Translation of upstream open reading frames in a model of neuronal differentiation

Caitlin M Rodriguez,Peter K Todd,Ryan E Mills,Sang Y Chun

doi:10.1186/s12864-019-5775-1

Caitlin M Rodriguez, Peter K Todd + Show 2 more

Open Access

https://doi.org/10.1186/s12864-019-5775-1

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Abstract

BackgroundUpstream open reading frames (uORFs) initiate translation within mRNA 5′ leaders, and have the potential to alter main coding sequence (CDS) translation on transcripts in which they reside. Ribosome profiling (RP) studies suggest that translating ribosomes are pervasive within 5′ leaders across model systems. However, the significance of this observation remains unclear. To explore a role for uORF usage in a model of neuronal differentiation, we performed RP on undifferentiated and differentiated human neuroblastoma cells.ResultsUsing a spectral coherence algorithm (SPECtre), we identify 4954 consistently translated uORFs across 31% of all neuroblastoma transcripts. These uORFs predominantly utilize non-AUG initiation codons and exhibit translational efficiencies (TE) comparable to annotated coding regions. On a population basis, the global impact of both AUG and non-AUG initiated uORFs on basal CDS translation were small, even when analysis is limited to conserved and consistently translated uORFs. However, uORFs did alter the translation of a subset of genes, including the Diamond-Blackfan Anemia associated ribosomal gene RPS24. With retinoic acid induced differentiation, we observed an overall positive correlation in translational shifts between uORF/CDS pairs. However, CDSs downstream of uORFs show smaller shifts in TE with differentiation relative to CDSs without a predicted uORF, suggesting that uORF translation buffers cell state dependent fluctuations in CDS translation.ConclusionThis work provides insights into the dynamic relationships and potential regulatory functions of uORF/CDS pairs in a model of neuronal differentiation.

Highlights

Upstream open reading frames initiate translation within mRNA 5′ leaders, and have the potential to alter main coding sequence (CDS) translation on transcripts in which they reside
Previous studies have used a similar protocol as a model for dopaminergic neuronal differentiation, Diff- retinoic acid differentiated (RA) treatment is thought to generate a more immature neuron-like cell than what can be achieved from a neural progenitor [26, 27, 30]
We observed an increase in expression of FMRP, a protein involved in neuronal function and translational control that is highly expressed in neurons relative to other cell types and tissues (Fig. 1e-f ) [34]

Summary

Introduction

Upstream open reading frames (uORFs) initiate translation within mRNA 5′ leaders, and have the potential to alter main coding sequence (CDS) translation on transcripts in which they reside. Ribosome profiling (RP) studies suggest that translating ribosomes are pervasive within 5′ leaders across model systems. Determining ribosomal occupancy across the transcriptome through ribosomal profiling (RP) provides us with a powerful tool for assessing the relationship between mRNA abundance. The 5′ leader (traditionally referred to as the 5′ untranslated region) of mRNAs are one well-studied source of protein synthesis regulation [6,7,8,9]. 5′ leaders can regulate the synthesis of the main coding sequence (CDS) product through a variety of mechanisms [6, 9]. Translation can initiate within 5′ leaders at upstream open reading frames (uORFS). In the case of uORFs that terminate after the CDS initiation site

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