Extended Data Fig. 12: Cell type-specific chromatin accessibility and interactions.
From: Rolling back human pluripotent stem cells to an eight-cell embryo-like stage
a–d. Genome browser tracks visualizing cell type-enriched (primed ESC, 4CL-day 12 naïve ESC, and non-8CLC and 8CLC in cluster 5 of stepwise e4CL-day 5 cells) chromatin accessibility (upper panel) and co-accessibility loops (middle panel) for the indicated classical pluripotency (a), naïve pluripotency (b) and classical totipotency loci (c), and the 8C-enriched lineage specifier GATA6 locus (d). Color intensities of the loops represent the significance level of peak co-accessibility. A violin plot showing the log normalized expression level in the same cell types is displayed in the bottom panel for each locus. e. Average normalized chromatin accessibility signal for the early human embryo-enriched TE MLT2A2 in early human embryo bulk ATAC-seq16 and pseudobulk of our scATAC-seq data. All reference datasets used in this study are summarized in Supplementary Table 8. f. UMAP visualization of gene score of all genes in the scATAC-seq of primed H9 ESC untreated (green) or converted by 4CL (day 12; blue) and 8CLC (red) detected in Fig. 2a. g. Trajectory based on gene score and DNA binding motif distribution along the stepwise process of 8CLC induction from primed ESC to 8CLC passing through 4CL-day 12 naïve ESC projected onto the UMAP of panel f. h. UMAP visualization based on panel g highlighting the gene score for primed (ZIC2) and shared naïve pluripotency/8CLC (DPPA3) and totipotency (ZNF280A) genes projected onto each individual cell of primed ESC untreated or converted by 4CL (day 12) and 8CLC detected in Fig. 2a
