title: Genome-wide prediction and analysis of yeast RNase III-dependent snoRNA processing signals.
abstract: In Saccharomyces cerevisiae, the maturation of both pre-rRNA and pre-small nucleolar RNAs (pre-snoRNAs) involves common factors, thereby providing a potential mechanism for the coregulation of snoRNA and rRNA synthesis. In this study, we examined the global impact of the double-stranded-RNA-specific RNase Rnt1p, which is required for pre-rRNA processing, on the maturation of all known snoRNAs. In silico searches for Rnt1p cleavage signals, and genome-wide analysis of the Rnt1p-dependent expression profile, identified seven new Rnt1p substrates. Interestingly, two of the newly identified Rnt1p-dependent snoRNAs, snR39 and snR59, are located in the introns of the ribosomal protein genes RPL7A and RPL7B. In vitro and in vivo experiments indicated that snR39 is normally processed from the lariat of RPL7A, suggesting that the expressions of RPL7A and snR39 are linked. In contrast, snR59 is produced by a direct cleavage of the RPL7B pre-mRNA, indicating that a single pre-mRNA transcript cannot be spliced to produce a mature RPL7B mRNA and processed by Rnt1p to produce a mature snR59 simultaneously. The results presented here reveal a new role of yeast RNase III in the processing of intron-encoded snoRNAs that permits independent regulation of the host mRNA and its associated snoRNA.
authors.affiliation: Université de Sherbrooke, Département de Microbiologie et d'Infectiologie, 3001 12e Ave nord, Sherbrooke, Québec J1H 5N4, Canada.
authors.forename: Ghada
authors.initials: G
authors.lastname: Ghazal
authors.forename: Dongling
authors.initials: D
authors.lastname: Ge
authors.forename: Julien
authors.initials: J
authors.lastname: Gervais-Bird
authors.forename: Jules
authors.initials: J
authors.lastname: Gagnon
authors.forename: Sherif
authors.initials: S
authors.lastname: Abou Elela
mesh_terms: D001483:Base Sequence; D019295:Computational Biology; D023281:Genomics; D007438:Introns / Q000235:genetics; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D012322:RNA Precursors / Q000235:genetics / Q000378:metabolism; D012326:RNA Splicing / Q000235:genetics / Q000502:physiology*; D012331:RNA, Fungal / Q000235:genetics / Q000378:metabolism; D020537:RNA, Small Nucleolar / Q000235:genetics / Q000378:metabolism*; D043244:Ribonuclease III / Q000502:physiology*; D012269:Ribosomal Proteins / Q000235:genetics*; D012441:Saccharomyces cerevisiae / Q000201:enzymology / Q000235:genetics* / Q000378:metabolism; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics* / Q000502:physiology*; D013379:Substrate Specificity; D014158:Transcription, Genetic
chemical_list: D012322:RNA Precursors; D012331:RNA, Fungal; D020537:RNA, Small Nucleolar; D012269:Ribosomal Proteins; D029701:Saccharomyces cerevisiae Proteins; C073617:RPL7A protein, S cerevisiae; C468367:RNT1 protein, S cerevisiae; D043244:Ribonuclease III