Fig. 4. Consolidation of RT is characterized by specific changes in histone modifications at RT troughs and RT peaks and is influenced by ZGA.

a, H3K36me3 coverage at the indicated replication features at different embryonic stages. b, H3K4me3 coverage at replication zones at each embryonic stage. c, Smoothed scatterplots showing correlation between RT values and transcript abundance (log₂(TPM)) at the indicated embryonic stages. Spearman’s correlation is indicated. Note that Spearman’s R measures not only linear, but also monotonic, relationships and is robust to outliers. d, Smoothed scatterplots showing correlation of RT values between control 2-cell embryos and those treated with α-amanitin (top) or DRB (bottom). DRB or α-amanitin was applied continuously from the zygote stage (17 h after human chorionic gonadotropin (hCG)) until collection at the 2-cell stage, to block both minor and major ZGA, as indicated in the schematic. Spearman’s correlation is indicated. e, RT profiles of 2-cell embryos overlayed with those from α-amanitin- and DRB-treated 2-cell embryos. Genomic positions of indicated gene classes according to DBTMEE⁵⁴ are shown as rectangles. f, Box plots showing the difference in RT values (ΔRT) between α-amanitin-treated and untreated 2-cell embryos at genomic bins overlapping only major ZGA genes, only maternal RNA genes or both gene classes compared with non-overlapping bins. g, Number of replication features in control 2-cell embryos and in embryos treated with α-amanitin or DRB. Box plots show median and IQR, whiskers depict the lowest and highest values within 1.5× IQR. n.d., not determined (data not available).