Poster abstracts

Poster number 110 submitted by Caitlin Rodriguez

Ribosome Profiling reveals a conditional role for upstream open reading frames in neuronal differentiation.

Caitlin M. Rodriguez (Department of Neurology, University of Michigan), Sang Y. Chun (Department of Computational Medicine and Bioinformatics, University of Michigan), Ryan E. Mills (Department of Computational Medicine and Bioinformatics, University of Michigan), Peter K. Todd (Department of Neurology, University of Michigan)

Abstract:
Ribosome profiling is a next-generation sequencing method that provides a transcriptome-wide snapshot of ribosome occupancy1. This technique demonstrates that fully assembled ribosomes frequently occupy the 5’ leader sequence outside of traditional open reading frames, suggesting a potential role for upstream opening reading frame (uORFs) in cellular functions2. To explore the potential role of uORFs in neuronal differentiation, we performed ribosome profiling in both undifferentiated and retinoic acid differentiated SH-SY5Y neuroblastoma cells. Using a novel spectral coherence-based classification algorithm to identify regions of active translation (SPECtre), we have identified a series of high confidence uORFs in SH-SY5Y cells, many of which exhibit initiation at non-AUG codons. Interestingly a subset of these transcripts exhibit a strong shift in uORF usage with retinoic acid differentiation as shown by increased conditional ribosome occupancy in the absence of concomitant changes in RNA abundance. 59% of these shifting transcripts demonstrate a negative correlation between uORF and main ORF occupancy with only 5% showing a positive relationship, corroborating the understanding that uORFs typically act to negatively regulate downstream transition3. Taken together, our findings suggest that uORF usage is a common feature in neuronal-like cells and that the use of uORFs is altered upon neuronal differentiation, suggesting a functional role for these processes in neuronal development.

References:
1. Ingolia, NT, et al.,Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling. Science. 324, 218-23 (2009).
2. Ingolia, NT, et al.,Ribosome Profiling of Mouse Embryonic Stem Cells Reveals the Complexity and Dynamics of Mammalian Proteomes. Cell. 147, 789-802 (2011).
3. Sonenberg, N and Hinnebusch, AG, Regulation of Translation Initiation in Eukaryotes: Mechanisms and Biological Targets, 136, 731-45 (2009).

Keywords: ribosome profiling, upstream open reading frame, translation