Fig. 4

Loss of mir430 transcription bodies causes premature gene activation.

a, Time of induction in WT embryos for the 716 genes that are upregulated in mir430^−/− + inj MiR430 versus WT embryos (at 256-cell stage). Expression at 256-cell stage is used as a reference. The genes are split into four groups based on when they are induced (n = 446 induced genes at 1,024-cell stage; n = 51 induced genes at Oblong; n = 83 genes induced at Sphere; n = 136 not induced). The percentage of genes in each group is indicated. Boxplots show median, quartiles, minimum and maximum, and 1.5× interquartile range. Individual points represent outliers. b, Scatterplot representing the fold change in expression between mir430^−/− + inj MiR430 and WT embryos at 256-cell stage on the y axis, and between 1,024-cell stage and 256-cell stage in WT embryos on the x axis. All upregulated genes are shown in grey, and genes induced at 1,024-cell stage (62%) are shown in blue. c, Heatmap of chromatin accessibility at 256-cell stage of the 716 genes that are upregulated in mir430^−/− + inj MiR430 embryos compared with WT embryos at the 256-cell stage, and—for comparison—the 716 most expressed genes in WT embryos at the 256-cell stage. Genes are ranked by accessibility. d, Graph showing the fraction of promoters of the 716 upregulated (in mir430^−/− + inj MiR430 versus WT at the 256-cell stage) and the 716 most expressed genes (in WT at 256-cell stage) amongst the x% most accessible promoters at 256-cell stage in WT embryos. The distribution of non-expressed genes as well as the non-differentially expressed genes (mir430^−/− + inj MiR430 versus WT at 256-cell stage) are shown for comparison. e, Scatterplot representing the enrichment ratio (log₂) of transcription factor motifs in the promoters (TSS ± 2 kb) of upregulated genes compared with the promoters of not expressed genes (y axis) and the percentage of promoters of the upregulated genes that have the motif (x axis). Only motifs whose corresponding protein is translated during early development²⁷ were considered, and only motifs with a P value < 0.05 and E-value ≤ 10 are shown. Motifs corresponding to the three pluripotency factors Nanog, Sox19b and Pou5f3 (POU5F1, Pou5f1, Pou5f1::Sox2, POU5F1B, POU2F1, POU2F1::SOX2) are labelled in red. Source numerical data are available in Source data and on GEO (GSE248237 and GSE130944).

Source data