Fig. 3: KAS-ATAC-seq quantitatively estimates the dsDNA openness in ATAC-seq peaks.

a Heatmap showing the ATAC-seq, KAS-ATAC-seq, log2 fold changes between KAS-ATAC-seq and ATAC-seq, and the DNA openness index (DOI) for proximal (left panel, n = 14,277) and distal (right panel, n = 41,007) ATAC-seq peaks. The DOI is determined as the proportion of KAS-ATAC-seq signal relative to the ATAC-seq signal at a specific CRE. Regions spanning 5 kb upstream and 5 kb downstream from the center of proximal and distal ATAC-seq peak were shown. b Density plot comparing the DNA openness index (DOI) of proximal (n = 14,277) and distal (n = 41,007) ATAC-seq peaks. c Metagene profiles showing the distribution of averaged ATAC-seq (upper panel) and KAS-ATAC-seq (lower panel) read density across ATAC-seq peaks categorized by high, medium, low, zero DNA openness index (DOI) in mESCs. Regions spanning 5 kb upstream and 5 kb downstream from the center of ATAC-seq peaks are displayed. d Table presenting the enriched sequence features on cis-regulatory elements (CREs) associated with varying levels of the DNA openness index (DOI). The hypergeometric test was used to calculate the p-values. e Boxplot illustrating the CpG density within proximal ATAC-seq peaks, categorized by high (n = 4386), medium (n = 4386), low (n = 4386), and zero (n = 2001) DNA openness index (DOI) in mESCs. The p-values were calculated using two-sided Student’s t-test. P-values < 0.0001 was shown as ****. The box shows 1st quartile, median and 3rd quartile, respectively. Whiskers extend to show the range from the 10th to the 90th percentile, with data points outside this range not shown. f Correlation heatmap showing Pearson correlation coefficients between the DNA openness index (DOI), ATAC-seq, KAS-ATAC-seq, RNA Pol II binding, and gene expression levels of genes with ATAC-seq peaks (n = 10,185). The gene expression levels of proximal ATAC-seq peaks target genes are determined using bulk cell RNA-seq data. The Pearson correlation coefficients were labeled on the correlation heatmap. g Scatterplot showing the Pearson correlation between DNA openness index (DOI) and gene expression (Gene expr, bulk cell RNA-seq) on genes with ATAC-seq peaks (n = 10,185). The Pearson correlation coefficient (R) and its associated two-sided p-value are displayed at the top of the plot. Points are color-coded in orange to indicate the gene density.