Fig. 5

The Xi reacquires chromatin accessibility during reprogramming to iPSCs. A Density plots showing regions with (i) allelic autosomal and (ii) X-linked chromatin accessibility ratios across different reprogramming time points from day 0 to iPSCs. Allelic chromatin accessibility ratios were calculated by dividing maternal read counts by total reads (Mus/Mus + Cast). The number of informative regions is 750. B Allelic ratio (Mus/Mus + Cast) of all X-linked annotated enhancer (blue) and promoter (red) regions that become biallelically accessible during iPSC reprogramming. C Allelic ratio (Mus/Mus + Cast) of all informative X-linked regions (n = 750) at each time point of iPSC reprogramming. Regions were grouped by k-means clustering. The bold line represents the average allelic ratio at each time point for regions within each cluster. D ATAC-seq tracks for allelic chromatin accessibility at promoter regions of representative X-linked gene regions that become biallelically accessible at different time points (day 0, day 12, escapees, and XCD) during reprogramming. The parental origin of the accessible allele is indicated in red for Cast and in blue for Mus. E Enrichment of TF motifs in X-linked biallelic accessible regions at different time points during reprogramming. Only significant enrichments (p value ≤ 0.05) are shown. The color gradient represents the percentage of regions with enriched motifs in the indicated group over 50,000 random background genome regions