Fig. 4: ST-MAGIC (+) demarcates the spatiotemporal changes in responsiveness to signaling pathways.

a Schematic overview of the morphogen gradient and the interpretation of signal transduction cascade in embryo patterning, and the in silico visualization using ST-MAGIC (+). b ST-MAGIC visualization of the distribution of WNT signaling ligand-Wnt3 (left) and the antagonist-Dkk1 (right) during mouse gastrulation. c The 2380 EpiLC-specific βCatenin binding peaks and the 801 linked genes were mapped to E6.5 and E7.5 embryo to show the spatiotemporal dynamics of chromatin responsiveness (left) and transcriptional output of WNT signaling (right). d ST-MAGIC visualization of the NODAL signaling ligand-Nodal and the antagonist-Cer1 during mouse gastrulation. e ST-MAGIC (+) visualization of embryoid body (EB)-specific Smad2/3 binding peaks (3635 peaks, left) and the linked genes (320 genes, right) reflecting the spatiotemporal transition of intrinsic chromatin responsiveness to NODAL signaling. f, g The spatiotemporal expression of Nodal (f) and the transition of intrinsic chromatin responsiveness to NODAL signaling (g). h The transition of intrinsic chromatin responsiveness to signaling is mostly related to E6.75_PS region (enriched with primitive streak cells) and E7.0_APS_M region (enriched with anterior primitive streak and nascent mesoderm). Left: the specific spatial locations of E6.75_PS and E7.0_APS_M region; middle: the cell type composition at indicated regions; top right: venn diagram showing the direct comparison of region-specific WNT signaling responsive peaks between E6.75_PS and E7.0_APS_M; bottom right: venn diagram showing the direct comparison of region-specific NODAL signaling responsive peaks between E6.75_PS and E7.0_APS_M. i. j. ST-MAGIC (+) visualization (i) and motif enrichment (j) of the 92 E7.0 APS_M specific WNT signaling responsive peaks during the late stage (E7.0, E7.25, E7.5) of mouse gastrulation. k The model describing the spatial evolution of WNT signaling responsiveness at late gastrulation. l, m ST-MAGIC (+) visualization (l) and motif enrichment (m) of the 291 E7.0 APS_M specific NODAL signaling responsive peaks during the late stage (E7.0, E7.25, E7.5) of mouse gastrulation. n The model describing the spatial evolution of NODAL signaling responsiveness during the late stage of mouse gastrulation.