Cell state transitions are decoupled from cell division during early embryo development [I]

As tissues develop, cells divide and differentiate concurrently. Conflicting evidence shows that cell division is either dispensable or required for formation of cell types. To determine the role of cell division in differentiation, we arrested the cell cycle in zebrafish embryos using two independent approaches and profiled them at single-cell resolution. We show that cell division is dispensable for differentiation of all embryonic tissues during initial cell type differentiation from early gastrulation to the end of segmentation. However, in the absence of cell division, differentiation slows down in some cell types, and cells exhibit global stress responses. While differentiation is robust to blocking cell division, the proportions of cells across cell states are not but show evidence of partial compensation. This work clarifies our understanding of the role of cell division in development and showcases the utility of combining embryo-wide perturbations with single-cell RNA sequencing to uncover the role of common biological processes across multiple tissues. Overall design: We arrested the cell cycle in zebrafish embryos at 6 hours post fertilization (hpf) using two independent approaches: a chemical approach (hydroxyurea and aphidicolin, HUA) and a genetic approach involving a loss-of-function mutation in the gene emi1 (allele hi2648). We tracked differentiation dynamics using single-cell RNA sequencing (scRNA-seq) on embryos spanning 6–24 hpf for HUA-treated and control embryos, and at 24 hpf for emi1 mutant embryos. Overall we have collected multiple replicates for control embryos (ABs) at 6, 8, 10, 14, 18, 21 and 24 hpf, for HUA treated at 8, 10, 14 and 24 hpf and for emi1 mutants at 24 hpf. Details about the samples can be found in the supplementary file "sample_information.txt"