Single-cell multiomics sequencing reveals the functional regulatory landscape of early embryos

Extensive epigenetic reprogramming occurs during preimplantation embryo development and is accompanied by zygotic genome activation (ZGA) and first cell fate specification. Recent studies using single-cell epigenome sequencing techniques have provided global views of the dynamics of different epigenetic layers during this period. However, it remains largely unclear how the drastic epigenetic reprogramming contributes to transcriptional regulatory network. Here, we developed a single-cell multiomics sequencing technology (scNOMeRe-seq) that enables profiling of genome-wide chromatin accessibility, DNA methylation and RNA expression in the same individual cell with improved performance compared to that of earlier techniques. We applied this method to analyze the global dynamics of different molecular layers and their associations in mouse preimplantation embryos. We found that global DNA methylation remodeling facilitates the reconstruction of genetic lineages in early embryos and revealed that the gradual increases in heterogeneity among blastomeres are driven by asymmetric cleavage. Allele-specific DNA methylation pattern is maintained throughout preimplantation development and is accompanied by allele-specific associations between DNA methylation and gene expression in the gene body that are inherited from oocytes and sperm. Through integrated analyses of the collective dynamics between gene expression and chromatin accessibility, we constructed a ZGA-associated regulatory network and revealed coordination among multiple epigenetic layers, transcription factors (TFs) and repeat elements that instruct the proper ZGA process. Moreover, we found that inner cell mass (ICM)/trophectoderm (TE) lineage-associated cis-regulatory elements are stepwise activated in blastomeres during post-ZGA embryo stages. TE lineage-specific TFs play dual roles in promoting the TE program while repressing the ICM program, thereby separating the TE lineage from the ICM lineage. Taken together, our findings not only depict the first single-cell triple-omics map of chromatin accessibility, DNA methylation and RNA expression during mouse preimplantation development but also enhance the fundamental understanding of epigenetic regulation in early embryos.