Surveillance of H/ACA snoRNA Transcripts in RNA Processing Mutants

Box H/ACA small nucleolar ribonucleoprotein particles (snoRNPs) are nucleolus-localized complexes that consist of four core proteins and an H/ACA small nucleolar RNA (snoRNA). Box H/ACA snoRNAs guide the pseudouridylation of ribosomal RNA and other stable RNAs. Formation of mature snoRNPs is carried out by several processing factors, including the nuclear exosome, which removes the 3’ extensions of snoRNAs. In instances of exosome dysfunction, such as deletion of the nuclear exosome components RRP47 or RRP6, 3’ extended species of snoRNAs are detected. This project investigates the assembly of H/ACA snoRNP complexes when exosome processing is disrupted—that is, without the RRP47 or RRP6 genes present—in order to further understand the biogenesis process of these complexes. When the H/ACA snoRNP assembly factor Naf1 is depleted in a strain with the exosome knockouts, we detect the degradation of the 3’ extended species of an H/ACA snoRNA but not of the mature snoRNA. This study aims to investigate whether this 3’ extended species is undergoing surveillance by the nonsense mediated decay (NMD) system, an evolutionarily conserved surveillance pathway that degrades aberrant mRNA with premature termination codons. By knocking out an essential factor in NMD (Upf1), it is possible to study whether the 3’ extended H/ACA species is identified as an NMD target. Furthermore, this study aims to study whether box H/ACA snoRNP core proteins will interact with the 3’ extended forms of the snoRNA present in the Naf1 depletion and exosome mutants to assess the assembly process of the snoRNPs.