Fig. 5: rCREs contain positional information within individual germ layers.
From: Spatial patterning of the epigenome during vertebrate gastrulation
a Stacked bar plot displaying cellular composition of groups of cells with high anterior vs posterior rCRE scores from the multiome dataset. b Projection of rCRE scores in the multiome UMAP. Aggregate accessibility of anterior rCREs is the strongest in ectodermal and endodermal cells, whereas posterior rCREs are on average more accessible in the mesodermal. c Cellular composition of 50-cell bins ordered from anterior to posterior using quadratic programming. A schematic sagittal section of the embryo depicts the uneven distribution of germ layers along the AP axis and the position of key midline structures, including the head process. d Immunohistochemistry for germ layer markers SOX2, SOX17, and TBXT show ectoderm and endoderm predominantly occupy anterior positions, while most of the posterior embryo is composed of mesoderm (n = 3/3). Scale bar: 200μm. e Immunohistochemistry for germ layer markers SOX2, SOX17, and TBXT at the anterior end of the embryo (n = 3/3). The prechordal plate is outlined and arrows indicate enriched SOX17 expression in this tissue. Scale bar: 100 μm. f Projection of anterior and posterior rCRE signatures in 708 neuroectodermal cells isolated from the multiome dataset. Axial markers of the neural ectoderm include OTX2, GBX2, and HOXA2. g Projection of normalized expression of OTX2, GBX2, and HOXA2 in neuroectodermal cells ordered from anterior to posterior using quadratic programming. Cell ordering recapitulates the expected expression patterns for axial markers of the central nervous system. h 1560 anterior rCREs and 1724 posterior rCREs are conserved between chicken and mouse. Conserved rCREs were used to order cells from the E7.5 mouse multiome dataset from Argelaguet et al.43 as 200-cell bins from anterior to posterior. i Heatmaps displaying accessibility of conserved rCREs in 200-cell bins ordered from anterior to posterior in the mouse gastrula. j Heatmaps displaying expression of OTX2, POU3F1, TBXT, and WNT3 in 200-cell bins ordered from anterior to posterior using rCRE accessibility. Conserved rCREs can be used for cell ordering and inference of expression patterns of axial genes in the cup-shaped murine gastrula.
