Novel Single-Cell Multiomics Approach to Analyze Replication Timing and Gene Expression in Mouse Preimplantation Embryos

Analysis of a cell’s replication timing (RT) provides insight into how genes replicate, early or late, during the S-phase of the cell cycle. RT is cell-type specific, inheritable, and has been correlated to gene expression in normal and diseased states. However, most studies have been limited to somatic cells. Very little is known about RT in early mouse embryos, and how it correlates with the start of transcription during zygote gene activation (ZGA), at the 2-cell stage. In this study, we used a novel in-house single-cell multiomics approach to simultaneously analyze RT and gene expression in individual cells of the mouse 1-cell, 2-cell, and 4-cell embryos. We demonstrated that RT was established at the 1-cell stage prior to ZGA. Surprisingly, we observed RT and gene expression correlation trends that were different in early totipotent embryos, compared to previously published studies in somatic cells. Late replicating regions correlated with higher gene expression and open chromatin in the early developing embryos. Lastly, we performed an integrated pseudo time trajectory analysis combining RT and gene expression information per cell.