Differential ribosome engagement profiling between undifferentiated and neuron-differentiated P19 cells

Translation is tightly regulated during differentiation. To gain insights into the mechanism regulating translational activity at the transcript level, we performed Ribosome Profiling of undifferentiated and neuron-differentiated P19 cells. Relative changes in translational activity between the undifferentiated and differentiated cells show an increase in the translational activity of the transcripts encoding for ribosomal proteins compared to the rest of the transcriptome. Thus, in this differentiation system, the biogenesis of the translational machinery is tightly controlled at the translational level. Overall design: P19 cells were differentiated into neuronal cells and then lyzed for material collection. Four biological replicates were collected before differentiation (D0), and four biological replicates were collected after six days of differentiation (D6). An RNA-seq library and a Ribosome Protected Fragment (RPF) library were generated for each sample. To estimate the change in ribosome engagement for each transcript between conditions, we compared the ratio of RFP reads to RNA-seq reads per transcript at D6 and D0.