Figures and data
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Mapping H3K4me2 in mouse (C57BL6/N) gametes and pre-implantation embryos.
(A) The IGV view showing the global landscape of H3K4me2 signals in mouse sperm, GV oocytes, MII oocytes, pre-implantation embryos. H3K4me2 data in sperm is from ENCODE (Lambrot R et al). ICM were isolated from blastocyst.
(B) Immunofluorescence of H3K4me2 in mouse(C57BL6/N) GV oocytes, MII oocytes, PN5 zygote, early 2-cell, late 2-cell, 4-cell, 8-cell, morula and blastocyst, scale bar is also shown.
(C) H3K4me2 enrichment near typical genes and their expression levels. H3K4me2 signal, ATAC-seq and Gene expression are shown.
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Comparison of the H3K4me2 between sperm and oocyte.
(A-B) Heatmaps showing H3K4me2 and H3K4me3 expressed genes between sperm and GV oocyte in promoter and distal region among different stages. CpG densities are also mapped and shown.
(C) The enriched GO terms of H3K4me2 marked genes in GV and sperm specific or shared genes, P value is also calculated and shown.
(D) The GREAT analysis result for distal peaks in GV and sperm specific or shared genes is shown. P value is also calculated and shown.
(E-F) The IGV views showing H3K4me2 expressions in GV and sperm specific or shared genes at representative promoters (left, shaded) or distal accessible regions (right, shaded).
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Resetting H3K4me2 during mouse pre-implantation development.
(A) H3K4me2 peaks number in mouse embryo stem cell(mESC), mouse gametes and pre-implantation embryos was calculated and shown.
(B) The IGV view showing H3K4me2 signals in mESC, mouse gametes and pre-implantation embryos, Ncc1 gene sites was shown.
(C) Venn diagrams showing the overlaps of H3K4me2 marked genes between sperm/GV oocytes, separately (left) or jointly (right), and 4-cell. The enriched GO terms for shared or nonoverlapping genes are also shown.
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Pervasive H3K4me2 in CpG-rich regulatory regions in mouse embryos.
(A-B) H3K4me2 and H3K4me3 enrichment near TSS (TSS ± 5kb) and PMD (3× PMD) in mouse gametes, pre-implantation embryos and mESC is shown.
(C) The IGV view showing promoter H3K4me2 signals and widespread distal H3K4me2 signals in mouse oocytes and early embryos.
(D) The IGV view showing H3K4me2 signals and DNA methylation distributions in mouse oocytes and early embryos at PMD (partially methylation district) region.
(E) Heat maps showing H3K4me2, H3K4me3 enrichment at the promoters in all stage shared and 4-cell/8-cell specific embryos. ATAC-seq, promoter CpG density and GO analysis results are also shown.
(F) Heatmaps showing stage-specifically expressed distal peaks of H3K4me2 among 8-cell, ICM and mESC. ATAC-seq is also shown.
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Chromatin states at specific stages and H3K4me2 mode chart during mouse maternal-to-zygotic transition.
(A) Heatmaps showing H3K4me2, H3K4me3 and ATAC-seq, “All active” and “All inactive” promoters and corresponding genes expression. CpG densities are also mapped and shown.
(B) The bar chart showing H3K4me2 distal peaks overlap with CcREs 4/8-cell stage. Random peaks are shown as a control.
(C) Heat maps showing the chromatin states of CcREs overlapping with H3K4me2 and H3K27ac distal peaks. Clustering was conducted using ATAC-seq, H3K4me2 in 4-cell, 8-cell and ICM stages. The GREAT analysis result for each cluster is shown (right). Mouse histone modified H3K27ac data refer to GEO database : GSE72784.
(D) Dynamic reprogramming of H3K4me2 during mouse parental-to-zygotic transition. A schematic model showing “H3K4me2 resetting” during parental-to-zygotic transition. After fertilization, the parental H3K4me2 is almost globally erased. De novo H3K4me2 promoters and distal regions in CpG-rich and DNA hypomethylation regions were re-established at late 2-cell stage, possibly as a priming chromatin state. This leads to resolution of primed promoters to “active” promoters with H3K4me3, or “poised”. A similar transition occurs for putative enhancers.
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Validation of H3K4me2 CUT&RUN data in Human K562 cell line, oocytes and early embryos.
(A) The IGV views showing H3K4me2 distributions by CUT&RUN using various numbers of Human K562 cell line. The ENCODE references are added for comparison. GEO accession: GSM733651.
(B) The Pearson correlation coefficients showing the comparison between CUT&RUN of H3K4me2 using various numbers of Human K562 cells and conventional ChIP–seq data from ENCODE.
(C) Scatter plots showing the correlations of biological replicates (n=2) of H3K4me2 signals (2kb-bin, whole genome) by CUT&RUN for each stage of mouse oocytes and early embryos. The Pearson correlation coefficients are also shown.
(D) Scatter plots comparing the H3K4me2 signals with ATAC-seq (Assay for Transposase-Accessible Chromatin with high throughput sequencing) at promoters or distal accessible regions in mouse oocytes and early embryos. Spearman correlation coefficients are also shown.
(E) Scatter plots comparing the H3K4me2 signals with H3K4me3 signals in mouse sperm, oocytes and early embryos. Spearman correlation coefficients are also shown.
(F) Hierarchical clustering of H3K4me2 mouse oocytes and early embryos. Pearson correlation was used to measure distances.
(G) Scatter plots comparing the H3K4me2 signals between 4-cell and 8-cell in mouse embryos. Spearman correlation coefficients are also shown.
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H3K4me2 in mouse gametes.
(A) Heatmaps showing H3K4me2 signals at all promoter regions (TSS ± 2.5kb) in mouse gametes. DNA methylation (TSS ± 2.5kb) is also mapped. DNA methlation data cited in GEO dataset: GSE56697.
(B) The box plots showing DNA methylation level at all promoter regions in mouse gametes. Random peaks are shown as a control. DNA methlation data cited in GEO dataset: GSE56697.
(C) Heatmaps showing H3K4me2 signals at all distal regions (peak ± 2kb) in mouse gametes. DNA methylation (peak ± 2kb) is also mapped. DNA methlation data cited in GEO dataset: GSE56697.
(D) The box plots showing DNA methylation level at all distal regions in mouse gametes. Random peaks are shown as a control. DNA methlation data cited in GEO dataset: GSE56697.
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H3K4me2 in late 2-cell embryos.
(A) Heatmaps showing the expression of H3K4me2 related regulators in mouse (based on published RNA-seq data40).
(B) The box plots showing DNA methylation level at all promoter regions and distal region in mouse 2-cell stage. Random peaks are shown as a control.
(C-D) Venn diagrams showing De novo 4-cell H3K4me2 promoter and distal peaks number.
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H3K4me2 in mouse 4/8-cell embryos.
(A) Scatter plots comparing the promoter and distal H3K4me2 signals with CpG densities in mouse gametes, 4-cell, 8-cell, ICM and mESC. The Spearman correlation coefficients are also shown.
(B) The box plots showing the CpG density and promoter/distal H3K4me2 peaks. Random peaks are shown as a control.
(C) The box plot showing DNA methylation in promoter and distal 4-cell H3K4me2 peaks. Random peaks are shown as a control.
(D) TF motifs identified from active enhancers in mouse early embryos (8-cell, ICM) and mESC. showing motif enrichment p value < 1e-20 at least at one stage were included. Circle size showing TF enrichment and the expression of the TF is color coded.
(E) Heatmaps showing stage-specifically expressed genes further classified by their H3K4me2 states (high, dynamic, and low). RNA-seq, H3K4me3 state, CpG densities and GO analysis results are also mapped and shown.
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Chromatin states at specific stages and distal CcREs.
(A) Box plots showing H3K4me2, H3K4me3 and ATAC-seq signals, “All active” and “All inactive” promoters in mouse gametes, embryos and mESC. CpG density for each group is also shown (right).
(B) The box plot showing the ATAC-seq, H3K4me2 and H3K27ac signals at putative active, poised or random enhancers in mouse gametes, early embryos or mESC, Mouse histone modified H3K27ac data refer to GEO database : GSE72784.
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CUT&RUN experimental sample information