TY - JOUR T1 - Novel Intronic Non-Coding RNAs Contribute to Maintenance of Phenotype in <em>Saccharomyces Cerevisiae</em> JF - bioRxiv DO - 10.1101/033076 SP - 033076 AU - Katarzyna B Hooks AU - Samina Naseeb AU - Sam Griffiths-Jones AU - Daniela Delneri Y1 - 2015/01/01 UR - http://biorxiv.org/content/early/2015/11/27/033076.abstract N2 - The Saccharomyces cerevisiae genome has undergone extensive intron loss during its evolutionary history. It has been suggested that the few remaining introns (in only 5% of protein-coding genes) are retained because of their impact on function under stress conditions. Here, we explore the possibility that novel non-coding RNA structures (ncRNAs) are embedded within intronic sequences and are contributing to phenotype and intron retention in yeast. We employed de novo RNA structure prediction tools to screen intronic sequences in S. cerevisiae and 36 other fungi. We identified and validated 19 new intronic RNAs via RNAseq and RT-PCR. Contrary to common belief that excised introns are rapidly degraded, we found that, in six cases, the excised introns were maintained intact in the cells. In other two cases we showed that the ncRNAs were further processed from their introns. RNAseq analysis confirmed higher expression of introns in the ribosomial protein genes containing predicted RNA structures. We deleted the novel intronic RNA structure within the GLC7 intron and showed that this predicted ncRNA, rather than the intron itself, is responsible for the cell’s ability to respond to salt stress. We also showed a direct association between the presence of the intronic ncRNA and GLC7 expression. Overall, these data support the notion that some introns may have been maintained in the genome because they harbour functional ncRNAs. ER -