Spatial Transcriptome for the Molecular Annotation of Lineage Fates and Cell Identity in Mid-gastrula Mouse Embryo

Abstract

Gastrulation of the mouse embryo entails progressive restriction of lineage potency and the organization of the lineage progenitors into a body plan. Here we performed a high-resolution RNA sequencing analysis on single mid-gastrulation mouse embryos to collate a spatial transcriptome that correlated with the regionalization of cell fates in the embryo. 3D rendition of the quantitative data enabled the visualization of the spatial pattern of all expressing genes in the epiblast in a digital whole-mount in situ format. The dataset also identified genes that (1) are co-expressed in a specific cell population, (2) display similar global pattern of expression, (3) have lineage markers, (4) mark domains of transcriptional and signaling activity associated with cell fates, and (5) can be used as zip codes for mapping the position of single cells isolated from the mid-gastrula stage embryo and the embryo-derived stem cells to the equivalent epiblast cells for delineating their prospective cell fates.

Single-cell analysis reveals lineage segregation in early post-implantation mouse embryos

“…Recently, two groups reported their single-cell transcriptomic analyses of mouse early post-implantation embryos (21,27,29). However, characteristics of the pre-MEN cells and the divergence between ME and DE cells were not included in these studies.…”

“…5D), suggesting that TFs of each group are systematically regulated. Because negative correlation often occurs between genes regulating alternative cellular states (21,48), the negative correlation between TFs of MC3 and MC1 (Otx2/Zfp516, Otx2/Tbx3, Otx2/Hand1, Foxa2/Lef1, Aff1/Tbx3, and Aff1/ Msx2) suggested that these TFs might account for the fate choice of DE and ME lineages. Mycn, which was expressed at a higher level in both Late EPI and ME cells than in DE cells (one sided Mann-Whitney U test, FDR Ͻ0.25), might also play a Fig.…”

“…S6C). In addition, two published studies (21,27) analyzed genes and signals involved in the anterior-posterior regionalization in the PS of E7.0 and E7.5 embryos. Our study extends this issue to an earlier stage (E6.5) and uncovers more aspects of signals and transcription factors that may govern the segregation of EXEM cells and embryonic ME cells.…”

“…The pairwise expression Pearson correlation coefficient (PCC) of TFs or pluripotency genes was used to calculate CSI scores (21,47). Hierarchical clustering was performed based on the CSI scores.…”

“…For examples, Wnt, Bmp4, FGF, and Nodal signaling are known to be critical for the cell lineage allocation and axis patterning in the post-implantation mouse embryo (1,(7)(8)(9)(15)(16)(17)(18)(19)(20)(21). However, the molecular basis for the cell-fate plasticity and lineage segregation remains elusive.…”