Fig. 3: Oocyte and embryo specific H2A.Z peaks are mainly found outside of genes.

a Heatmaps of H2A.Z enrichment at aggregated and clustered H2A.Z peaks from all developmental stages, except for the zygote to 4-cell stages, which had relatively lower library complexities compared to the other samples. Z-score of CpG density at peaks is also shown. Blast., blastocyst. b Z-scores of histone marks^35,36,71 and ATAC-seq^37,38,39 at clustered peaks. c Bubble plots showing overlap of LADs²² and clusters of H2A.Z peaks compared to an average distribution across all clusters. p-values were calculated by two-sided Chi-Square tests, Benjamini-Hochberg adjusted for multiple testing. Bubbles corresponding to a p-value < 0.05 were excluded from the plot. d 2D-histograms showing the genome-wide occurrence of each cluster of H2A.Z peaks (color) in relation to the mean Replication Status (RS) of the maternal (X-axis) and paternal (Y-axis) genomes²⁵ in individual 2-cell embryos. # and * indicates noteworthy sex-specific differences, where low and high peak-occurrences, respectively, largely follow the maternal RS, but not the paternal. Data was analyzed in 40 kbp bins, and the subset of bins overlapping with LADs is shown (n = 21,966). For the non-overlapping subset, see Supplementary Fig. 4d. e 2D-histogram showing the genome-wide occurrence of cluster 3 H2A.Z peaks (color) in relation to the mean maternal RS (X-axis) in individual 2-cell embryos and H3K27me3 levels in MII oocytes (Y-axis). Data was analyzed in 40 kbp bins, and the subset of bins overlapping with LADs is shown (n = 21,966). For the non-overlapping subset, see Supplementary Fig. 4d.f Overlap between peaks in each cluster and indicated genic features. g Heatmap of gene ontology (GO) analysis for H2A.Z peak annotated genes. -log₁₀ transformed adjusted p-values of gene ontology biological process terms (X-axis) are visualized across H2A.Z peak clusters (Y-axis). Biological processes with a cumulative-log₁₀ adjusted p-value in all clusters greater than 150 are visualized and labeled as general biological processes for clarity. One-tailed Fisher’s exact test was used to calculate the p-values, followed by multiple testing correction with g:SCS. h Overview of the fraction of peaks that overlap with genomic features. i Overview of the fraction of peaks that overlap with major classes of repetitive elements. Assoc., associated.