Human DCM-time machine unravels cell state changes during primitive gut tube differentiation

Cell state changes in development and differentiation are directed by gene and enhancer activity changes, the dynamics of which are difficult to study in real time. To be able to define lineage paths and monitor time resolved cell state changes during pluripotent stem cell differentiation, we introduced the DCM-time machine technology (DCM-TM) into human induced pluripotent stem cells (iPSCs). We demonstrate that, at time of induction, human DCM-TM labels active genes and enhancers. In addition, we find that the majority of the DCM methylation labels are propagated during S-phase, which makes it well suited to trace gene and enhancer activity during cell state changes. As proof of concept, we applied the DCM-time machine to study differentiation from iPSCs towards definitive endoderm and primitive gut tube cells. In a comparative analysis with scRNA-seq, we show the capacity of the system to label gene and enhancer activity during differentiation and trace back gene and enhancer activity over time across multiple cell divisions. In addition, we demonstrate that combining DCMTM with methylated DNA sequencing (MeD-seq) enables the detection of CpG methylation changes, which can be correlated with gene and enhancer activity dynamics. Human DCM-TM provides a novel genome-wide lineage tracing tool for iPSCs and will be a significant contribution to the understanding of healthy and pathogenic embryonic development.