Fig. 2: Characterization of ZTA during zebrafish early embryogenesis.

a Number and abundance of zygotically activated TE-alone, TE-gene and gene transcripts across the 11 developmental stages. Two zygotic TE activation (ZTA) stages (1k-cell and oblong) are marked by arrows. Boxplots show expression distribution of each type of transcripts from the 64-cell to shield stages. Wilcoxon rank sum tests, two-sided are used to test the significant differences among gene, TE-gene and TE-alone. The total number of transcripts at each stage is 3563, 11,132, 10,415, 10,187, 14,352, 14,275, 13,050, 15,539, 16,936 in the corresponding boxplots. b Heatmap showing the expression similarity (Pearson’s correlation) between adjacent developmental stages for TE-alone, TE-gene, and gene transcripts, respectively, with red boxes highlighting the low similarity. c WISH experiments showing the activation stages with the representative TE subfamilies. Abundances estimated by long reads are drawn for each subfamily with the bar plot. d Widespread TE-alone and gene expression loss after α-Amanitin treatment at the sphere and shield stages. WT wide type, Zygotic strictly zygotic genes, Maternal maternal genes. e Widespread TE-alone and gene expression loss in the triple LOF (loss-of-function: maternal zygotic MZpou5f1 mutant with translation-blocking morpholinos for Nanog and SoxB1) at the sphere and shield stages. MO morpholino, MZ maternal zygotic. f Widespread TE-alone and gene expression loss at the sphere and shield stages following CHX (cycloheximide) treatment to block translation of zygotic genes. g Downregulated zygotic activation in zebrafish ERV subfamilies at the shield stage following CHX treatments.