Mullti-omics profiling of mouse gastrulation at single-cell resolution

From time-to-time, these GEITP pages have discussed topics of developmental biology (such as this paper) — because there are many similarities to evolution (and both involve gene-environment interactions). Early mammalian developmental stages include: [a] Zygotic stage (zygote is formed when sperm and egg fuse); [b] Blastocyst stage (single-celled zygote begins to divide into a solid cluster of cells, which then becomes a hollow ball called a blastocyst (which attaches to endometrium of the mother’s uterus); [c] Gastrulation stage (single-cell-layered blastula is re-organized into a multi-layered structure called the gastrula, which includes the inner cell mass). Formation of the three primary germ cell layers (endoderm, mesoderm, exoderm) during gastrulation is an essential step in establishing the vertebrate body plan; this process is known to be associated with major transcriptional changes (DNA being transcribed into RNA).

Global epigenetic reprogramming accompanies these changes [which were studied in the attached paper]. Authors describe a “single-cell multi-omics map” of chromatin accessibility, DNA methylation, and RNA expression during the onset of gastrulation in mouse embryos. The initial exit from pluripotency (ability of a cell to develop into any of the three primary germ cell layers) coincides with the establishment of a global repressive epigenetic landscape — followed by emergence of lineage-specific epigenetic patterns during gastrulation. Cells — committed to mesoderm and endoderm — undergo widespread coordinated epigenetic rearrangements at enhancer marks, driven by ten-eleven translocation (TET)-mediated demethylation and concomitant increase in chromatin accessibility. In contrast, the methylation and chromatin accessibility landscape of ectodermal cells is already established in the early epiblast (the outermost layer of the gastrula — before it differentiates into ectoderm and mesoderm).

Hence, regulatory elements associated with each germ layer are either epigenetically primed, or remodeled — before cell-fate decisions — which provides the molecular framework for a hierarchical emergence of the primary germ layers. Recent technological advances have enabled the profiling of multiple molecular layers at single-cell resolution, providing novel opportunities to study the relationship between the transcriptome (DNA —> mRNA) and epigenome (genes involved in DNA methylation, RNA interference, histone modifications, chromatin remodeling) during cell-fate decisions. Authors [see attached article] studied single-cell nucleosome-, methylome- and transcriptome-sequencing (scNMT-seq) to profile 1,105 single cells isolated from mouse embryos at four developmental stages [embryonic day (E)4.5, E5.5, E6.5 and E7.5] representing the exit from pluripotency and primary germ-layer specification. Cells were assigned to a specific lineage by mapping their RNA-expression profiles to a comprehensive single-cell atlas for each developmental stage. Using dimensionality reduction, authors show that all three molecular layers contain sufficient information to separate cells by stage and by lineage identity.

To relate epigenetic changes to the transcriptional dynamics across stages, authors calculated — for each gene and across all embryonic cells — correlations between RNA expression and corresponding DNA methylation, or chromatin accessibility, at the gene’s promoter region. Out of 5,000 genes tested, authors identified 125 genes, the expression of which showed significant correlation with promoter DNA methylation, and 52 genes with expression significantly correlated with chromatin accessibility. These loci largely comprise markers of early pluripotency and germ cells (e.g. Dppa4, Zfp42, Tex19.1 and Pou3f1), which are repressed, coinciding with the global increase in methylation, and decrease in chromatin accessibility. In addition, authors identified Trap1a and Zfp981 genes, which so far have unknown roles in development. In summary, this mind-boggling study (mind-boggling because it boggles our minds what can now be done at the single-cell level) shows that regulatory elements (associated with each germ layer) are either epigenetically primed, or remodeled — before cell-fate decisions occur, providing a molecular framework for a hierarchical emergence of the three primary germ cell layers. 😊


Nature 19/26 Dec 2019; 576: 487-491

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