Figure 6. Developmental dynamics of H3K27me3.

(A) Heatmap of developmentally regulated H3K27me3 regions in E14 and P39 control samples. CPM – counts per million; R1/2 – replicates. (B) Bar plots show the numbers of developmental differentially modified H3K27me3 regions (E14 vs. P39) that overlap developmental differentially methylated regions (DMRs) (P0 vs. P39, left panel), and the numbers of developmental DMRs that overlap developmental differentially modified H3K27me3 regions (right panel). (C–E) Normalized H3K27me3 signal (fold-changes compared to P39 control), and mCG, mCH differences (compared to the average of the two replicates from P39 control) in peaks that overlap with E14 vs. P39 developmental loss-of-H3K27me3 regions (C), developmental gain-of-H3K27me3 regions (D), or increased H3K27me3 in P39 Dnmt3a cKO (E).

Figure 6—figure supplement 1. Regions prone to alteration of H3K27me3 by Dnmt3a conditional knockout (cKO) were distinct from the regions affected by developmentally dynamic H3K27me3.

(A) Differentially modified H3K27me3 regions during development in control samples. (B) Top 10 most enriched biological process terms from the Gene Ontology in the genes associated with differentially modified H3K27me3 regions during development in control samples. Gene-region association was predicted by GREAT (McLean et al., 2010). FDR, false discovery rate; the vertical dashed line shows the threshold of FDR = 0.05. (C) Correlations of P39 H3K27me3 signal fold-changes of Dnmt3a cKO vs. control and developmental H3K27me3 signal fold-changes of P39 vs. E14 in H3K27me3 chromatin immunoprecipitation sequencing (ChIP-seq) peaks. Note that peaks with big absolute fold-changes in P39 cKO vs. P39 control are generally not changed much in P39 control vs. E14 control, and vice versa. Replicates 1 and 2 of P39 control are used in the y and x axis, respectively, to avoid double-dipping. The smoothed line is fitted using a generalized additive model, and the shaded area shows the 95% confidence interval of the fit. r, Spearman correlation coefficient. (D) The developmental H3K27me3 signal fold-changes are not affected by Dnmt3a cKO. r, Spearman correlation coefficient. (E–G) Boxplots to show the distribution of H3K27me3 signal, mCG, and mCH levels in peaks that overlaps with E14 vs. P39 developmental loss-of-H3K27me3 regions (E), peaks that overlap with developmental gain-of-H3K27me3 regions (F), and peaks that overlap with increased H3K27me3 regions in P39 Dnmt3a cKO (G). Asterisks show the significances from paired t-tests (***, p<0.001). ∆ values are the mean of the differences for the two groups in comparison (group on the right vs. group on the left).

Figure 6—figure supplement 2. Correlations of chromatin immunoprecipitation sequencing (ChIP-seq) signals across replicates.

Correlations were computed with ChIP-seq counts in 1 kb genomic bins (A) and in peaks (B) across replicates. r, Spearman correlation coefficient. n, number of peaks. RPKM, reads per kilobase million.