Extended Data Fig. 1: H2A.Z dynamics during oogenesis.
a, Scatter plots showing the correlations between biological replicates of H2A.Z CATCH-seq. b, Heatmaps showing the enrichment of H2A.Z signals at genic regions and expression levels of genes classified into 4 clusters. Actively expressed genes were defined by [RPKM > 1], while lowly expressed genes are [0.1 < RPKM < 1], and inactive genes are [RPKM < 0.1] in all stages, respectively. The remaining genes were defined as variably expressed genes. The RNA-seq datasets were from Veselovska et al.41. c, Box plots showing the H2A.Z signal intensity at the promoters of the 4 clusters. The center lines in the boxes represent median values. The box edges, upper and lower whiskers indicate the interquartile range (IQR, from the 25th to 75th percentile), the maximal value smaller than 1.5 x the IQR above the 75th percentile, and the minimal value larger than 1.5 x the IQR below the 25th percentile, respectively. P-value was calculated by two-sided t-test. d, Transcription factor motifs identified at intergenic ncH2A.Z-H3K27ac dual-marked regions (left). Right bubble plots represent the expression level of TFs in FGOs and the statistical significance of the motif enrichment (P-value of hypergeometric test with one-sided). e, The proportion of the number of merged H2A.Z domains when merging adjacent peaks at each different distance from 1- to 12-kb. After summing the number of merged domains at each different distance from 1- to 12-kb, the number of merged domains at each distance was divided by the total number. f, Heatmap showing the global Pearson correlations between H2A.Z and H3K4me3 in four stages during oogenesis. The bin size is 5 kb. g, Violin plot showing the “skewing distance” of each H2A.Z peak. h, Representative images of 5-ethynyl uridine (EU) incorporation assay to validate transcriptional inhibition. 10d-GOs were first treated with 0.2% DMSO, 100 µM 5,6-dichlorobenzimidazole (DRB), or 100 µg/mL α-amanitin for 2 hrs, incubated with a medium containing EU and the respective inhibitors for additional 2 hrs, and then fixed. Bar plot indicates quantification of the EU signal intensity. The data are representative of a single time experiment using 10 (DMSO), 12 (DRB), and 10 (amanitin) oocytes. Scale bar, 20 µm. i, Genome browser views of H2A.Z and H3K4me3 landscapes in 5d-GO, 10d-GO, 15d-GO, and 28d-FGO oocytes, as well as their dynamic profiles in mouse preimplantation embryos. The H2A.Z ChIP-seq datasets are from Liu et al.17. The H3K4me3 ChIP-seq datasets in oocytes and preimplantation embryos are from Hanna et al.7 and Dahl et al.8, respectively. Broad ncH3K4me3 domains are highlighted.
