Ribosomal profiling in single cells reveals cell-cycle dependent translational pausing

In recent years novel single-cell sequencing methods have allowed an in-depth analysis of the diversity of cell types and cell states in a wide range of organisms. These novel tools predominantly focus on sequencing the genomes, epigenomes, and transcriptomes of single cells. However, despite recent progress in detecting proteins by mass spectrometry with single-cell resolution, it remains a major challenge to measure translation in individual cells. Building upon existing ribosome profiling protocols, we majorly increased the sensitivity of these assays allowing ribosome profiling in single cells. Integrated with a machine learning approach, this technology achieves single codon resolution in individual cells. We validate this method by demonstrating that limitation for a particular amino acid causes ribosome pausing at a subset of the codons representing this amino acid. Interestingly, this pausing is only observed in a sub-population of cells correlating to its cell-cycle state. We further corroborate this phenomenon in non-limiting conditions and detect pronounced GAA pausing during mitosis. Finally, we demonstrate the applicability of this technique to rare primary enteroendocrine cells. This new technology provides the first steps towards determining the contribution of the translational process to the astonishing diversity between seemingly identical cells. Ribosome profiling in single HEK293T and hTERT-RPE1 FUCCI cells.