Extended Data Fig. 2: Chromatin accessibility dynamics across the human placenta.
From: Spatial multiomic landscape of the human placenta at molecular resolution
a, Left: FOXP1 expression in 3D trophoblast organoids (TB-ORG, n = 4). WB analyses of TB-ORG protein lysates under stemness and EVT differentiation conditions (DIFF1= EVT differentiation under TGF-beta (TGFβ) inhibition; DIFF2=EVT differentiation under TGFβ activation) detect FOXP1 in TB-ORG under stemness conditions and its almost absence in EVTs. Right: siRNA-based downregulation of FOXP1 in trophoblast stem cells (TSCs) under stemness conditions, showing that siRNA treatment of FOXP1 reduces proliferation (CCNA2) and provokes markers for STB differentiation of TSCs (CGB, ENDOU). n = 3 independent TSC lines, two replicates each. Data are represented as mean values +/− SD. Normal distribution was tested using Kolmogorov-Smirnov test and subsequent unpaired t-tests were applied. P-values are depicted in the blots. b, Visual comparison of gene expression (RNA) and gene activity score (ATAC) UMAP plots for LY6E, with accompanying spatial visualization using STARmap-ISH (n = 3). Stippled line demarcates villous core from vCTBs. c, UMAP representation of novel trophoblast-associated microRNAs miR23B (vCTB) and miR7973-1 (STB), identified by snATAC-seq analyses. Verification of expression was performed through qPCR in isolated vCTB (TP63), STB (CGB), and EVT cells (Methods) (n = 3 donors). Per donor, qPCR was repeated twice (TP63, CGB), six times (miRNA23B), and four times (miRNA7973), respectively. Data are represented as mean values +/− SD. Kolmogorov-Smirnov test (normal distribution) was followed by either Friedman test and Dunn’s multiple comparison (non-parametric miRNA23b and CGB), or one-way ANOVA and Geisser-Greenhouse correction (miRNA7973 and TP63). P-values are depicted in the blots. d, Heatmap showing differentially accessible genes across clusters. All differentially accessible genes from snATAC-seq are listed in Supplementary Table 3. e, Corresponding gene expression (Gene Expression Matrix) and gene accessibility (Gene Score Matrix) of TF motifs from intercluster motif enrichment comparisons, ChromVAR analyses, and identified positive TF regulators. Intercluster motif enrichments can be found in Supplementary Table 4, while ChromVAR enrichments and positive TF regulators can be found in Supplementary Table 5. f, Positive TF regulators identified based on gene activity scores. Positive TF regulator motifs such as BACH2, GCM1, TFAP2C, TEAD1, and MESP2 are significantly enriched. Specific motifs and enrichment values can be found in Supplementary Table 5.
