Fig. 2

Dynamics of H3K27ac and H3K4me1 ChIP-seq signals across mouse gastrulation. A and B: PCA analysis of the average H3K27ac (A) and H3K4me1 (B) ChIP-seq signals of each subpopulation at different developmental stages except for the ExE cluster. C and D: Alluvial plots showing the global dynamics of H3K27ac (C) and H3K4me1 (D) ChIP-seq signals during ectoderm lineage specification. The number of total ectoderm-specific H3K27ac (C) and H3K4me1 (D) peaks in all stages was shown. GO enrichment analysis of the genes adjacent to EHF-specific ectoderm peaks was shown on the right panel. The colorful codes in the vertical columns represent specific ChIP-seq peaks at each stage, and the green ribbons indicate the flow of ectoderm-specific ChIP-seq signals from the previous stage along the sampled time points. E and F: Alluvial plots showing the global dynamics of H3K27ac (E) and H3K4me1 (F) ChIP-seq signals during endoderm lineage specification. The number of total endoderm-specific H3K27ac (E) and H3K4me1 (F) peaks in all stages was shown. GO enrichment analysis of the genes adjacent to EHF-specific endoderm peaks was shown on the right panel. The colorful codes in the vertical columns represent specific ChIP-seq peaks at each stage, and the blue ribbons indicate the flow of endoderm-specific ChIP-seq signals from the previous stage along the sampled time points. G and H: Alluvial plots showing the global dynamics of H3K27ac (G) and H3K4me1 (H) ChIP-seq signals during mesoderm lineage specification. The number of total mesoderm-specific H3K27ac (G) and H3K4me1 (H) peaks in all stages was shown. GO enrichment analysis of the genes adjacent to EHF-specific mesoderm peaks was shown on the right panel. The colorful codes in the vertical columns represent specific ChIP-seq peaks at each stage, and the red ribbons indicate the flow of mesoderm-specific ChIP-seq signals from the previous stage along the sampled time points. I and J: Line plot showing cluster-specific H3K27ac (I) and H3K4me1 (J) ChIP-seq signals in Epiblast cells. ChIP-seq signals were calculated within 50 bp window around the ± 1 kb of the peak centers. Total 61, 3,174, 1,264, 2,226 H3K27ac peaks in the epiblast (Epi cluster), ectoderm (both NE1 and NE2 clusters), endoderm (DE cluster), and mesoderm (MM cluster), respectively, and 7,137, 176, 548, 21,567 H3K4me1 peaks in the epiblast (Epi_L cluster), ectoderm (NE_L), endoderm (EN_L), and mesoderm (ME_L), respectively, were used for signal calculations