Fig. 5: KAS-ATAC-seq accurately captures the transcriptional dynamics of ssDNA promoters and SSTEs during neural differentiation.

a Schematic of the in vitro neural differentiation procedure from mouse embryonic stem cells (mESCs) to neural progenitor cells (NPCs). b Snapshot of UCSC genome browser tracks displaying the ATAC-seq and KAS-ATAC-seq data for a representative region. c Principal component analysis (PCA) plot of ATAC-seq (left panel) and KAS-ATAC-seq (right panel) data generated using cells harvested at different time points indicated during the in vitro neural differentiation process. d, e Heatmaps of time-course ATAC-seq and KAS-ATAC-seq profiles during the neural differentiation of mESCs into NPCs, using significantly dynamic CREs (up- and down-regulated), clustered on the basis of the KAS-ATAC-seq data. Each row represents a promoter (d) and SSTE (e) and each column represents a time point. The row order is the same between ATAC-seq (left panel) and KAS-ATAC-seq (right panel). Asterisks represent peak time points of promoters in the heatmaps of ATAC-seq and KAS-ATAC-seq data. f Line graph depicting the z-scores of C3 (n = 1140) and C4 (n = 1863) promoters in the clustered heatmap of dynamic promoters (d). The z-scores were calculated using ATAC-seq data (blue) and KAS-ATAC-seq data (red) at various stages of the mouse neural differentiation. g Line graph depicting the z-scores of C4 SSTEs (n = 1151) in the clustered heatmap of dynamic SSTEs (e). h Table presenting the enriched motifs of TFs identified on cluster 3&4 (C3&4) immediate-early activated promoters in the clustered heatmap (d) during the mouse neural differentiation. The hypergeometric test was used to calculate the p-values. i Metagene profile showing the averaged read density of Elk4 ChIP-seq data over different promoter clusters in the clustered heatmap (d) during the mouse neural differentiation. j Bubble plots showing the fold changes of gene expression levels between consecutive stages for genes with newly generated and stable ssDNA and non-ssDNA CREs defined by KAS-ATAC-seq and ATAC-seq data during the mouse neural differentiation from mESCs to EBs and NPCs (D0 to D8). The color key, ranging from blue to red, indicates the median of fold changes of gene expression levels from low to high, respectively.