Fig. 3: In early development, proteins enter nuclei sequentially correlating with the onset of their nuclear functions.

a–c Embryos developed at 16 °C. a Left: Protein abundance dynamics of previously reported ZGA key regulatory factors change little from fertilization to the ZGA^15,16. Right: These regulators are among the earliest proteins to titrate into embryonic nuclei. Shown are fits of individual ZGA regulators and the median fit of the core histones (H2a, H2b, H3, and H4) and their isoforms with 50% spread. b RNA polymerase III (Pol III) and II (Pol II) enter nuclei at different times of development, which corresponds to the respective appearances of their first downstream transcripts. Left: Proteomics data show that Pol III subunits titrate into nuclei before Pol II subunits. Shown are median and 50% spread of unique subunits. Right: The first tRNA transcripts, transcribed by Pol III, and snRNA, transcribed by Pol II, show corresponding timing to the nuclear entry of their corresponding polymerases. The RNA measurements are quantified from Newport and Kirschner’s RNA gel of newly synthesized transcripts¹³. Error bars indicate standard deviation of five snRNA species (snRNA U1, U2, U4, U5, U6). c Timing of the nuclear import of TFs in the mesendoderm gene regulatory network corresponds to the timing of their activation. Left: Transcriptional activation order in early Xenopus embryos (Adapted drawing from Charney et al.²⁴ and^43,44). Middle: MS-quantification of nuclear import in early development for these TFs. Right: Scatter plot of rank between the measured nuclear entry T_embryo1/2 by MS and the reported temporal gene regulatory network shows strong agreement (Spearman correlation of 0.87, two-tailed p-value = 0.005).