Universality of cell differentiation trajectories revealed by a reconstruction of transcriptional uncertainty landscapes from single-cell transcriptomic data

We employed our previously-described single-cell gene expression analysis CALISTA (Clustering And Lineage Inference in Single-Cell Transcriptional Analysis) to evaluate transcriptional uncertainty at the single-cell level using a stochastic mechanistic model of gene expression. We reconstructed a transcriptional uncertainty landscape during cell differentiation by visualizing single-cell transcriptional uncertainty surface over a two dimensional representation of the single-cell gene expression data. The reconstruction of transcriptional uncertainty landscapes for ten publicly available single-cell gene expression datasets from cell differentiation processes with linear, single or multi-branching cell lineage, reveals universal features in the cell differentiation trajectory that include: (i) a peak in single-cell uncertainty during transition states, and in systems with bifurcating differentiation trajectories, each branching point represents a state of high transcriptional uncertainty; (ii) a positive correlation of transcriptional uncertainty with transcriptional burst size and frequency; (iii) an increase in RNA velocity preceeding the increase in the cell transcriptional uncertainty. Finally, we provided biological interpretations of the universal rise-then-fall profile of the transcriptional uncertainty landscape, including a link with the Waddington’s epigenetic landscape, that is generalizable to every cell differentiation system.