sc-LAB2FATE · Revealing plasticity of developmental cell fate decisions by single-cell RNA labelling

Every time an egg is fertilised, the cellular diversity of an animal must be rebuilt from scratch. Therefore, a central question in developmental biology is how cells differentiate to acquire distinct fates. A combination of genetics, molecular biology, and microscopy approaches has led to fundamental discoveries. Recently, single-cell genomics has enabled the analysis of transcriptional differentiation trajectories at unprecedented scale and resolution. However, ordering single cells by transcriptome similarity only gives ensemble averages of differentiation trajectories and not the full spectrum of cell state transitions. It then remains unclear whether cells can commit to their fate at different stages of development or change differentiation trajectories. The sc-LAB2FATE project proposes to measure how single-cell transcriptomes change over time in living zebrafish embryos using a new RNA labelling methodology. This will reveal the full spectrum of differentiation trajectories during gastrulation, allowing to see not only the major routes of differentiation, but also rare alternative trajectories. Single-cell RNA labelling, biochemical nucleoside conversion and sequencing will be used to measure mRNA kinetics and transcriptome dynamics of zebrafish embryos at single-cell resolution. Spontaneous cell fate changes during normal development will be contrasted with induced cell fate changes upon cell transplantation from different cell types to decipher signalling interactions. This project will leverage single-cell genomics and traditional approaches in developmental biology to build a conceptual framework for analysing embryonic development as both a genetically programmed and a self-organised phenomenon, and to provide a general blueprint of how one can study perturbation response using metabolic labelling in living systems.