Ensembles of genome-coverage single-cell histone modifications reveal epigenetic lineages during mouse preimplantation development

We applied TACIT to profile seven histone modifications at single-cell resolution in mouse early embryos from zygotes to blastocysts. Profound epigenetic resetting during early embryo development from fertilization to blastocyst ensures zygotic genome activation and also begets progressive cellular heterogeneities1-6. Mapping single-cell epigenomic profiles of core histone modifications covering each individual cell onto the lineage tree (epigenetic lineages) is a fundamental goal in developmental biology. Here, we develop a method, TACIT, achieving genome-coverage single-cell profiling of seven histone modifications in mouse early embryos from zygotes to blastocysts. TACIT yields up to half million fragments per cell with peaks equivalent of bulk assays. Integrating these single-cell histone modifications with scRNA-seq data7, we chart a cell-kinship informed epigenetic lineage landscape. Multimodal chromatin state annotations show that the ZGA onset at early 2-cell stage already primes heterogeneities in totipotency. Epigenetic lineages also allow for nominating totipotency gene regulatory networks including stage-specific transposable elements and putative transcription factors (TFs). In addition, machine learning models together with single-cell co-profiles of multiple histone modifications facilitate prediction of the earliest cell branching toward inner cell mass (ICM) and trophectoderm (TE) in latent multimodal space as well as feature regulatory elements and previously unknown lineage-specifying TFs. Together, our work reconstructs single-cell holistic epigenetic lineages, elucidating multimodal regulation of cellular heterogeneities and cell fate priming during mouse pre-implantation development.