title: Transcriptome wide annotation of eukaryotic RNase III reactivity and degradation signals.
abstract: Detection and validation of the RNA degradation signals controlling transcriptome stability are essential steps for understanding how cells regulate gene expression. Here we present complete genomic and biochemical annotations of the signals required for RNA degradation by the dsRNA specific ribonuclease III (Rnt1p) and examine its impact on transcriptome expression. Rnt1p cleavage signals are randomly distributed in the yeast genome, and encompass a wide variety of sequences, indicating that transcriptome stability is not determined by the recurrence of a fixed cleavage motif. Instead, RNA reactivity is defined by the sequence and structural context in which the cleavage sites are located. Reactive signals are often associated with transiently expressed genes, and their impact on RNA expression is linked to growth conditions. Together, the data suggest that Rnt1p reactivity is triggered by malleable RNA degradation signals that permit dynamic response to changes in growth conditions.
authors: Université de Sherbrooke Centre of Excellence in RNA Biology, Département de microbiologie et d'infectiologie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec, Canada.
authors: Jules
authors: J
authors: Gagnon
authors: Université de Sherbrooke Centre of Excellence in RNA Biology, Département de microbiologie et d'infectiologie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec, Canada.
authors: Mathieu
authors: M
authors: Lavoie
authors: Université de Sherbrooke Centre of Excellence in RNA Biology, Département de microbiologie et d'infectiologie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec, Canada.
authors: Mathieu
authors: M
authors: Catala
authors: Université de Sherbrooke Centre of Excellence in RNA Biology, Département de microbiologie et d'infectiologie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec, Canada.
authors: Francis
authors: F
authors: Malenfant
authors: Université de Sherbrooke Centre of Excellence in RNA Biology, Département de microbiologie et d'infectiologie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec, Canada.
authors: Sherif Abou
authors: SA
authors: Elela
mesh_terms: D001483:Base Sequence; D015966:Gene Expression Regulation, Fungal; D058977:Molecular Sequence Annotation; D009690:Nucleic Acid Conformation; D020871:RNA Stability / Q000235:genetics*; D012330:RNA, Double-Stranded / Q000235:genetics; D012331:RNA, Fungal / Q000235:genetics; D043244:Ribonuclease III / Q000096:biosynthesis / Q000235:genetics*; D012441:Saccharomyces cerevisiae / Q000235:genetics*; D029701:Saccharomyces cerevisiae Proteins / Q000096:biosynthesis / Q000235:genetics*; D013379:Substrate Specificity; D059467:Transcriptome / Q000235:genetics*
chemical_list: D012330:RNA, Double-Stranded; D012331:RNA, Fungal; D029701:Saccharomyces cerevisiae Proteins; C468367:RNT1 protein, S cerevisiae; D043244:Ribonuclease III