Fig. 4

H3K27ac and H3K27me3 reprogramming and chromatin accessibility change shape early embryogenesis. a Waterfall plots showing the number of genes first upregulated at different stages compared with DPA0. Representative genes were listed. b Chromatin accessibility and histone modification profiles of downregulated (left) and upregulated (right) genes. c Overlap between downregulated genes and corresponding active histone modification marks decreasing. d Expression levels of different gene sets generated from c. e GO enrichment for 2696 downregulated genes whose active histone modification marks decreased (c) (top) and 1643 upregulated genes which gained pACRs (f) (bottom). f Overlap between up-regulated genes and corresponding chromatin accessibility gains. g Correlation between gained pACRs and up-regulated genes based on 1643 genes overlapped. Genes were ranked by RNA-seq fold change and separated into 50 bins. h Dynamic of H3K27me3 modification in Chr. 6 during embryogenesis, with resetting at DPA4 and regaining at DAP8. i IGV showing histone modifications and chromatin accessibility changes on embryo developmental essential genes. j Overlap between genes with H3K27me3 decreasing at DPA4 and increasing at DPA8. k Correlation between H3K27me3 decreasing and target genes’ activation from DAP4 to DPA2. Genes were ranked by RNA-seq fold change and separated into 50 bins. H3K27me3 loss with mRNA level increased genes are shown in red color, while loss of H3K27me3 without mRNA changed is shown in blue color, while gray color indicates no change of H3K27me3. l Overlap among genes with downregulated H3K27me3 and up-regulated ATAC-seq and H3K27ac modification (top) and altered expression levels of different gene sets (bottom). m Synchronous pattern between the gain of chromatin accessibility and elevation of gene expression on the basis of H3K27me3 decreasing at DPA4. Several developmental essential genes were highlighted. Fisher exact test was used for significance calling for c, f, j, and l, Pearson test was used for g. Mann–Whitney U test (two-sided) was used for difference comparison in d and l, * p <  = 0.05; **p <  = 0.01; ***p <  = 0.001; ****p <  = 0.0001