Fig. 3

Fig. 3 Four types of TdARs by pioneer-like activity of Pou5f3, SoxB1, and Nanog.

a Four groups of TdARs by non-redundant requirements for Pou5f3 and/or Nanog for chromatin accessibility. b Frequencies of PSN motifs in the 4 groups. Note that 2.P and 3.N groups are the most enriched in the Pou5f3- and Nanog- specific motifs, respectively (colored boxes). c 2.P and 3.N groups are the mostly occupied by Pou5f3/SoxB1 and Nanog, respectively (gray dashed lines). Summary ChIP-seq profiles for indicated TFs (rpkm). d PSN establish accessible chromatin starting from major ZGA (3 hpf). ATAC-seq summary profiles in WT and MZtriple at 3, 3.7, and 4.3 hpf (rpkm). Note that chromatin in group 4.- regions in MZtriple is more accessible than in the other groups (gray dashed line). e GC content in four groups is significantly different: note that Pou5f3 is required in two groups with the lowest GC. p-values for two-sided Tukey-Kramer test; p-value for 1-way ANOVA was <2e⁻¹⁶. Groups were derived from at two to four independent ATAC-seq experiments in each of the four genotypes. n “1.PN” = 3748, n ”2.P” = 4524, n ”3.N” = 8335, n “4.-” = 3524. The lower dashed line shows the median genomic control GC content, upper line – median GC content of ARs upregulated in MZtriple. The centers of the box plots correspond to the median values, the lower and upper bounds of the box correspond to the 25th and 75th percentiles, the upper whisker extends from the upper bound to the largest value no further than 1.5 * IQR (inter-quartile range), the lower whisker extends from the lower bound to the smallest value at most 1.5 * IQR. Outlying points beyond the end of the whiskers are plotted individually. f Percentages of TdARs, for four groups, on which chromatin accessibility could be rescued by microinjection of different concentrations of single TFs into 1-cell stage MZnps embryos⁵. RNA concentrations: low, normal, high for Pou5f3 and Nanog normal and high for Sox19b⁵. g Percentages of TdARs, for four groups, which could be rescued by microinjection of double or triple combinations of P,S and N TFs into 1-cell stage MZnps embryos⁵. TFs in normal concentration. h Schematic drawing of four types of regulation of chromatin accessibility, percentage of each group from all TdARs is shown. “OR” – logical operator. Nanog and Sox19b are redundantly required for more regions within group 4.-, than Pou5f3. Source data are provided as a Source Data file 1 (a–g).