNA. Thedual functionality enables simultaneous regulation of both the spliceosome andribosome while the parasite cycles between the insect and mammalian hosts. Thestudy proposes that functional flexibility of H/ACA RNA maybe general to guide noveltargets under ambient conditions.