Extended Data Figure 9: CAF-1 suppression induces specific depletion of H3K9me3 at somatic heterochromatin domains.

a, Scatter plots comparing H3K9me3 enrichment nearby ATAC-seq sensitive and super-enhancer regions between control (Ren.713) and Chaf1a knockdown cells (Chaf1a.164 and Chaf1a.2122) at day 3 of reprogramming. Values reflect normalized H3K9me3 ChIP signal (IP/input) for 5-kb genomic regions overlapping ATAC-seq sensitive regions (red), super-enhancer regions (orange) and regions within 50-kb upstream and downstream of super-enhancers (black). b, Scatter plots comparing H3K9me3 enrichment over transposable element (TE) families in control and Chaf1a knockdown cells at day 3 of reprogramming. Values reflect normalized H3K9me3 ChIP-seq signal (IP/input) over families of TEs in the mouse genome. c, Heatmap shows the relative changes (z-normalized) of TE family expression as estimated by RNA sequencing in control and Chaf1a knockdown cells at day 0, 3 and 6 of reprogramming. Data are clustered using the k-means algorithm. d, Cumulative histogram showing the relative fraction of reprogramming-resistant regions (RRRs)²⁹ (x axis) that display negative or positive enrichment (fold change) of average H3K9me3 signal at day 3 of reprogramming in control and Chaf1a knockdown cells. Note that more RRRs exhibit depletion of H3K9me3 in Chaf1a knockdown samples. e, H3K9me3 ChIP-seq analysis of RRRs after 0 and 3 days of reprogramming. Box plots depict representative RRRs on chromosome 7 (P < 0.05 for both shRNAs). See also Fig. 5d. f, Histogram plot showing activation of UAS–Oct4–GFP transgene upon suppression of Chaf1b (shRNA⁺ line) in the presence of Gal4–VP16 fusion protein. See Fig. 5f for quantification.