Transcriptome Wide Annotation of Eukaryotic RNase III Reactivity and Degradation Signals [ncRNA-Seq]

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 stability. Rnt1p cleavage signals are randomly distributed in the yeast genome and encompass wide variety of sequence 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 stability of the yeast transcriptome is regulated by malleable RNA degradation signals that permit dynamic response to changes in growth conditions. Overall design: Total RNA from rnt1d strain was divided in two samples. One sample was treated with purified Rnt1p. The other was only incubated with buffer. The two samples were then enriched for small RNA.