Fig. 4: Genes pre-marked by H3K4me3 are expressed early during zygotic genome activation.

a Heatmap of expression of zygotic genes in egg, spermatid, and different timepoints during ZGA grouped by their first detected expression timepoint during ZGA (6 hpf: n = 183, 7 hpf: n = 239, 8 hpf: n = 260, 9 hpf: n = 174). Zygotic genes = Gamete+Zygotic (GZ) + Zygotic-Specific (ZS). b Results of statistical tests for association between H3K4me3 dynamics groups and gene groups based on their first-detected expression timepoint during ZGA (6-9 hpf). P-values are calculated with one-sided Fisher’s Exact Test for positive association and FDR adjusted. c Results of statistical tests for association between RNA dynamics groups and gene groups based on their first-detected expression timepoint during ZGA (6-9 hpf). d (Top) H3K4me3 around TSS (± 1kb) for expression timing gene groups at each timepoint - spermatid, sperm, pre-ZGA, post-ZGA. Values displayed as mean ± SE. (Bottom) H3K4me3 promoter enrichment in each group for each time point. Statistical test: one-sided Wilcoxon rank-sum test with alternative hypothesis that values of left distribution tend to be larger than right distribution; p: (****) ≤ 0.0001, (***) ≤ 0.001, (**) ≤ 0.01, (*) ≤ 0.05; n.s. are p > 0.05. Box plots show the median (center line), 25–75th percentiles (box), whiskers extending to 1.5× the interquartile range, and outliers as individual points.