Genome editing by dual nucleases records deep lineage hierarchy with high fidelity.
Single-cell lineage tracing based on CRISPR/Cas9 gene editing tracks both cell states and genetic lineages at a single-cell resolution. We developed DuTracer, a single-cell lineage tracing method, to avoid rapid target exhaustion and barcode information dropout. Firstly, we introduced this system into HEK293T cells and initiated DuTracer for tracing. We collected single-cell transcriptome and barcode amplicon, demonstrating that this system could record more hierarchical information with minimal inter-site deletions. Subsequently, we applied DuTracer to a mouse embryoid body differentiation model to track lineage transitions of different cell types. We revealed cell potency hierarchy during the stochastic differentiation process of mES cells. Overall design: For HEK293T cells, we sequentially induced the gene editing of Cas12a and Cas9 and harvested the cells at D22. For embryoid body (EB) differentiation, we designed six induction strategies. We sampled cells at different time points between D8 and D14 to capture potential differentiation cascades. Single cell RNA-seq was performed using BGI DNBelab C4 kits. For all seven libraries, the obtained cDNAs were split into two halves. One half was used to generate the RNA-seq libraries and the other half was used to make amplicon libraries.