Poster abstracts
Poster number 120 submitted by Jenna Smith
Translation of small open reading frames within unannotated RNA transcripts in Saccharomyces cerevisiae
Jenna E. Smith (Center for RNA Molecular Biology, Case Western Reserve University, Cleveland, OH), Juan R. Alvarez-Dominguez, Wenqian Hu (Whitehead Institute for Biomedical Research, Cambridge, MA), Sarah Geisler, Nicholas Kline, Nathan Huynh (Center for RNA Molecular Biology, Case Western Reserve University, Cleveland, OH), Jeff Coller (Center for RNA Molecular Biology, Case Western Reserve University, Cleveland, OH), Kristian E. Baker (Center for RNA Molecular Biology, Case Western Reserve University, Cleveland, OH)
Abstract:
High-throughput gene expression analysis has revealed that eukaryotic cells express many previously unidentified and largely uncharacterized transcripts. In most cases, these transcripts are bioinformatically predicted to lack protein-coding capacity. Here, we investigate >1100 unannotated transcripts in yeast predicted to be non-coding. We show that a majority of these RNAs associate with polyribosomes to an extent more similar to mRNAs than classical, well-characterized non-coding RNAs. Furthermore, ribosome profiling demonstrates that many of these RNAs are directly bound by ribosomes, with a number demonstrating periodicity of ribosome footprints indicative of bona fide translation. Location of ribosome footprints facilitated the identification of putative open-reading frames 10-96 codons in length within a number of unannotated RNAs. We directly demonstrate translation of a subset of these open-reading frames through detection of the predicted polypeptide. Consistent with their translation, many unannotated RNAs are targeted for degradation by the translation-dependent, nonsense-mediated RNA decay (NMD) pathway. Based upon ribosome profiling, we predict these RNAs are targets for NMD due to long 3’ ribosome-free regions. Inspection of mammalian lncRNAs reveals that a subset are also sensitive to NMD, indicating translation of non-coding transcripts in higher eukaryotes. These data demonstrate that transcripts considered to lack coding potential do in fact engage translating ribosomes. An intriguing possibility is that this translation serves either as a mechanism to regulate the metabolism or function of these RNAs or to produce short proteins, potentially expanding the proteome of yeast and other eukaryotes.
Keywords: lncRNA, Nonsense-mediated RNA decay, Translation