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

Abstract

17Extensive epigenetic reprogramming occurs during preimplantation embryo development and is 18 accompanied by zygotic genome activation (ZGA) and first cell fate specification. Recent studies 19 using single-cell epigenome sequencing techniques have provided global views of the dynamics of 20 different epigenetic layers during this period. However, it remains largely unclear how the drastic 21 epigenetic reprogramming contributes to transcriptional regulatory network. Here, we developed a 22 single-cell multiomics sequencing technology (scNOMeRe-seq) that enables profiling of genome-23 wide chromatin accessibility, DNA methylation and RNA expression in the same individual cell 24 with improved performance compared to that of earlier techniques. We applied this method to 25 analyze the global dynamics of different molecular layers and their associations in mouse 26 preimplantation embryos. We found that global DNA methylation remodeling facilitates the 27 reconstruction of genetic lineages in early embryos and revealed that the gradual increases in 28 heterogeneity among blastomeres are driven by asymmetric cleavage. Allele-specific DNA 29 methylation pattern is maintained throughout preimplantation development and is accompanied by 30 allele-specific associations between DNA methylation and gene expression in the gene body that 31 are inherited from oocytes and sperm. Through integrated analyses of the collective dynamics 32 between gene expression and chromatin accessibility, we constructed a ZGA-associated regulatory 33 network and revealed coordination among multiple epigenetic layers, transcription factors (TFs) 34 and repeat elements that instruct the proper ZGA process. Moreover, we found that inner cell mass 35 (ICM)/trophectoderm (TE) lineage-associated cis-regulatory elements are stepwise activated in 36 blastomeres during post-ZGA embryo stages. TE lineage-specific TFs play dual roles in promoting 37 the TE program while repressing the ICM program, thereby separating the TE lineage from the ICM 38 lineage. Taken together, our findings not only depict the first single-cell triple-omics map of 39 chromatin accessibility, DNA methylation and RNA expression during mouse preimplantation 40 development but also enhance the fundamental understanding of epigenetic regulation in early 41 embryos. 42 43

Multi-omics integration and regulatory inference for unpaired single-cell data with a graph-linked unified embedding framework

“…Recent advances in experimental multi-omics technologies have increased the availability of paired data [8][9][10][11]30 . While most of the current simultaneous multi-omics protocols still suffer from lower data quality or throughput than that of single-omics methods 54 , paired cells can be highly informative in anchoring different omics layers and should be utilized in conjunction with unpaired cells whenever available.…”

“…While simultaneous assays are emerging recently [8][9][10][11] , different omics are usually measured independently and produce unpaired data, which calls for effective and efficient in silico multi-omics integration 12,13 .…”

Recent advances in single‐cell multimodal analysis to study immune cells

“…Single‐nucleus chromatin accessibility and mRNA expression sequencing can also be used to understand gene regulation, as this technology provides high‐throughput sequencing of the transcriptome and chromatin accessibility in the same cell 49 . Other advances can be applied for a different problem of characterizing molecular cell state, and include those utilizing transcriptomics (mRNA) as one of its modalities, in addition to either DNA, 50 protein expression, 10,51 chromatin accessibility 52,53 or DNA methylation 54–57 . Lineage tracing of immune cells that do not carry a natural bar code, such as TCR or B‐cell receptor, can also benefit from recent technologies using synthetic barcodes, such as CellTagging which uses a lentiviral approach 58 .…”

The synergistic coordination of DNA 5-hydroxylmethylcytosine and RNA 5-methycytosine regulates human foetal development

“…3a, e). Chromatin accessibility of cis-regulatory sequences drives cell differentiation and zygotic genome activation (ZGA) by regulating gene expression in early mammalian embryos [7][8][9]13 . Studies have shown that post-translational modi cations, such as histone acetylation and ubiquitination, enhance chromatin accessibility by disrupting chromatin folding and globule formation 47,48 .…”